From e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 Mon Sep 17 00:00:00 2001
From: Bonface
Date: Thu, 15 Feb 2024 06:09:54 -0600
Subject: Update dataset RTF Files.
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general/datasets/AKXDGeno/summary.rtf | 1 -
.../datasets/B139_K_1206_M/experiment-design.rtf | 3 -
general/datasets/B139_K_1206_M/summary.rtf | 1 -
.../datasets/B139_K_1206_R/experiment-design.rtf | 3 -
general/datasets/B139_K_1206_R/summary.rtf | 1 -
.../datasets/B150_K_0406_R/experiment-design.rtf | 3 -
general/datasets/B150_K_0406_R/summary.rtf | 1 -
general/datasets/B1LI0809M5/summary.rtf | 1 -
general/datasets/B1LI0809R/summary.rtf | 1 -
general/datasets/B1MI0809M5/summary.rtf | 1 -
general/datasets/B1MI0809R/summary.rtf | 1 -
general/datasets/B30_K_1206_M/acknowledgment.rtf | 3 -
general/datasets/B30_K_1206_M/cases.rtf | 1748 -----
.../datasets/B30_K_1206_M/experiment-design.rtf | 62 -
general/datasets/B30_K_1206_M/notes.rtf | 14 -
general/datasets/B30_K_1206_M/platform.rtf | 3 -
general/datasets/B30_K_1206_M/processing.rtf | 49 -
general/datasets/B30_K_1206_M/summary.rtf | 5 -
general/datasets/B30_K_1206_M/tissue.rtf | 9 -
general/datasets/B30_K_1206_R/acknowledgment.rtf | 3 -
general/datasets/B30_K_1206_R/cases.rtf | 1748 -----
.../datasets/B30_K_1206_R/experiment-design.rtf | 62 -
general/datasets/B30_K_1206_R/notes.rtf | 14 -
general/datasets/B30_K_1206_R/platform.rtf | 3 -
general/datasets/B30_K_1206_R/processing.rtf | 49 -
general/datasets/B30_K_1206_R/summary.rtf | 5 -
general/datasets/B30_K_1206_R/tissue.rtf | 9 -
general/datasets/B30_K_1206_Rn/acknowledgment.rtf | 3 -
general/datasets/B30_K_1206_Rn/cases.rtf | 1748 -----
.../datasets/B30_K_1206_Rn/experiment-design.rtf | 62 -
general/datasets/B30_K_1206_Rn/notes.rtf | 14 -
general/datasets/B30_K_1206_Rn/platform.rtf | 3 -
general/datasets/B30_K_1206_Rn/processing.rtf | 49 -
general/datasets/B30_K_1206_Rn/summary.rtf | 5 -
general/datasets/B30_K_1206_Rn/tissue.rtf | 9 -
.../datasets/B6BTBRF2Publish/acknowledgment.rtf | 1 -
general/datasets/B6BTBRF2Publish/summary.rtf | 5 -
.../datasets/B6d2oncilm_0412/experiment-type.rtf | 1 -
general/datasets/BHHBF2Geno/summary.rtf | 1 -
general/datasets/BRF2_M_0304_M/acknowledgment.rtf | 3 -
general/datasets/BRF2_M_0304_M/cases.rtf | 3 -
.../datasets/BRF2_M_0304_M/experiment-design.rtf | 1 -
general/datasets/BRF2_M_0304_M/notes.rtf | 5 -
general/datasets/BRF2_M_0304_M/platform.rtf | 1154 ----
general/datasets/BRF2_M_0304_M/processing.rtf | 16 -
general/datasets/BRF2_M_0304_M/summary.rtf | 1 -
general/datasets/BRF2_M_0304_M/tissue.rtf | 1 -
general/datasets/BRF2_M_0304_P/acknowledgment.rtf | 3 -
general/datasets/BRF2_M_0304_P/cases.rtf | 3 -
.../datasets/BRF2_M_0304_P/experiment-design.rtf | 1 -
general/datasets/BRF2_M_0304_P/notes.rtf | 5 -
general/datasets/BRF2_M_0304_P/platform.rtf | 1154 ----
general/datasets/BRF2_M_0304_P/processing.rtf | 16 -
general/datasets/BRF2_M_0304_P/summary.rtf | 1 -
general/datasets/BRF2_M_0304_P/tissue.rtf | 1 -
general/datasets/BRF2_M_0304_R/acknowledgment.rtf | 3 -
general/datasets/BRF2_M_0304_R/cases.rtf | 3 -
.../datasets/BRF2_M_0304_R/experiment-design.rtf | 1 -
general/datasets/BRF2_M_0304_R/notes.rtf | 5 -
general/datasets/BRF2_M_0304_R/platform.rtf | 1154 ----
general/datasets/BRF2_M_0304_R/processing.rtf | 16 -
general/datasets/BRF2_M_0304_R/summary.rtf | 1 -
general/datasets/BRF2_M_0304_R/tissue.rtf | 1 -
general/datasets/BRF2_M_0805_M/acknowledgment.rtf | 5 -
general/datasets/BRF2_M_0805_M/cases.rtf | 3 -
general/datasets/BRF2_M_0805_M/notes.rtf | 3 -
general/datasets/BRF2_M_0805_M/platform.rtf | 1154 ----
general/datasets/BRF2_M_0805_M/processing.rtf | 26 -
general/datasets/BRF2_M_0805_M/summary.rtf | 1 -
general/datasets/BRF2_M_0805_M/tissue.rtf | 1 -
general/datasets/BRF2_M_0805_P/acknowledgment.rtf | 5 -
general/datasets/BRF2_M_0805_P/cases.rtf | 3 -
general/datasets/BRF2_M_0805_P/notes.rtf | 3 -
general/datasets/BRF2_M_0805_P/platform.rtf | 1154 ----
general/datasets/BRF2_M_0805_P/processing.rtf | 26 -
general/datasets/BRF2_M_0805_P/summary.rtf | 1 -
general/datasets/BRF2_M_0805_P/tissue.rtf | 1 -
general/datasets/BRF2_M_0805_R/acknowledgment.rtf | 5 -
general/datasets/BRF2_M_0805_R/cases.rtf | 3 -
general/datasets/BRF2_M_0805_R/notes.rtf | 3 -
general/datasets/BRF2_M_0805_R/platform.rtf | 1154 ----
general/datasets/BRF2_M_0805_R/processing.rtf | 26 -
general/datasets/BRF2_M_0805_R/summary.rtf | 1 -
general/datasets/BRF2_M_0805_R/tissue.rtf | 1 -
general/datasets/BR_M2_1106_R/acknowledgment.rtf | 3 -
general/datasets/BR_M2_1106_R/cases.rtf | 5 -
general/datasets/BR_M2_1106_R/notes.rtf | 2 -
general/datasets/BR_M2_1106_R/platform.rtf | 3 -
general/datasets/BR_M2_1106_R/processing.rtf | 7 -
general/datasets/BR_M2_1106_R/summary.rtf | 5 -
general/datasets/BR_M2_1106_R/tissue.rtf | 2751 --------
.../datasets/BR_U_0304_DPMMR/acknowledgment.rtf | 1 -
general/datasets/BR_U_0304_DPMMR/cases.rtf | 232 -
general/datasets/BR_U_0304_DPMMR/notes.rtf | 1 -
general/datasets/BR_U_0304_DPMMR/platform.rtf | 14 -
general/datasets/BR_U_0304_DPMMR/processing.rtf | 11 -
general/datasets/BR_U_0304_DPMMR/summary.rtf | 1 -
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general/datasets/BR_U_0304_DPMR/acknowledgment.rtf | 1 -
general/datasets/BR_U_0304_DPMR/cases.rtf | 232 -
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general/datasets/BR_U_0304_DPMR/platform.rtf | 14 -
general/datasets/BR_U_0304_DPMR/processing.rtf | 11 -
general/datasets/BR_U_0304_DPMR/summary.rtf | 1 -
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general/datasets/BR_U_0304_R/acknowledgment.rtf | 1 -
general/datasets/BR_U_0304_R/cases.rtf | 232 -
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general/datasets/BR_U_0304_R/platform.rtf | 14 -
general/datasets/BR_U_0304_R/processing.rtf | 11 -
general/datasets/BR_U_0304_R/summary.rtf | 1 -
general/datasets/BR_U_0304_R/tissue.rtf | 1 -
general/datasets/BR_U_0304_RR/acknowledgment.rtf | 1 -
general/datasets/BR_U_0304_RR/cases.rtf | 232 -
general/datasets/BR_U_0304_RR/notes.rtf | 1 -
general/datasets/BR_U_0304_RR/platform.rtf | 14 -
general/datasets/BR_U_0304_RR/processing.rtf | 11 -
general/datasets/BR_U_0304_RR/summary.rtf | 1 -
general/datasets/BR_U_0304_RR/tissue.rtf | 1 -
general/datasets/BR_U_0405_SS/acknowledgment.rtf | 1 -
general/datasets/BR_U_0405_SS/cases.rtf | 232 -
general/datasets/BR_U_0405_SS/notes.rtf | 1 -
general/datasets/BR_U_0405_SS/platform.rtf | 14 -
general/datasets/BR_U_0405_SS/processing.rtf | 11 -
general/datasets/BR_U_0405_SS/summary.rtf | 1 -
general/datasets/BR_U_0405_SS/tissue.rtf | 1 -
general/datasets/BR_U_0805_M/acknowledgment.rtf | 1 -
general/datasets/BR_U_0805_M/cases.rtf | 232 -
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general/datasets/BR_U_0805_M/platform.rtf | 14 -
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general/datasets/BR_U_0805_M/summary.rtf | 1 -
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general/datasets/BR_U_0805_P/acknowledgment.rtf | 1 -
general/datasets/BR_U_0805_P/cases.rtf | 232 -
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general/datasets/BR_U_0805_R/acknowledgment.rtf | 1 -
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general/datasets/BR_U_0805_R/summary.rtf | 1 -
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general/datasets/BR_U_0903_DPM/acknowledgment.rtf | 1 -
general/datasets/BR_U_0903_DPM/cases.rtf | 230 -
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general/datasets/BR_U_0903_DPM/platform.rtf | 1 -
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general/datasets/BR_U_0903_M/cases.rtf | 230 -
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general/datasets/BR_U_0903_M/processing.rtf | 27 -
general/datasets/BR_U_0903_M/summary.rtf | 1 -
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general/datasets/BR_U_0903_P/cases.rtf | 230 -
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general/datasets/BR_U_0903_P/platform.rtf | 1 -
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general/datasets/BR_U_0903_R/acknowledgment.rtf | 1 -
general/datasets/BR_U_0903_R/cases.rtf | 230 -
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general/datasets/BR_U_0903_R/processing.rtf | 27 -
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general/datasets/BR_U_1203_DPMR/acknowledgment.rtf | 1 -
general/datasets/BR_U_1203_DPMR/cases.rtf | 232 -
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general/datasets/BR_U_1203_DPMR/platform.rtf | 14 -
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general/datasets/BR_U_1203_DPMR/summary.rtf | 1 -
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general/datasets/BR_U_1203_H2/acknowledgment.rtf | 1 -
general/datasets/BR_U_1203_H2/cases.rtf | 232 -
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general/datasets/BR_U_1203_P/acknowledgment.rtf | 1 -
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general/datasets/BR_U_1203_R/cases.rtf | 232 -
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general/datasets/BR_U_1203_R/platform.rtf | 14 -
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general/datasets/BR_U_1203_RR/acknowledgment.rtf | 1 -
general/datasets/BR_U_1203_RR/cases.rtf | 232 -
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general/datasets/BR_U_1203_RR/platform.rtf | 14 -
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general/datasets/BR_U_1203_RR/summary.rtf | 1 -
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.../datasets/BXD_GLA_0911/experiment-design.rtf | 9 -
general/datasets/BXD_GLA_0911/summary.rtf | 58 -
general/datasets/Br_U_0303_M/acknowledgment.rtf | 1 -
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general/datasets/Br_U_0503_M/cases.rtf | 216 -
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general/datasets/CANDLE_NB_0711/tissue.rtf | 1 -
general/datasets/CB_M_0104_M/acknowledgment.rtf | 15 -
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general/datasets/CB_M_0104_M/platform.rtf | 3 -
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general/datasets/CB_M_0104_M/summary.rtf | 3 -
general/datasets/CB_M_0104_M/tissue.rtf | 376 --
general/datasets/CB_M_0104_P/acknowledgment.rtf | 15 -
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general/datasets/CB_M_0104_P/processing.rtf | 17 -
general/datasets/CB_M_0104_P/summary.rtf | 3 -
general/datasets/CB_M_0104_P/tissue.rtf | 376 --
general/datasets/CB_M_0104_R/acknowledgment.rtf | 15 -
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general/datasets/CB_M_0104_R/processing.rtf | 17 -
general/datasets/CB_M_0104_R/summary.rtf | 3 -
general/datasets/CB_M_0104_R/tissue.rtf | 376 --
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.../HQFNeoc_0208_RankInv/experiment-design.rtf | 937 ---
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.../HQFNeoc_1210_RankInv/experiment-design.rtf | 937 ---
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general/datasets/HXB_Adrenal_1208/tissue.rtf | 530 --
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general/datasets/HXB_Heart_1208/summary.rtf | 19 -
general/datasets/HXB_Heart_1208/tissue.rtf | 530 --
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general/datasets/HZI_0408_M/cases.rtf | 784 ---
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diff --git a/general/datasets/AKXDGeno/summary.rtf b/general/datasets/AKXDGeno/summary.rtf
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-Download the entire AKXD genotype file used in GeneNetwork (n = 1352 markers with useful strain distribution pattens from a total of 5448 informative markers). We have modified the orginal Wellcome-CTC genotypes by adding selected microsatellite markers. We have also curate the data and have removed somewhat improbable double-recombinant haplotypes and by imputing genotypes for a few untyped strains using very tightly linked markers. This genotype "smoothing" may remove some genuine recombinations and may result in linkage maps that will be very slightly conservative.
diff --git a/general/datasets/B139_K_1206_M/experiment-design.rtf b/general/datasets/B139_K_1206_M/experiment-design.rtf
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-A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community.
-
-By integrating barley genotypic, phenotypic and mRNA abundance data sets directly within GeneNetwork's analytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (barley) in a database that has been designed for an animal model species (mouse) with a well established genome sequence, we prove the importance of the concept and practice of modular development and interoperability of software engineering for biological data sets.
diff --git a/general/datasets/B139_K_1206_M/summary.rtf b/general/datasets/B139_K_1206_M/summary.rtf
deleted file mode 100644
index 54d0d52..0000000
--- a/general/datasets/B139_K_1206_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org webcite. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits). Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them.
diff --git a/general/datasets/B139_K_1206_R/experiment-design.rtf b/general/datasets/B139_K_1206_R/experiment-design.rtf
deleted file mode 100644
index b80f1da..0000000
--- a/general/datasets/B139_K_1206_R/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community.
-
-By integrating barley genotypic, phenotypic and mRNA abundance data sets directly within GeneNetwork's analytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (barley) in a database that has been designed for an animal model species (mouse) with a well established genome sequence, we prove the importance of the concept and practice of modular development and interoperability of software engineering for biological data sets.
diff --git a/general/datasets/B139_K_1206_R/summary.rtf b/general/datasets/B139_K_1206_R/summary.rtf
deleted file mode 100644
index 54d0d52..0000000
--- a/general/datasets/B139_K_1206_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org webcite. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits). Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them.
diff --git a/general/datasets/B150_K_0406_R/experiment-design.rtf b/general/datasets/B150_K_0406_R/experiment-design.rtf
deleted file mode 100644
index b80f1da..0000000
--- a/general/datasets/B150_K_0406_R/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community.
-
-By integrating barley genotypic, phenotypic and mRNA abundance data sets directly within GeneNetwork's analytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (barley) in a database that has been designed for an animal model species (mouse) with a well established genome sequence, we prove the importance of the concept and practice of modular development and interoperability of software engineering for biological data sets.
diff --git a/general/datasets/B150_K_0406_R/summary.rtf b/general/datasets/B150_K_0406_R/summary.rtf
deleted file mode 100644
index 54d0d52..0000000
--- a/general/datasets/B150_K_0406_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org webcite. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits). Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them.
diff --git a/general/datasets/B1LI0809M5/summary.rtf b/general/datasets/B1LI0809M5/summary.rtf
deleted file mode 100644
index 134e635..0000000
--- a/general/datasets/B1LI0809M5/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 79, Name: Barley1 Leaf INOC TTKS (Aug09)
\ No newline at end of file
diff --git a/general/datasets/B1LI0809R/summary.rtf b/general/datasets/B1LI0809R/summary.rtf
deleted file mode 100644
index 134e635..0000000
--- a/general/datasets/B1LI0809R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 79, Name: Barley1 Leaf INOC TTKS (Aug09)
\ No newline at end of file
diff --git a/general/datasets/B1MI0809M5/summary.rtf b/general/datasets/B1MI0809M5/summary.rtf
deleted file mode 100644
index 134e635..0000000
--- a/general/datasets/B1MI0809M5/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 79, Name: Barley1 Leaf INOC TTKS (Aug09)
\ No newline at end of file
diff --git a/general/datasets/B1MI0809R/summary.rtf b/general/datasets/B1MI0809R/summary.rtf
deleted file mode 100644
index 134e635..0000000
--- a/general/datasets/B1MI0809R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 79, Name: Barley1 Leaf INOC TTKS (Aug09)
\ No newline at end of file
diff --git a/general/datasets/B30_K_1206_M/acknowledgment.rtf b/general/datasets/B30_K_1206_M/acknowledgment.rtf
deleted file mode 100644
index 5d9cc73..0000000
--- a/general/datasets/B30_K_1206_M/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant SCR/910/04 The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
-
diff --git a/general/datasets/B30_K_1206_M/cases.rtf b/general/datasets/B30_K_1206_M/cases.rtf
deleted file mode 100644
index 1425413..0000000
--- a/general/datasets/B30_K_1206_M/cases.rtf
+++ /dev/null
@@ -1,1748 +0,0 @@
-
-The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
-
-The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
-1) pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
-2) 'minimapper' subset - MINI;
-3) lines that have expression data removed - ERROR:
-
-
-
-
- | Order # |
- Line ID |
- Permanent Oregon ID |
- Cross direction |
-
- CEL file names
- |
- Mini-mapper set |
- Error check |
-
-
- | embryo data-set |
- leaf data-set |
- embryo data-set |
- leaf data-set |
-
-
- | 1 |
- SM001 |
- 2907001 |
- Steptoe/Morex(BxF) |
- AD_SCRI_82.CEL |
- |
- |
- OK |
- |
-
-
- | 2 |
- SM002 |
- 2907002 |
- Steptoe/Morex(BxF) |
- AD_SCRI_1.CEL |
- |
- |
- OK |
- |
-
-
- | 3 |
- SM003 |
- 2907003 |
- Morex/Steptoe(CxF) |
- AD_SCRI_19.CEL |
- |
- |
- OK |
- |
-
-
- | 4 |
- SM004 |
- 2907004 |
- Morex/Steptoe(CxF) |
- AD_SCRI_3.CEL |
- 0521-1_SetA1.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 5 |
- SM005 |
- 2907005 |
- Steptoe/Morex(BxH) |
- AD_SCRI_88.CEL |
- |
- |
- OK |
- |
-
-
- | 6 |
- SM006 |
- 2907006 |
- Morex/Steptoe(CxF) |
- AD_SCRI_48.CEL |
- |
- |
- OK |
- |
-
-
- | 7 |
- SM007 |
- 2907007 |
- Steptoe/Morex(BxH) |
- AD_SCRI_35.CEL |
- 0521-2_SetA2.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 8 |
- SM009 |
- 2907009 |
- Steptoe/Morex(BxF) |
- AD_SCRI_2.CEL |
- |
- |
- OK |
- |
-
-
- | 9 |
- SM010 |
- 2907010 |
- Morex/Steptoe(IxE) |
- AD_SCRI_42.CEL |
- |
- |
- OK |
- |
-
-
- | 10 |
- SM011 |
- 2907011 |
- Steptoe/Morex(QxG) |
- AD_SCRI_10.CEL |
- |
- |
- OK |
- |
-
-
- | 11 |
- SM012 |
- 2907012 |
- Morex/Steptoe(CxF) |
- AD_SCRI_45.CEL |
- 0521-3_SetA3.CEL |
- SMmini |
- ERROR |
- ERROR |
-
-
- | 12 |
- SM013 |
- 2907013 |
- Morex/Steptoe(IxE) |
- AD_SCRI_78.CEL |
- 0521-4_SetA4.CEL |
- SMmini |
- ERROR |
- ERROR |
-
-
- | 13 |
- SM014 |
- 2907014 |
- Steptoe/Morex(BxH) |
- AD_SCRI_18.CEL |
- |
- |
- OK |
- |
-
-
- | 14 |
- SM015 |
- 2907015 |
- Steptoe/Morex(BxH) |
- AD_SCRI_5.CEL |
- |
- |
- OK |
- |
-
-
- | 15 |
- SM016 |
- 2907016 |
- Steptoe/Morex(BxH) |
- AD_SCRI_21.CEL |
- |
- |
- OK |
- |
-
-
- | 16 |
- SM020 |
- 2907020 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_77.CEL |
- |
- |
- OK |
- |
-
-
- | 17 |
- SM021 |
- 2907021 |
- Morex/Steptoe(IxE) |
- AD_SCRI_30.CEL |
- |
- |
- OK |
- |
-
-
- | 18 |
- SM022 |
- 2907022 |
- Morex/Steptoe(IxE) |
- AD_SCRI_31.CEL |
- 0521-5_SetA5.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 19 |
- SM023 |
- 2907023 |
- Steptoe/Morex(BxH) |
- AD_SCRI_32.CEL |
- |
- |
- OK |
- |
-
-
- | 20 |
- SM024 |
- 2907024 |
- Morex/Steptoe(IxE) |
- AD_SCRI_33.CEL |
- 0521-6_SetA6.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 21 |
- SM025 |
- 2907025 |
- Morex/Steptoe(CxF) |
- AD_SCRI_34.CEL |
- |
- |
- OK |
- |
-
-
- | 22 |
- SM027 |
- 2907027 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_12.CEL |
- 0521-7_SetA7.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 23 |
- SM030 |
- 2907030 |
- Morex/Steptoe(IxE) |
- AD_SCRI_79.CEL |
- |
- |
- OK |
- |
-
-
- | 24 |
- SM031 |
- 2907031 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_16.CEL |
- |
- |
- OK |
- |
-
-
- | 25 |
- SM032 |
- 2907032 |
- Morex/Steptoe(IxE) |
- AD_SCRI_13.CEL |
- |
- |
- OK |
- |
-
-
- | 26 |
- SM035 |
- 2907035 |
- Morex/Steptoe(CxF) |
- AD_SCRI_15.CEL |
- |
- |
- ERROR |
- |
-
-
- | 27 |
- SM039 |
- 2907039 |
- Morex/Steptoe(CxF) |
- AD_SCRI_41.CEL |
- |
- |
- OK |
- |
-
-
- | 28 |
- SM040 |
- 2907040 |
- Steptoe/Morex(BxH) |
- AD_SCRI_83.CEL |
- |
- |
- OK |
- |
-
-
- | 29 |
- SM041 |
- 2907041 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_11_redo.CEL |
- 0521-8_SetA8.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 30 |
- SM042 |
- 2907042 |
- Morex/Steptoe(CxF) |
- AD_SCRI_57.CEL |
- |
- |
- OK |
- |
-
-
- | 31 |
- SM043 |
- 2907043 |
- Morex/Steptoe(JxE) |
- AD_SCRI_49.CEL |
- 0521-9_SetA9.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 32 |
- SM044 |
- 2907044 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_50.CEL |
- 0521-10_SetA10.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 33 |
- SM045 |
- 2907045 |
- Steptoe/Morex(BxH) |
- AD_SCRI_51.CEL |
- |
- |
- OK |
- |
-
-
- | 34 |
- SM046 |
- 2907046 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_52.CEL |
- 0521-11_SetA11.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 35 |
- SM048 |
- 2907048 |
- Steptoe/Morex(BxF) |
- AD_SCRI_53.CEL |
- |
- |
- ERROR |
- |
-
-
- | 36 |
- SM050 |
- 2907050 |
- Morex/Steptoe(IxE) |
- AD_SCRI_46.CEL |
- |
- |
- OK |
- |
-
-
- | 37 |
- SM054 |
- 2907054 |
- Morex/Steptoe(CxF) |
- AD_SCRI_60.CEL |
- |
- |
- OK |
- |
-
-
- | 38 |
- SM055 |
- 2907055 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_55.CEL |
- |
- |
- OK |
- |
-
-
- | 39 |
- SM056 |
- 2907056 |
- Steptoe/Morex(BxH) |
- AD_SCRI_23.CEL |
- |
- |
- OK |
- |
-
-
- | 40 |
- SM057 |
- 2907057 |
- Morex/Steptoe(CxF) |
- AD_SCRI_24.CEL |
- |
- |
- OK |
- |
-
-
- | 41 |
- SM058 |
- 2907058 |
- Steptoe/Morex(BxF) |
- AD_SCRI_22.CEL |
- |
- |
- OK |
- |
-
-
- | 42 |
- SM059 |
- 2907059 |
- Steptoe/Morex(BxH) |
- AD_SCRI_27.CEL |
- |
- |
- OK |
- |
-
-
- | 43 |
- SM061 |
- 2907061 |
- Morex/Steptoe(LxF) |
- AD_SCRI_81.CEL |
- 0521-12_SetA12.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 44 |
- SM062 |
- 2907062 |
- Morex/Steptoe(CxF) |
- AD_SCRI_44.CEL |
- |
- |
- OK |
- |
-
-
- | 45 |
- SM063 |
- 2907063 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_40.CEL |
- 0521-13_SetA13.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 46 |
- SM064 |
- 2907064 |
- Morex/Steptoe(CxF) |
- AD_SCRI_87_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 47 |
- SM065 |
- 2907065 |
- Morex/Steptoe(CxF) |
- AD_SCRI_54.CEL |
- |
- |
- OK |
- |
-
-
- | 48 |
- SM067 |
- 2907067 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_73.CEL |
- |
- |
- OK |
- |
-
-
- | 49 |
- SM068 |
- 2907068 |
- Steptoe/Morex(OxG) |
- AD_SCRI_56.CEL |
- |
- |
- ERROR |
- |
-
-
- | 50 |
- SM069 |
- 2907069 |
- Steptoe/Morex(BxH) |
- AD_SCRI_71.CEL |
- |
- |
- OK |
- |
-
-
- | 51 |
- SM070 |
- 2907070 |
- Steptoe/Morex(BxF) |
- AD_SCRI_64.CEL |
- |
- |
- OK |
- |
-
-
- | 52 |
- SM071 |
- 2907071 |
- Steptoe/Morex(BxH) |
- AD_SCRI_58.CEL |
- |
- |
- OK |
- |
-
-
- | 53 |
- SM072 |
- 2907072 |
- Morex/Steptoe(CxF) |
- AD_SCRI_59.CEL |
- |
- |
- OK |
- |
-
-
- | 54 |
- SM073 |
- 2907073 |
- Steptoe/Morex(BxF) |
- AD_SCRI_74.CEL |
- 0521-14_SetA14.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 55 |
- SM074 |
- 2907074 |
- Morex/Steptoe(CxF) |
- AD_SCRI_25.CEL |
- 0521-15_SetA15.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 56 |
- SM075 |
- 2907075 |
- Steptoe/Morex(QxG) |
- AD_SCRI_120.CEL |
- |
- |
- OK |
- |
-
-
- | 57 |
- SM076 |
- 2907076 |
- Steptoe/Morex(BxF) |
- AD_SCRI_112.CEL |
- |
- |
- OK |
- |
-
-
- | 58 |
- SM077 |
- 2907077 |
- Morex/Steptoe(CxF) |
- AD_SCRI_142.CEL |
- |
- |
- OK |
- |
-
-
- | 59 |
- SM078 |
- 2907078 |
- Steptoe/Morex(BxF) |
- AD_SCRI_86.CEL |
- |
- |
- OK |
- |
-
-
- | 60 |
- SM079 |
- 2907079 |
- Morex/Steptoe(CxF) |
- AD_SCRI_153.CEL |
- 0521-16_SetA16.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 61 |
- SM080 |
- 2907080 |
- Steptoe/Morex(BxF) |
- AD_SCRI_107.CEL |
- |
- |
- OK |
- |
-
-
- | 62 |
- SM081 |
- 2907081 |
- Morex/Steptoe(CxF) |
- AD_SCRI_105.CEL |
- |
- |
- OK |
- |
-
-
- | 63 |
- SM082 |
- 2907082 |
- Steptoe/Morex(BxF) |
- AD_SCRI_97.CEL |
- |
- |
- OK |
- |
-
-
- | 64 |
- SM083 |
- 2907083 |
- Steptoe/Morex(BxF) |
- AD_SCRI_89.CEL |
- |
- |
- OK |
- |
-
-
- | 65 |
- SM084 |
- 2907084 |
- Morex/Steptoe(CxF) |
- AD_SCRI_155.CEL |
- |
- |
- OK |
- |
-
-
- | 66 |
- SM085 |
- 2907085 |
- Morex/Steptoe(IxE) |
- AD_SCRI_149.CEL |
- 0521-17_SetA17.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 67 |
- SM087 |
- 2907087 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_113.CEL |
- |
- |
- OK |
- |
-
-
- | 68 |
- SM088 |
- 2907088 |
- Morex/Steptoe(CxF) |
- AD_SCRI_93.CEL |
- 0521-18_SetA18.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 69 |
- SM089 |
- 2907089 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_148.CEL |
- 0521-19_SetA19.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 70 |
- SM091 |
- 2907091 |
- Morex/Steptoe(CxF) |
- AD_SCRI_110.CEL |
- |
- |
- OK |
- |
-
-
- | 71 |
- SM092 |
- 2907092 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_7.CEL |
- |
- |
- OK |
- |
-
-
- | 72 |
- SM093 |
- 2907093 |
- Steptoe/Morex(BxF) |
- AD_SCRI_122.CEL |
- |
- |
- OK |
- |
-
-
- | 73 |
- SM094 |
- 2907094 |
- Morex/Steptoe(CxF) |
- AD_SCRI_150.CEL |
- |
- |
- OK |
- |
-
-
- | 74 |
- SM097 |
- 2907097 |
- Morex/Steptoe(CxF) |
- AD_SCRI_158.CEL |
- |
- |
- OK |
- |
-
-
- | 75 |
- SM098 |
- 2907098 |
- Morex/Steptoe(CxF) |
- AD_SCRI_121.CEL |
- |
- |
- OK |
- |
-
-
- | 76 |
- SM099 |
- 2907099 |
- Steptoe/Morex(QxG) |
- AD_SCRI_137.CEL |
- |
- |
- OK |
- |
-
-
- | 77 |
- SM103 |
- 2907103 |
- Morex/Steptoe(IxE) |
- AD_SCRI_156.CEL |
- |
- |
- OK |
- |
-
-
- | 78 |
- SM104 |
- 2907104 |
- Steptoe/Morex(BxH) |
- AD_SCRI_70.CEL |
- |
- |
- ERROR |
- |
-
-
- | 79 |
- SM105 |
- 2907105 |
- Morex/Steptoe(IxE) |
- AD_SCRI_69.CEL |
- |
- |
- OK |
- |
-
-
- | 80 |
- SM110 |
- 2907110 |
- Morex/Steptoe(CxF) |
- AD_SCRI_75.CEL |
- |
- |
- ERROR |
- |
-
-
- | 81 |
- SM112 |
- 2907112 |
- Steptoe/Morex(BxF) |
- AD_SCRI_84.CEL |
- |
- |
- OK |
- |
-
-
- | 82 |
- SM116 |
- 2907116 |
- Morex/Steptoe(CxF) |
- AD_SCRI_117.CEL |
- 0521-20_SetA20.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 83 |
- SM120 |
- 2907120 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_138.CEL |
- |
- |
- OK |
- |
-
-
- | 84 |
- SM124 |
- 2907124 |
- Steptoe/Morex(BxF) |
- AD_SCRI_146.CEL |
- |
- |
- OK |
- |
-
-
- | 85 |
- SM125 |
- 2907125 |
- Morex/Steptoe(IxE) |
- AD_SCRI_43.CEL |
- |
- |
- OK |
- |
-
-
- | 86 |
- SM126 |
- 2907126 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_144_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 87 |
- SM127 |
- 2907127 |
- Steptoe/Morex(BxH) |
- AD_SCRI_129.CEL |
- |
- |
- OK |
- |
-
-
- | 88 |
- SM129 |
- 2907129 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_132.CEL |
- |
- |
- OK |
- |
-
-
- | 89 |
- SM130 |
- 2907130 |
- Morex/Steptoe(CxF) |
- AD_SCRI_101.CEL |
- 0521-21_SetA21.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 90 |
- SM131 |
- 2907131 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_102.CEL |
- |
- |
- OK |
- |
-
-
- | 91 |
- SM132 |
- 2907132 |
- Steptoe/Morex(QxG) |
- AD_SCRI_4_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 92 |
- SM133 |
- 2907133 |
- Morex/Steptoe(CxF) |
- AD_SCRI_157.CEL |
- |
- |
- OK |
- |
-
-
- | 93 |
- SM134 |
- 2907134 |
- Morex/Steptoe(IxE) |
- AD_SCRI_159.CEL |
- |
- |
- OK |
- |
-
-
- | 94 |
- SM135 |
- 2907135 |
- Steptoe/Morex(BxF) |
- AD_SCRI_72.CEL |
- 0521-22_SetA22.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 95 |
- SM136 |
- 2907136 |
- Steptoe/Morex(QxG) |
- AD_SCRI_123.CEL |
- 0521-23_SetA23.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 96 |
- SM137 |
- 2907137 |
- Steptoe/Morex(BxH) |
- AD_SCRI_39.CEL |
- |
- |
- OK |
- |
-
-
- | 97 |
- SM139 |
- 2907139 |
- Morex/Steptoe(CxF) |
- AD_SCRI_133.CEL |
- |
- |
- OK |
- |
-
-
- | 98 |
- SM140 |
- 2907140 |
- Morex/Steptoe(CxF) |
- AD_SCRI_134.CEL |
- 0521-24_SetA24.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 99 |
- SM141 |
- 2907141 |
- Steptoe/Morex(BxH) |
- AD_SCRI_136.CEL |
- 0521-25_SetA25.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 100 |
- SM142 |
- 2907142 |
- Morex/Steptoe(IxE) |
- AD_SCRI_6.CEL |
- |
- |
- OK |
- |
-
-
- | 101 |
- SM143 |
- 2907143 |
- Steptoe/Morex(BxH) |
- AD_SCRI_145.CEL |
- |
- |
- OK |
- |
-
-
- | 102 |
- SM144 |
- 2907144 |
- Steptoe/Morex(BxF) |
- AD_SCRI_103.CEL |
- |
- |
- OK |
- |
-
-
- | 103 |
- SM145 |
- 2907145 |
- Steptoe/Morex(QxG) |
- AD_SCRI_108.CEL |
- |
- |
- OK |
- |
-
-
- | 104 |
- SM146 |
- 2907146 |
- Morex/Steptoe(BxF) |
- AD_SCRI_91.CEL |
- 0521-26_SetA26.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 105 |
- SM147 |
- 2907147 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_139.CEL |
- |
- |
- OK |
- |
-
-
- | 106 |
- SM149 |
- 2907149 |
- Steptoe/Morex(BxF) |
- AD_SCRI_131.CEL |
- |
- |
- ERROR |
- |
-
-
- | 107 |
- SM150 |
- 2907150 |
- Morex/Steptoe(CxF) |
- AD_SCRI_37.CEL |
- |
- |
- OK |
- |
-
-
- | 108 |
- SM151 |
- 2907151 |
- Morex/Steptoe(IxE) |
- AD_SCRI_28.CEL |
- |
- |
- OK |
- |
-
-
- | 109 |
- SM152 |
- 2907152 |
- Steptoe/Morex(BxH) |
- AD_SCRI_9_redo.CEL |
- 0521-27_SetA27.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 110 |
- SM153 |
- 2907153 |
- Steptoe/Morex(BxH) |
- AD_SCRI_135.CEL |
- |
- |
- OK |
- |
-
-
- | 111 |
- SM154 |
- 2907154 |
- Steptoe/Morex(BxH) |
- AD_SCRI_114.CEL |
- |
- |
- OK |
- |
-
-
- | 112 |
- SM155 |
- 2907155 |
- Steptoe/Morex(BxH) |
- AD_SCRI_119.CEL |
- 0521-28_SetA28.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 113 |
- SM156 |
- 2907156 |
- Steptoe/Morex(BxH) |
- AD_SCRI_140.CEL |
- |
- |
- OK |
- |
-
-
- | 114 |
- SM157 |
- 2907157 |
- Morex/Steptoe(CxF) |
- AD_SCRI_106_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 115 |
- SM158 |
- 2907158 |
- Morex/Steptoe(CxF) |
- AD_SCRI_65.CEL |
- |
- |
- OK |
- |
-
-
- | 116 |
- SM159 |
- 2907159 |
- Morex/Steptoe(IxE) |
- AD_SCRI_168.CEL |
- |
- |
- OK |
- |
-
-
- | 117 |
- SM160 |
- 2907160 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_47.CEL |
- 0521-29_SetA29.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 118 |
- SM161 |
- 2907161 |
- Steptoe/Morex(BxH) |
- AD_SCRI_76.CEL |
- |
- |
- ERROR |
- |
-
-
- | 119 |
- SM162 |
- 2907162 |
- Morex/Steptoe(CxF) |
- AD_SCRI_147.CEL |
- |
- |
- OK |
- |
-
-
- | 120 |
- SM164 |
- 2907164 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_128.CEL |
- |
- |
- OK |
- |
-
-
- | 121 |
- SM165 |
- 2907165 |
- Steptoe/Morex(BxH) |
- AD_SCRI_143.CEL |
- |
- |
- OK |
- OK |
-
-
- | 122 |
- SM166 |
- 2907166 |
- Morex/Steptoe(CxF) |
- AD_SCRI_115.CEL |
- |
- |
- OK |
- |
-
-
- | 123 |
- SM167 |
- 2907167 |
- Steptoe/Morex(BxH) |
- AD_SCRI_127.CEL |
- 0521-30_SetA30.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 124 |
- SM168 |
- 2907168 |
- Steptoe/Morex(BxH) |
- AD_SCRI_130.CEL |
- |
- |
- OK |
- |
-
-
- | 125 |
- SM169 |
- 2907169 |
- Morex/Steptoe(CxF) |
- AD_SCRI_118.CEL |
- 0521-31_SetA31.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 126 |
- SM170 |
- 2907170 |
- Steptoe/Morex(BxF) |
- AD_SCRI_151.CEL |
- |
- |
- OK |
- |
-
-
- | 127 |
- SM171 |
- 2907171 |
- Steptoe/Morex(BxF) |
- AD_SCRI_165.CEL |
- |
- |
- ERROR |
- |
-
-
- | 128 |
- SM172 |
- 2907172 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_152.CEL |
- |
- |
- ERROR |
- |
-
-
- | 129 |
- SM173 |
- 2907173 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_104.CEL |
- 0521-32_SetA32.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 130 |
- SM174 |
- 2907174 |
- Steptoe/Morex(BxH) |
- AD_SCRI_154.CEL |
- |
- |
- OK |
- |
-
-
- | 131 |
- SM176 |
- 2907176 |
- Morex/Steptoe(CxF) |
- AD_SCRI_141.CEL |
- |
- |
- OK |
- |
-
-
- | 132 |
- SM177 |
- 2907177 |
- Morex/Steptoe(CxF) |
- AD_SCRI_111.CEL |
- 0521-33_SetA33.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 133 |
- SM179 |
- 2907179 |
- Morex/Steptoe(CxF) |
- AD_SCRI_166.CEL |
- |
- |
- OK |
- |
-
-
- | 134 |
- SM180 |
- 2907180 |
- Morex/Steptoe(IxE) |
- AD_SCRI_161.CEL |
- |
- |
- OK |
- |
-
-
- | 135 |
- SM181 |
- 2907181 |
- Morex/Steptoe(IxE) |
- AD_SCRI_162.CEL |
- |
- |
- OK |
- |
-
-
- | 136 |
- SM182 |
- 2907182 |
- Morex/Steptoe(CxF) |
- AD_SCRI_163.CEL |
- |
- |
- OK |
- |
-
-
- | 137 |
- SM183 |
- 2907183 |
- Morex/Steptoe(CxF) |
- AD_SCRI_164.CEL |
- |
- |
- OK |
- |
-
-
- | 138 |
- SM184 |
- 2907184 |
- Morex/Steptoe(IxE) |
- AD_SCRI_160.CEL |
- 0521-34_SetA34.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 139 |
- SM185 |
- 2907185 |
- Morex/Steptoe(IxE) |
- AD_SCRI_167.CEL |
- |
- |
- OK |
- |
-
-
- | 140 |
- SM186 |
- 2907186 |
- Morex/Steptoe(IxE) |
- AD_SCRI_62.CEL |
- |
- |
- OK |
- |
-
-
- | 141 |
- SM187 |
- 2907187 |
- Morex/Steptoe(IxE) |
- AD_SCRI_61.CEL |
- |
- |
- OK |
- |
-
-
- | 142 |
- SM188 |
- 2907188 |
- Morex/Steptoe(CxF) |
- AD_SCRI_63.CEL |
- |
- |
- OK |
- |
-
-
- | 143 |
- SM189 |
- 2907189 |
- Steptoe/Morex(QxG) |
- AD_SCRI_80.CEL |
- |
- |
- OK |
- |
-
-
- | 144 |
- SM193 |
- 2907193 |
- Morex/Steptoe(IxE) |
- AD_SCRI_36.CEL |
- |
- |
- OK |
- |
-
-
- | 145 |
- SM194 |
- 2907194 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_29.CEL |
- |
- |
- OK |
- |
-
-
- | 146 |
- SM196 |
- 2907196 |
- Steptoe/Morex(BxF) |
- AD_SCRI_26.CEL |
- |
- |
- OK |
- |
-
-
- | 147 |
- SM197 |
- 2907197 |
- Steptoe/Morex(BxF) |
- AD_SCRI_85.CEL |
- |
- |
- OK |
- |
-
-
- | 148 |
- SM198 |
- 2907198 |
- Morex/Steptoe(IxE) |
- AD_SCRI_8.CEL |
- |
- |
- OK |
- |
-
-
- | 149 |
- SM199 |
- 2907199 |
- Steptoe/Morex(BxF) |
- AD_SCRI_20.CEL |
- |
- |
- OK |
- |
-
-
- | 150 |
- SM200 |
- 2907200 |
- Morex/Steptoe(IxE) |
- AD_SCRI_38.CEL |
- 0521-35_SetA35.CEL |
- SMmini |
- OK |
- OK |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_17.CEL |
- 0521-36_SetA36.CEL |
- |
- |
- |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_66.CEL |
- 0521-37_SetA37.CEL |
- |
- |
- |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_68.CEL |
- 0521-38_SetA38.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_116.CEL |
- 0521-39_SetA39.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_14.CEL |
- 0521-40_SetA40.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_67.CEL |
- 0521-41_SetA41.CEL |
- |
- |
- |
-
-
-
-
-
-
diff --git a/general/datasets/B30_K_1206_M/experiment-design.rtf b/general/datasets/B30_K_1206_M/experiment-design.rtf
deleted file mode 100644
index e743086..0000000
--- a/general/datasets/B30_K_1206_M/experiment-design.rtf
+++ /dev/null
@@ -1,62 +0,0 @@
-
-RNA Sample Processing:
-
-Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
-
-
-☠Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
-☠Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
-☠Incubate samples at 60oC for 10 minutes, vortexing three times.
-☠Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
-☠While centrifuging, label new set of 15 ml tubes
-☠Transfer supernatant to 15 ml centrifuge tube
-☠Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
-seconds, and incubate at room temperature for 5 minutes.
-☠Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
-☠While centrifuging, label new 15 ml tubes
-☠Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
-☠Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
-☠Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
-☠Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
-4000 rpm for 15 minutes @ 4oC.
-☠Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
-☠Air-dry the pellet for 10 minutes, inverted on a kimwipe.
-☠Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
-few times.
-☠Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
-☠Set water bath to 37oC.
-☠Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
-☠Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
-☠Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
-☠Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
-☠Label 15 ml tubes from the kit and place midi columns in them
-☠Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
-☠Discard the flow-through.
-☠Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
-incubate for 3 min
-☠Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
-☠Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
-gently, incubate for 3 min
-☠Centrifuge for 10 min at 3000 rpm, remove flow-through
-☠Centrifuge again for another 5 min.
-☠Label new 15 ml tubes from the kit.
-☠Transfer the RNA easy column to a new tube and pipet 250 ul volume of
-RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
-☠Centrifuge for 5 min at 3000 rpm.
-☠To the same tube add again 250 ul H2O, incubate for 1 min.
-☠Centrifuge for 5 min at 3000 rpm.
-☠Label two sets of 1.5 ml Eppendorf tubes.
-☠Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
-
-Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
-
-Replication and Sample Balance:
-
-3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
-
-Experimental Design and Batch Structure:
-
-
-
-The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs: E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
-
diff --git a/general/datasets/B30_K_1206_M/notes.rtf b/general/datasets/B30_K_1206_M/notes.rtf
deleted file mode 100644
index 46cff8f..0000000
--- a/general/datasets/B30_K_1206_M/notes.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Arnis Druka
-Genetics Programme
-Scottish Crop Research Institute
-Invergowrie, Dundee DD2 5DA
-Angus, Scotland, United Kingdom
-Tel +44 01382 562731
-Fax +44 01382 568587
-adruka@scri.sari.ac.uk
-
-
-
-This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
-
diff --git a/general/datasets/B30_K_1206_M/platform.rtf b/general/datasets/B30_K_1206_M/platform.rtf
deleted file mode 100644
index a935318..0000000
--- a/general/datasets/B30_K_1206_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
-
diff --git a/general/datasets/B30_K_1206_M/processing.rtf b/general/datasets/B30_K_1206_M/processing.rtf
deleted file mode 100644
index d8d039a..0000000
--- a/general/datasets/B30_K_1206_M/processing.rtf
+++ /dev/null
@@ -1,49 +0,0 @@
-
-
-
-
- |
- Types of the expression data-sets
- |
-
- Data processing description
- |
-
-
- Barley1 Embryo gcRMA SCRI (Dec 06)
- Barley1 Leaf gcRMA SCRI (Dec 06) |
-
-
-
- The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
-
-
- |
-
-
- Barley1 Embryo MAS 5.0 SCRI (Dec 06)
- Barley1 Leaf MAS 5.0 SCRI (Dec 06) |
-
-
-
- The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
-
-
- |
-
-
- Barley1 Embryo0 gcRMA SCRI (Apr 06)
- Barley1 Leaf gcRMAn SCRI (Dec 06) |
-
- The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
-
-
- - Values below 0.01 were set to 0.01.
- - Each measurement was divided by the 50.0th percentile of all measurements in that sample.
- - Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
-
- |
-
-
-
-
diff --git a/general/datasets/B30_K_1206_M/summary.rtf b/general/datasets/B30_K_1206_M/summary.rtf
deleted file mode 100644
index 67f4fab..0000000
--- a/general/datasets/B30_K_1206_M/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Barley1 Leaf MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
-
-
-The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip (GEO GPL1340).
-
diff --git a/general/datasets/B30_K_1206_M/tissue.rtf b/general/datasets/B30_K_1206_M/tissue.rtf
deleted file mode 100644
index a8351e8..0000000
--- a/general/datasets/B30_K_1206_M/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
-
-To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
-
-To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
-
-
-
diff --git a/general/datasets/B30_K_1206_R/acknowledgment.rtf b/general/datasets/B30_K_1206_R/acknowledgment.rtf
deleted file mode 100644
index 5d9cc73..0000000
--- a/general/datasets/B30_K_1206_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant SCR/910/04 The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
-
diff --git a/general/datasets/B30_K_1206_R/cases.rtf b/general/datasets/B30_K_1206_R/cases.rtf
deleted file mode 100644
index 1425413..0000000
--- a/general/datasets/B30_K_1206_R/cases.rtf
+++ /dev/null
@@ -1,1748 +0,0 @@
-
-The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
-
-The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
-1) pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
-2) 'minimapper' subset - MINI;
-3) lines that have expression data removed - ERROR:
-
-
-
-
- | Order # |
- Line ID |
- Permanent Oregon ID |
- Cross direction |
-
- CEL file names
- |
- Mini-mapper set |
- Error check |
-
-
- | embryo data-set |
- leaf data-set |
- embryo data-set |
- leaf data-set |
-
-
- | 1 |
- SM001 |
- 2907001 |
- Steptoe/Morex(BxF) |
- AD_SCRI_82.CEL |
- |
- |
- OK |
- |
-
-
- | 2 |
- SM002 |
- 2907002 |
- Steptoe/Morex(BxF) |
- AD_SCRI_1.CEL |
- |
- |
- OK |
- |
-
-
- | 3 |
- SM003 |
- 2907003 |
- Morex/Steptoe(CxF) |
- AD_SCRI_19.CEL |
- |
- |
- OK |
- |
-
-
- | 4 |
- SM004 |
- 2907004 |
- Morex/Steptoe(CxF) |
- AD_SCRI_3.CEL |
- 0521-1_SetA1.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 5 |
- SM005 |
- 2907005 |
- Steptoe/Morex(BxH) |
- AD_SCRI_88.CEL |
- |
- |
- OK |
- |
-
-
- | 6 |
- SM006 |
- 2907006 |
- Morex/Steptoe(CxF) |
- AD_SCRI_48.CEL |
- |
- |
- OK |
- |
-
-
- | 7 |
- SM007 |
- 2907007 |
- Steptoe/Morex(BxH) |
- AD_SCRI_35.CEL |
- 0521-2_SetA2.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 8 |
- SM009 |
- 2907009 |
- Steptoe/Morex(BxF) |
- AD_SCRI_2.CEL |
- |
- |
- OK |
- |
-
-
- | 9 |
- SM010 |
- 2907010 |
- Morex/Steptoe(IxE) |
- AD_SCRI_42.CEL |
- |
- |
- OK |
- |
-
-
- | 10 |
- SM011 |
- 2907011 |
- Steptoe/Morex(QxG) |
- AD_SCRI_10.CEL |
- |
- |
- OK |
- |
-
-
- | 11 |
- SM012 |
- 2907012 |
- Morex/Steptoe(CxF) |
- AD_SCRI_45.CEL |
- 0521-3_SetA3.CEL |
- SMmini |
- ERROR |
- ERROR |
-
-
- | 12 |
- SM013 |
- 2907013 |
- Morex/Steptoe(IxE) |
- AD_SCRI_78.CEL |
- 0521-4_SetA4.CEL |
- SMmini |
- ERROR |
- ERROR |
-
-
- | 13 |
- SM014 |
- 2907014 |
- Steptoe/Morex(BxH) |
- AD_SCRI_18.CEL |
- |
- |
- OK |
- |
-
-
- | 14 |
- SM015 |
- 2907015 |
- Steptoe/Morex(BxH) |
- AD_SCRI_5.CEL |
- |
- |
- OK |
- |
-
-
- | 15 |
- SM016 |
- 2907016 |
- Steptoe/Morex(BxH) |
- AD_SCRI_21.CEL |
- |
- |
- OK |
- |
-
-
- | 16 |
- SM020 |
- 2907020 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_77.CEL |
- |
- |
- OK |
- |
-
-
- | 17 |
- SM021 |
- 2907021 |
- Morex/Steptoe(IxE) |
- AD_SCRI_30.CEL |
- |
- |
- OK |
- |
-
-
- | 18 |
- SM022 |
- 2907022 |
- Morex/Steptoe(IxE) |
- AD_SCRI_31.CEL |
- 0521-5_SetA5.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 19 |
- SM023 |
- 2907023 |
- Steptoe/Morex(BxH) |
- AD_SCRI_32.CEL |
- |
- |
- OK |
- |
-
-
- | 20 |
- SM024 |
- 2907024 |
- Morex/Steptoe(IxE) |
- AD_SCRI_33.CEL |
- 0521-6_SetA6.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 21 |
- SM025 |
- 2907025 |
- Morex/Steptoe(CxF) |
- AD_SCRI_34.CEL |
- |
- |
- OK |
- |
-
-
- | 22 |
- SM027 |
- 2907027 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_12.CEL |
- 0521-7_SetA7.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 23 |
- SM030 |
- 2907030 |
- Morex/Steptoe(IxE) |
- AD_SCRI_79.CEL |
- |
- |
- OK |
- |
-
-
- | 24 |
- SM031 |
- 2907031 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_16.CEL |
- |
- |
- OK |
- |
-
-
- | 25 |
- SM032 |
- 2907032 |
- Morex/Steptoe(IxE) |
- AD_SCRI_13.CEL |
- |
- |
- OK |
- |
-
-
- | 26 |
- SM035 |
- 2907035 |
- Morex/Steptoe(CxF) |
- AD_SCRI_15.CEL |
- |
- |
- ERROR |
- |
-
-
- | 27 |
- SM039 |
- 2907039 |
- Morex/Steptoe(CxF) |
- AD_SCRI_41.CEL |
- |
- |
- OK |
- |
-
-
- | 28 |
- SM040 |
- 2907040 |
- Steptoe/Morex(BxH) |
- AD_SCRI_83.CEL |
- |
- |
- OK |
- |
-
-
- | 29 |
- SM041 |
- 2907041 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_11_redo.CEL |
- 0521-8_SetA8.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 30 |
- SM042 |
- 2907042 |
- Morex/Steptoe(CxF) |
- AD_SCRI_57.CEL |
- |
- |
- OK |
- |
-
-
- | 31 |
- SM043 |
- 2907043 |
- Morex/Steptoe(JxE) |
- AD_SCRI_49.CEL |
- 0521-9_SetA9.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 32 |
- SM044 |
- 2907044 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_50.CEL |
- 0521-10_SetA10.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 33 |
- SM045 |
- 2907045 |
- Steptoe/Morex(BxH) |
- AD_SCRI_51.CEL |
- |
- |
- OK |
- |
-
-
- | 34 |
- SM046 |
- 2907046 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_52.CEL |
- 0521-11_SetA11.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 35 |
- SM048 |
- 2907048 |
- Steptoe/Morex(BxF) |
- AD_SCRI_53.CEL |
- |
- |
- ERROR |
- |
-
-
- | 36 |
- SM050 |
- 2907050 |
- Morex/Steptoe(IxE) |
- AD_SCRI_46.CEL |
- |
- |
- OK |
- |
-
-
- | 37 |
- SM054 |
- 2907054 |
- Morex/Steptoe(CxF) |
- AD_SCRI_60.CEL |
- |
- |
- OK |
- |
-
-
- | 38 |
- SM055 |
- 2907055 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_55.CEL |
- |
- |
- OK |
- |
-
-
- | 39 |
- SM056 |
- 2907056 |
- Steptoe/Morex(BxH) |
- AD_SCRI_23.CEL |
- |
- |
- OK |
- |
-
-
- | 40 |
- SM057 |
- 2907057 |
- Morex/Steptoe(CxF) |
- AD_SCRI_24.CEL |
- |
- |
- OK |
- |
-
-
- | 41 |
- SM058 |
- 2907058 |
- Steptoe/Morex(BxF) |
- AD_SCRI_22.CEL |
- |
- |
- OK |
- |
-
-
- | 42 |
- SM059 |
- 2907059 |
- Steptoe/Morex(BxH) |
- AD_SCRI_27.CEL |
- |
- |
- OK |
- |
-
-
- | 43 |
- SM061 |
- 2907061 |
- Morex/Steptoe(LxF) |
- AD_SCRI_81.CEL |
- 0521-12_SetA12.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 44 |
- SM062 |
- 2907062 |
- Morex/Steptoe(CxF) |
- AD_SCRI_44.CEL |
- |
- |
- OK |
- |
-
-
- | 45 |
- SM063 |
- 2907063 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_40.CEL |
- 0521-13_SetA13.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 46 |
- SM064 |
- 2907064 |
- Morex/Steptoe(CxF) |
- AD_SCRI_87_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 47 |
- SM065 |
- 2907065 |
- Morex/Steptoe(CxF) |
- AD_SCRI_54.CEL |
- |
- |
- OK |
- |
-
-
- | 48 |
- SM067 |
- 2907067 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_73.CEL |
- |
- |
- OK |
- |
-
-
- | 49 |
- SM068 |
- 2907068 |
- Steptoe/Morex(OxG) |
- AD_SCRI_56.CEL |
- |
- |
- ERROR |
- |
-
-
- | 50 |
- SM069 |
- 2907069 |
- Steptoe/Morex(BxH) |
- AD_SCRI_71.CEL |
- |
- |
- OK |
- |
-
-
- | 51 |
- SM070 |
- 2907070 |
- Steptoe/Morex(BxF) |
- AD_SCRI_64.CEL |
- |
- |
- OK |
- |
-
-
- | 52 |
- SM071 |
- 2907071 |
- Steptoe/Morex(BxH) |
- AD_SCRI_58.CEL |
- |
- |
- OK |
- |
-
-
- | 53 |
- SM072 |
- 2907072 |
- Morex/Steptoe(CxF) |
- AD_SCRI_59.CEL |
- |
- |
- OK |
- |
-
-
- | 54 |
- SM073 |
- 2907073 |
- Steptoe/Morex(BxF) |
- AD_SCRI_74.CEL |
- 0521-14_SetA14.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 55 |
- SM074 |
- 2907074 |
- Morex/Steptoe(CxF) |
- AD_SCRI_25.CEL |
- 0521-15_SetA15.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 56 |
- SM075 |
- 2907075 |
- Steptoe/Morex(QxG) |
- AD_SCRI_120.CEL |
- |
- |
- OK |
- |
-
-
- | 57 |
- SM076 |
- 2907076 |
- Steptoe/Morex(BxF) |
- AD_SCRI_112.CEL |
- |
- |
- OK |
- |
-
-
- | 58 |
- SM077 |
- 2907077 |
- Morex/Steptoe(CxF) |
- AD_SCRI_142.CEL |
- |
- |
- OK |
- |
-
-
- | 59 |
- SM078 |
- 2907078 |
- Steptoe/Morex(BxF) |
- AD_SCRI_86.CEL |
- |
- |
- OK |
- |
-
-
- | 60 |
- SM079 |
- 2907079 |
- Morex/Steptoe(CxF) |
- AD_SCRI_153.CEL |
- 0521-16_SetA16.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 61 |
- SM080 |
- 2907080 |
- Steptoe/Morex(BxF) |
- AD_SCRI_107.CEL |
- |
- |
- OK |
- |
-
-
- | 62 |
- SM081 |
- 2907081 |
- Morex/Steptoe(CxF) |
- AD_SCRI_105.CEL |
- |
- |
- OK |
- |
-
-
- | 63 |
- SM082 |
- 2907082 |
- Steptoe/Morex(BxF) |
- AD_SCRI_97.CEL |
- |
- |
- OK |
- |
-
-
- | 64 |
- SM083 |
- 2907083 |
- Steptoe/Morex(BxF) |
- AD_SCRI_89.CEL |
- |
- |
- OK |
- |
-
-
- | 65 |
- SM084 |
- 2907084 |
- Morex/Steptoe(CxF) |
- AD_SCRI_155.CEL |
- |
- |
- OK |
- |
-
-
- | 66 |
- SM085 |
- 2907085 |
- Morex/Steptoe(IxE) |
- AD_SCRI_149.CEL |
- 0521-17_SetA17.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 67 |
- SM087 |
- 2907087 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_113.CEL |
- |
- |
- OK |
- |
-
-
- | 68 |
- SM088 |
- 2907088 |
- Morex/Steptoe(CxF) |
- AD_SCRI_93.CEL |
- 0521-18_SetA18.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 69 |
- SM089 |
- 2907089 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_148.CEL |
- 0521-19_SetA19.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 70 |
- SM091 |
- 2907091 |
- Morex/Steptoe(CxF) |
- AD_SCRI_110.CEL |
- |
- |
- OK |
- |
-
-
- | 71 |
- SM092 |
- 2907092 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_7.CEL |
- |
- |
- OK |
- |
-
-
- | 72 |
- SM093 |
- 2907093 |
- Steptoe/Morex(BxF) |
- AD_SCRI_122.CEL |
- |
- |
- OK |
- |
-
-
- | 73 |
- SM094 |
- 2907094 |
- Morex/Steptoe(CxF) |
- AD_SCRI_150.CEL |
- |
- |
- OK |
- |
-
-
- | 74 |
- SM097 |
- 2907097 |
- Morex/Steptoe(CxF) |
- AD_SCRI_158.CEL |
- |
- |
- OK |
- |
-
-
- | 75 |
- SM098 |
- 2907098 |
- Morex/Steptoe(CxF) |
- AD_SCRI_121.CEL |
- |
- |
- OK |
- |
-
-
- | 76 |
- SM099 |
- 2907099 |
- Steptoe/Morex(QxG) |
- AD_SCRI_137.CEL |
- |
- |
- OK |
- |
-
-
- | 77 |
- SM103 |
- 2907103 |
- Morex/Steptoe(IxE) |
- AD_SCRI_156.CEL |
- |
- |
- OK |
- |
-
-
- | 78 |
- SM104 |
- 2907104 |
- Steptoe/Morex(BxH) |
- AD_SCRI_70.CEL |
- |
- |
- ERROR |
- |
-
-
- | 79 |
- SM105 |
- 2907105 |
- Morex/Steptoe(IxE) |
- AD_SCRI_69.CEL |
- |
- |
- OK |
- |
-
-
- | 80 |
- SM110 |
- 2907110 |
- Morex/Steptoe(CxF) |
- AD_SCRI_75.CEL |
- |
- |
- ERROR |
- |
-
-
- | 81 |
- SM112 |
- 2907112 |
- Steptoe/Morex(BxF) |
- AD_SCRI_84.CEL |
- |
- |
- OK |
- |
-
-
- | 82 |
- SM116 |
- 2907116 |
- Morex/Steptoe(CxF) |
- AD_SCRI_117.CEL |
- 0521-20_SetA20.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 83 |
- SM120 |
- 2907120 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_138.CEL |
- |
- |
- OK |
- |
-
-
- | 84 |
- SM124 |
- 2907124 |
- Steptoe/Morex(BxF) |
- AD_SCRI_146.CEL |
- |
- |
- OK |
- |
-
-
- | 85 |
- SM125 |
- 2907125 |
- Morex/Steptoe(IxE) |
- AD_SCRI_43.CEL |
- |
- |
- OK |
- |
-
-
- | 86 |
- SM126 |
- 2907126 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_144_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 87 |
- SM127 |
- 2907127 |
- Steptoe/Morex(BxH) |
- AD_SCRI_129.CEL |
- |
- |
- OK |
- |
-
-
- | 88 |
- SM129 |
- 2907129 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_132.CEL |
- |
- |
- OK |
- |
-
-
- | 89 |
- SM130 |
- 2907130 |
- Morex/Steptoe(CxF) |
- AD_SCRI_101.CEL |
- 0521-21_SetA21.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 90 |
- SM131 |
- 2907131 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_102.CEL |
- |
- |
- OK |
- |
-
-
- | 91 |
- SM132 |
- 2907132 |
- Steptoe/Morex(QxG) |
- AD_SCRI_4_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 92 |
- SM133 |
- 2907133 |
- Morex/Steptoe(CxF) |
- AD_SCRI_157.CEL |
- |
- |
- OK |
- |
-
-
- | 93 |
- SM134 |
- 2907134 |
- Morex/Steptoe(IxE) |
- AD_SCRI_159.CEL |
- |
- |
- OK |
- |
-
-
- | 94 |
- SM135 |
- 2907135 |
- Steptoe/Morex(BxF) |
- AD_SCRI_72.CEL |
- 0521-22_SetA22.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 95 |
- SM136 |
- 2907136 |
- Steptoe/Morex(QxG) |
- AD_SCRI_123.CEL |
- 0521-23_SetA23.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 96 |
- SM137 |
- 2907137 |
- Steptoe/Morex(BxH) |
- AD_SCRI_39.CEL |
- |
- |
- OK |
- |
-
-
- | 97 |
- SM139 |
- 2907139 |
- Morex/Steptoe(CxF) |
- AD_SCRI_133.CEL |
- |
- |
- OK |
- |
-
-
- | 98 |
- SM140 |
- 2907140 |
- Morex/Steptoe(CxF) |
- AD_SCRI_134.CEL |
- 0521-24_SetA24.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 99 |
- SM141 |
- 2907141 |
- Steptoe/Morex(BxH) |
- AD_SCRI_136.CEL |
- 0521-25_SetA25.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 100 |
- SM142 |
- 2907142 |
- Morex/Steptoe(IxE) |
- AD_SCRI_6.CEL |
- |
- |
- OK |
- |
-
-
- | 101 |
- SM143 |
- 2907143 |
- Steptoe/Morex(BxH) |
- AD_SCRI_145.CEL |
- |
- |
- OK |
- |
-
-
- | 102 |
- SM144 |
- 2907144 |
- Steptoe/Morex(BxF) |
- AD_SCRI_103.CEL |
- |
- |
- OK |
- |
-
-
- | 103 |
- SM145 |
- 2907145 |
- Steptoe/Morex(QxG) |
- AD_SCRI_108.CEL |
- |
- |
- OK |
- |
-
-
- | 104 |
- SM146 |
- 2907146 |
- Morex/Steptoe(BxF) |
- AD_SCRI_91.CEL |
- 0521-26_SetA26.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 105 |
- SM147 |
- 2907147 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_139.CEL |
- |
- |
- OK |
- |
-
-
- | 106 |
- SM149 |
- 2907149 |
- Steptoe/Morex(BxF) |
- AD_SCRI_131.CEL |
- |
- |
- ERROR |
- |
-
-
- | 107 |
- SM150 |
- 2907150 |
- Morex/Steptoe(CxF) |
- AD_SCRI_37.CEL |
- |
- |
- OK |
- |
-
-
- | 108 |
- SM151 |
- 2907151 |
- Morex/Steptoe(IxE) |
- AD_SCRI_28.CEL |
- |
- |
- OK |
- |
-
-
- | 109 |
- SM152 |
- 2907152 |
- Steptoe/Morex(BxH) |
- AD_SCRI_9_redo.CEL |
- 0521-27_SetA27.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 110 |
- SM153 |
- 2907153 |
- Steptoe/Morex(BxH) |
- AD_SCRI_135.CEL |
- |
- |
- OK |
- |
-
-
- | 111 |
- SM154 |
- 2907154 |
- Steptoe/Morex(BxH) |
- AD_SCRI_114.CEL |
- |
- |
- OK |
- |
-
-
- | 112 |
- SM155 |
- 2907155 |
- Steptoe/Morex(BxH) |
- AD_SCRI_119.CEL |
- 0521-28_SetA28.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 113 |
- SM156 |
- 2907156 |
- Steptoe/Morex(BxH) |
- AD_SCRI_140.CEL |
- |
- |
- OK |
- |
-
-
- | 114 |
- SM157 |
- 2907157 |
- Morex/Steptoe(CxF) |
- AD_SCRI_106_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 115 |
- SM158 |
- 2907158 |
- Morex/Steptoe(CxF) |
- AD_SCRI_65.CEL |
- |
- |
- OK |
- |
-
-
- | 116 |
- SM159 |
- 2907159 |
- Morex/Steptoe(IxE) |
- AD_SCRI_168.CEL |
- |
- |
- OK |
- |
-
-
- | 117 |
- SM160 |
- 2907160 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_47.CEL |
- 0521-29_SetA29.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 118 |
- SM161 |
- 2907161 |
- Steptoe/Morex(BxH) |
- AD_SCRI_76.CEL |
- |
- |
- ERROR |
- |
-
-
- | 119 |
- SM162 |
- 2907162 |
- Morex/Steptoe(CxF) |
- AD_SCRI_147.CEL |
- |
- |
- OK |
- |
-
-
- | 120 |
- SM164 |
- 2907164 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_128.CEL |
- |
- |
- OK |
- |
-
-
- | 121 |
- SM165 |
- 2907165 |
- Steptoe/Morex(BxH) |
- AD_SCRI_143.CEL |
- |
- |
- OK |
- OK |
-
-
- | 122 |
- SM166 |
- 2907166 |
- Morex/Steptoe(CxF) |
- AD_SCRI_115.CEL |
- |
- |
- OK |
- |
-
-
- | 123 |
- SM167 |
- 2907167 |
- Steptoe/Morex(BxH) |
- AD_SCRI_127.CEL |
- 0521-30_SetA30.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 124 |
- SM168 |
- 2907168 |
- Steptoe/Morex(BxH) |
- AD_SCRI_130.CEL |
- |
- |
- OK |
- |
-
-
- | 125 |
- SM169 |
- 2907169 |
- Morex/Steptoe(CxF) |
- AD_SCRI_118.CEL |
- 0521-31_SetA31.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 126 |
- SM170 |
- 2907170 |
- Steptoe/Morex(BxF) |
- AD_SCRI_151.CEL |
- |
- |
- OK |
- |
-
-
- | 127 |
- SM171 |
- 2907171 |
- Steptoe/Morex(BxF) |
- AD_SCRI_165.CEL |
- |
- |
- ERROR |
- |
-
-
- | 128 |
- SM172 |
- 2907172 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_152.CEL |
- |
- |
- ERROR |
- |
-
-
- | 129 |
- SM173 |
- 2907173 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_104.CEL |
- 0521-32_SetA32.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 130 |
- SM174 |
- 2907174 |
- Steptoe/Morex(BxH) |
- AD_SCRI_154.CEL |
- |
- |
- OK |
- |
-
-
- | 131 |
- SM176 |
- 2907176 |
- Morex/Steptoe(CxF) |
- AD_SCRI_141.CEL |
- |
- |
- OK |
- |
-
-
- | 132 |
- SM177 |
- 2907177 |
- Morex/Steptoe(CxF) |
- AD_SCRI_111.CEL |
- 0521-33_SetA33.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 133 |
- SM179 |
- 2907179 |
- Morex/Steptoe(CxF) |
- AD_SCRI_166.CEL |
- |
- |
- OK |
- |
-
-
- | 134 |
- SM180 |
- 2907180 |
- Morex/Steptoe(IxE) |
- AD_SCRI_161.CEL |
- |
- |
- OK |
- |
-
-
- | 135 |
- SM181 |
- 2907181 |
- Morex/Steptoe(IxE) |
- AD_SCRI_162.CEL |
- |
- |
- OK |
- |
-
-
- | 136 |
- SM182 |
- 2907182 |
- Morex/Steptoe(CxF) |
- AD_SCRI_163.CEL |
- |
- |
- OK |
- |
-
-
- | 137 |
- SM183 |
- 2907183 |
- Morex/Steptoe(CxF) |
- AD_SCRI_164.CEL |
- |
- |
- OK |
- |
-
-
- | 138 |
- SM184 |
- 2907184 |
- Morex/Steptoe(IxE) |
- AD_SCRI_160.CEL |
- 0521-34_SetA34.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 139 |
- SM185 |
- 2907185 |
- Morex/Steptoe(IxE) |
- AD_SCRI_167.CEL |
- |
- |
- OK |
- |
-
-
- | 140 |
- SM186 |
- 2907186 |
- Morex/Steptoe(IxE) |
- AD_SCRI_62.CEL |
- |
- |
- OK |
- |
-
-
- | 141 |
- SM187 |
- 2907187 |
- Morex/Steptoe(IxE) |
- AD_SCRI_61.CEL |
- |
- |
- OK |
- |
-
-
- | 142 |
- SM188 |
- 2907188 |
- Morex/Steptoe(CxF) |
- AD_SCRI_63.CEL |
- |
- |
- OK |
- |
-
-
- | 143 |
- SM189 |
- 2907189 |
- Steptoe/Morex(QxG) |
- AD_SCRI_80.CEL |
- |
- |
- OK |
- |
-
-
- | 144 |
- SM193 |
- 2907193 |
- Morex/Steptoe(IxE) |
- AD_SCRI_36.CEL |
- |
- |
- OK |
- |
-
-
- | 145 |
- SM194 |
- 2907194 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_29.CEL |
- |
- |
- OK |
- |
-
-
- | 146 |
- SM196 |
- 2907196 |
- Steptoe/Morex(BxF) |
- AD_SCRI_26.CEL |
- |
- |
- OK |
- |
-
-
- | 147 |
- SM197 |
- 2907197 |
- Steptoe/Morex(BxF) |
- AD_SCRI_85.CEL |
- |
- |
- OK |
- |
-
-
- | 148 |
- SM198 |
- 2907198 |
- Morex/Steptoe(IxE) |
- AD_SCRI_8.CEL |
- |
- |
- OK |
- |
-
-
- | 149 |
- SM199 |
- 2907199 |
- Steptoe/Morex(BxF) |
- AD_SCRI_20.CEL |
- |
- |
- OK |
- |
-
-
- | 150 |
- SM200 |
- 2907200 |
- Morex/Steptoe(IxE) |
- AD_SCRI_38.CEL |
- 0521-35_SetA35.CEL |
- SMmini |
- OK |
- OK |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_17.CEL |
- 0521-36_SetA36.CEL |
- |
- |
- |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_66.CEL |
- 0521-37_SetA37.CEL |
- |
- |
- |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_68.CEL |
- 0521-38_SetA38.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_116.CEL |
- 0521-39_SetA39.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_14.CEL |
- 0521-40_SetA40.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_67.CEL |
- 0521-41_SetA41.CEL |
- |
- |
- |
-
-
-
-
-
-
diff --git a/general/datasets/B30_K_1206_R/experiment-design.rtf b/general/datasets/B30_K_1206_R/experiment-design.rtf
deleted file mode 100644
index e743086..0000000
--- a/general/datasets/B30_K_1206_R/experiment-design.rtf
+++ /dev/null
@@ -1,62 +0,0 @@
-
-RNA Sample Processing:
-
-Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
-
-
-☠Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
-☠Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
-☠Incubate samples at 60oC for 10 minutes, vortexing three times.
-☠Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
-☠While centrifuging, label new set of 15 ml tubes
-☠Transfer supernatant to 15 ml centrifuge tube
-☠Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
-seconds, and incubate at room temperature for 5 minutes.
-☠Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
-☠While centrifuging, label new 15 ml tubes
-☠Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
-☠Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
-☠Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
-☠Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
-4000 rpm for 15 minutes @ 4oC.
-☠Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
-☠Air-dry the pellet for 10 minutes, inverted on a kimwipe.
-☠Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
-few times.
-☠Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
-☠Set water bath to 37oC.
-☠Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
-☠Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
-☠Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
-☠Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
-☠Label 15 ml tubes from the kit and place midi columns in them
-☠Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
-☠Discard the flow-through.
-☠Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
-incubate for 3 min
-☠Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
-☠Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
-gently, incubate for 3 min
-☠Centrifuge for 10 min at 3000 rpm, remove flow-through
-☠Centrifuge again for another 5 min.
-☠Label new 15 ml tubes from the kit.
-☠Transfer the RNA easy column to a new tube and pipet 250 ul volume of
-RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
-☠Centrifuge for 5 min at 3000 rpm.
-☠To the same tube add again 250 ul H2O, incubate for 1 min.
-☠Centrifuge for 5 min at 3000 rpm.
-☠Label two sets of 1.5 ml Eppendorf tubes.
-☠Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
-
-Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
-
-Replication and Sample Balance:
-
-3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
-
-Experimental Design and Batch Structure:
-
-
-
-The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs: E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
-
diff --git a/general/datasets/B30_K_1206_R/notes.rtf b/general/datasets/B30_K_1206_R/notes.rtf
deleted file mode 100644
index 46cff8f..0000000
--- a/general/datasets/B30_K_1206_R/notes.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Arnis Druka
-Genetics Programme
-Scottish Crop Research Institute
-Invergowrie, Dundee DD2 5DA
-Angus, Scotland, United Kingdom
-Tel +44 01382 562731
-Fax +44 01382 568587
-adruka@scri.sari.ac.uk
-
-
-
-This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
-
diff --git a/general/datasets/B30_K_1206_R/platform.rtf b/general/datasets/B30_K_1206_R/platform.rtf
deleted file mode 100644
index a935318..0000000
--- a/general/datasets/B30_K_1206_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
-
diff --git a/general/datasets/B30_K_1206_R/processing.rtf b/general/datasets/B30_K_1206_R/processing.rtf
deleted file mode 100644
index d8d039a..0000000
--- a/general/datasets/B30_K_1206_R/processing.rtf
+++ /dev/null
@@ -1,49 +0,0 @@
-
-
-
-
- |
- Types of the expression data-sets
- |
-
- Data processing description
- |
-
-
- Barley1 Embryo gcRMA SCRI (Dec 06)
- Barley1 Leaf gcRMA SCRI (Dec 06) |
-
-
-
- The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
-
-
- |
-
-
- Barley1 Embryo MAS 5.0 SCRI (Dec 06)
- Barley1 Leaf MAS 5.0 SCRI (Dec 06) |
-
-
-
- The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
-
-
- |
-
-
- Barley1 Embryo0 gcRMA SCRI (Apr 06)
- Barley1 Leaf gcRMAn SCRI (Dec 06) |
-
- The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
-
-
- - Values below 0.01 were set to 0.01.
- - Each measurement was divided by the 50.0th percentile of all measurements in that sample.
- - Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
-
- |
-
-
-
-
diff --git a/general/datasets/B30_K_1206_R/summary.rtf b/general/datasets/B30_K_1206_R/summary.rtf
deleted file mode 100644
index 67f4fab..0000000
--- a/general/datasets/B30_K_1206_R/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Barley1 Leaf MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
-
-
-The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip (GEO GPL1340).
-
diff --git a/general/datasets/B30_K_1206_R/tissue.rtf b/general/datasets/B30_K_1206_R/tissue.rtf
deleted file mode 100644
index a8351e8..0000000
--- a/general/datasets/B30_K_1206_R/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
-
-To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
-
-To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
-
-
-
diff --git a/general/datasets/B30_K_1206_Rn/acknowledgment.rtf b/general/datasets/B30_K_1206_Rn/acknowledgment.rtf
deleted file mode 100644
index 5d9cc73..0000000
--- a/general/datasets/B30_K_1206_Rn/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant SCR/910/04 The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
-
diff --git a/general/datasets/B30_K_1206_Rn/cases.rtf b/general/datasets/B30_K_1206_Rn/cases.rtf
deleted file mode 100644
index 1425413..0000000
--- a/general/datasets/B30_K_1206_Rn/cases.rtf
+++ /dev/null
@@ -1,1748 +0,0 @@
-
-The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
-
-The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
-1) pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
-2) 'minimapper' subset - MINI;
-3) lines that have expression data removed - ERROR:
-
-
-
-
- | Order # |
- Line ID |
- Permanent Oregon ID |
- Cross direction |
-
- CEL file names
- |
- Mini-mapper set |
- Error check |
-
-
- | embryo data-set |
- leaf data-set |
- embryo data-set |
- leaf data-set |
-
-
- | 1 |
- SM001 |
- 2907001 |
- Steptoe/Morex(BxF) |
- AD_SCRI_82.CEL |
- |
- |
- OK |
- |
-
-
- | 2 |
- SM002 |
- 2907002 |
- Steptoe/Morex(BxF) |
- AD_SCRI_1.CEL |
- |
- |
- OK |
- |
-
-
- | 3 |
- SM003 |
- 2907003 |
- Morex/Steptoe(CxF) |
- AD_SCRI_19.CEL |
- |
- |
- OK |
- |
-
-
- | 4 |
- SM004 |
- 2907004 |
- Morex/Steptoe(CxF) |
- AD_SCRI_3.CEL |
- 0521-1_SetA1.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 5 |
- SM005 |
- 2907005 |
- Steptoe/Morex(BxH) |
- AD_SCRI_88.CEL |
- |
- |
- OK |
- |
-
-
- | 6 |
- SM006 |
- 2907006 |
- Morex/Steptoe(CxF) |
- AD_SCRI_48.CEL |
- |
- |
- OK |
- |
-
-
- | 7 |
- SM007 |
- 2907007 |
- Steptoe/Morex(BxH) |
- AD_SCRI_35.CEL |
- 0521-2_SetA2.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 8 |
- SM009 |
- 2907009 |
- Steptoe/Morex(BxF) |
- AD_SCRI_2.CEL |
- |
- |
- OK |
- |
-
-
- | 9 |
- SM010 |
- 2907010 |
- Morex/Steptoe(IxE) |
- AD_SCRI_42.CEL |
- |
- |
- OK |
- |
-
-
- | 10 |
- SM011 |
- 2907011 |
- Steptoe/Morex(QxG) |
- AD_SCRI_10.CEL |
- |
- |
- OK |
- |
-
-
- | 11 |
- SM012 |
- 2907012 |
- Morex/Steptoe(CxF) |
- AD_SCRI_45.CEL |
- 0521-3_SetA3.CEL |
- SMmini |
- ERROR |
- ERROR |
-
-
- | 12 |
- SM013 |
- 2907013 |
- Morex/Steptoe(IxE) |
- AD_SCRI_78.CEL |
- 0521-4_SetA4.CEL |
- SMmini |
- ERROR |
- ERROR |
-
-
- | 13 |
- SM014 |
- 2907014 |
- Steptoe/Morex(BxH) |
- AD_SCRI_18.CEL |
- |
- |
- OK |
- |
-
-
- | 14 |
- SM015 |
- 2907015 |
- Steptoe/Morex(BxH) |
- AD_SCRI_5.CEL |
- |
- |
- OK |
- |
-
-
- | 15 |
- SM016 |
- 2907016 |
- Steptoe/Morex(BxH) |
- AD_SCRI_21.CEL |
- |
- |
- OK |
- |
-
-
- | 16 |
- SM020 |
- 2907020 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_77.CEL |
- |
- |
- OK |
- |
-
-
- | 17 |
- SM021 |
- 2907021 |
- Morex/Steptoe(IxE) |
- AD_SCRI_30.CEL |
- |
- |
- OK |
- |
-
-
- | 18 |
- SM022 |
- 2907022 |
- Morex/Steptoe(IxE) |
- AD_SCRI_31.CEL |
- 0521-5_SetA5.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 19 |
- SM023 |
- 2907023 |
- Steptoe/Morex(BxH) |
- AD_SCRI_32.CEL |
- |
- |
- OK |
- |
-
-
- | 20 |
- SM024 |
- 2907024 |
- Morex/Steptoe(IxE) |
- AD_SCRI_33.CEL |
- 0521-6_SetA6.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 21 |
- SM025 |
- 2907025 |
- Morex/Steptoe(CxF) |
- AD_SCRI_34.CEL |
- |
- |
- OK |
- |
-
-
- | 22 |
- SM027 |
- 2907027 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_12.CEL |
- 0521-7_SetA7.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 23 |
- SM030 |
- 2907030 |
- Morex/Steptoe(IxE) |
- AD_SCRI_79.CEL |
- |
- |
- OK |
- |
-
-
- | 24 |
- SM031 |
- 2907031 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_16.CEL |
- |
- |
- OK |
- |
-
-
- | 25 |
- SM032 |
- 2907032 |
- Morex/Steptoe(IxE) |
- AD_SCRI_13.CEL |
- |
- |
- OK |
- |
-
-
- | 26 |
- SM035 |
- 2907035 |
- Morex/Steptoe(CxF) |
- AD_SCRI_15.CEL |
- |
- |
- ERROR |
- |
-
-
- | 27 |
- SM039 |
- 2907039 |
- Morex/Steptoe(CxF) |
- AD_SCRI_41.CEL |
- |
- |
- OK |
- |
-
-
- | 28 |
- SM040 |
- 2907040 |
- Steptoe/Morex(BxH) |
- AD_SCRI_83.CEL |
- |
- |
- OK |
- |
-
-
- | 29 |
- SM041 |
- 2907041 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_11_redo.CEL |
- 0521-8_SetA8.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 30 |
- SM042 |
- 2907042 |
- Morex/Steptoe(CxF) |
- AD_SCRI_57.CEL |
- |
- |
- OK |
- |
-
-
- | 31 |
- SM043 |
- 2907043 |
- Morex/Steptoe(JxE) |
- AD_SCRI_49.CEL |
- 0521-9_SetA9.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 32 |
- SM044 |
- 2907044 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_50.CEL |
- 0521-10_SetA10.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 33 |
- SM045 |
- 2907045 |
- Steptoe/Morex(BxH) |
- AD_SCRI_51.CEL |
- |
- |
- OK |
- |
-
-
- | 34 |
- SM046 |
- 2907046 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_52.CEL |
- 0521-11_SetA11.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 35 |
- SM048 |
- 2907048 |
- Steptoe/Morex(BxF) |
- AD_SCRI_53.CEL |
- |
- |
- ERROR |
- |
-
-
- | 36 |
- SM050 |
- 2907050 |
- Morex/Steptoe(IxE) |
- AD_SCRI_46.CEL |
- |
- |
- OK |
- |
-
-
- | 37 |
- SM054 |
- 2907054 |
- Morex/Steptoe(CxF) |
- AD_SCRI_60.CEL |
- |
- |
- OK |
- |
-
-
- | 38 |
- SM055 |
- 2907055 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_55.CEL |
- |
- |
- OK |
- |
-
-
- | 39 |
- SM056 |
- 2907056 |
- Steptoe/Morex(BxH) |
- AD_SCRI_23.CEL |
- |
- |
- OK |
- |
-
-
- | 40 |
- SM057 |
- 2907057 |
- Morex/Steptoe(CxF) |
- AD_SCRI_24.CEL |
- |
- |
- OK |
- |
-
-
- | 41 |
- SM058 |
- 2907058 |
- Steptoe/Morex(BxF) |
- AD_SCRI_22.CEL |
- |
- |
- OK |
- |
-
-
- | 42 |
- SM059 |
- 2907059 |
- Steptoe/Morex(BxH) |
- AD_SCRI_27.CEL |
- |
- |
- OK |
- |
-
-
- | 43 |
- SM061 |
- 2907061 |
- Morex/Steptoe(LxF) |
- AD_SCRI_81.CEL |
- 0521-12_SetA12.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 44 |
- SM062 |
- 2907062 |
- Morex/Steptoe(CxF) |
- AD_SCRI_44.CEL |
- |
- |
- OK |
- |
-
-
- | 45 |
- SM063 |
- 2907063 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_40.CEL |
- 0521-13_SetA13.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 46 |
- SM064 |
- 2907064 |
- Morex/Steptoe(CxF) |
- AD_SCRI_87_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 47 |
- SM065 |
- 2907065 |
- Morex/Steptoe(CxF) |
- AD_SCRI_54.CEL |
- |
- |
- OK |
- |
-
-
- | 48 |
- SM067 |
- 2907067 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_73.CEL |
- |
- |
- OK |
- |
-
-
- | 49 |
- SM068 |
- 2907068 |
- Steptoe/Morex(OxG) |
- AD_SCRI_56.CEL |
- |
- |
- ERROR |
- |
-
-
- | 50 |
- SM069 |
- 2907069 |
- Steptoe/Morex(BxH) |
- AD_SCRI_71.CEL |
- |
- |
- OK |
- |
-
-
- | 51 |
- SM070 |
- 2907070 |
- Steptoe/Morex(BxF) |
- AD_SCRI_64.CEL |
- |
- |
- OK |
- |
-
-
- | 52 |
- SM071 |
- 2907071 |
- Steptoe/Morex(BxH) |
- AD_SCRI_58.CEL |
- |
- |
- OK |
- |
-
-
- | 53 |
- SM072 |
- 2907072 |
- Morex/Steptoe(CxF) |
- AD_SCRI_59.CEL |
- |
- |
- OK |
- |
-
-
- | 54 |
- SM073 |
- 2907073 |
- Steptoe/Morex(BxF) |
- AD_SCRI_74.CEL |
- 0521-14_SetA14.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 55 |
- SM074 |
- 2907074 |
- Morex/Steptoe(CxF) |
- AD_SCRI_25.CEL |
- 0521-15_SetA15.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 56 |
- SM075 |
- 2907075 |
- Steptoe/Morex(QxG) |
- AD_SCRI_120.CEL |
- |
- |
- OK |
- |
-
-
- | 57 |
- SM076 |
- 2907076 |
- Steptoe/Morex(BxF) |
- AD_SCRI_112.CEL |
- |
- |
- OK |
- |
-
-
- | 58 |
- SM077 |
- 2907077 |
- Morex/Steptoe(CxF) |
- AD_SCRI_142.CEL |
- |
- |
- OK |
- |
-
-
- | 59 |
- SM078 |
- 2907078 |
- Steptoe/Morex(BxF) |
- AD_SCRI_86.CEL |
- |
- |
- OK |
- |
-
-
- | 60 |
- SM079 |
- 2907079 |
- Morex/Steptoe(CxF) |
- AD_SCRI_153.CEL |
- 0521-16_SetA16.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 61 |
- SM080 |
- 2907080 |
- Steptoe/Morex(BxF) |
- AD_SCRI_107.CEL |
- |
- |
- OK |
- |
-
-
- | 62 |
- SM081 |
- 2907081 |
- Morex/Steptoe(CxF) |
- AD_SCRI_105.CEL |
- |
- |
- OK |
- |
-
-
- | 63 |
- SM082 |
- 2907082 |
- Steptoe/Morex(BxF) |
- AD_SCRI_97.CEL |
- |
- |
- OK |
- |
-
-
- | 64 |
- SM083 |
- 2907083 |
- Steptoe/Morex(BxF) |
- AD_SCRI_89.CEL |
- |
- |
- OK |
- |
-
-
- | 65 |
- SM084 |
- 2907084 |
- Morex/Steptoe(CxF) |
- AD_SCRI_155.CEL |
- |
- |
- OK |
- |
-
-
- | 66 |
- SM085 |
- 2907085 |
- Morex/Steptoe(IxE) |
- AD_SCRI_149.CEL |
- 0521-17_SetA17.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 67 |
- SM087 |
- 2907087 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_113.CEL |
- |
- |
- OK |
- |
-
-
- | 68 |
- SM088 |
- 2907088 |
- Morex/Steptoe(CxF) |
- AD_SCRI_93.CEL |
- 0521-18_SetA18.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 69 |
- SM089 |
- 2907089 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_148.CEL |
- 0521-19_SetA19.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 70 |
- SM091 |
- 2907091 |
- Morex/Steptoe(CxF) |
- AD_SCRI_110.CEL |
- |
- |
- OK |
- |
-
-
- | 71 |
- SM092 |
- 2907092 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_7.CEL |
- |
- |
- OK |
- |
-
-
- | 72 |
- SM093 |
- 2907093 |
- Steptoe/Morex(BxF) |
- AD_SCRI_122.CEL |
- |
- |
- OK |
- |
-
-
- | 73 |
- SM094 |
- 2907094 |
- Morex/Steptoe(CxF) |
- AD_SCRI_150.CEL |
- |
- |
- OK |
- |
-
-
- | 74 |
- SM097 |
- 2907097 |
- Morex/Steptoe(CxF) |
- AD_SCRI_158.CEL |
- |
- |
- OK |
- |
-
-
- | 75 |
- SM098 |
- 2907098 |
- Morex/Steptoe(CxF) |
- AD_SCRI_121.CEL |
- |
- |
- OK |
- |
-
-
- | 76 |
- SM099 |
- 2907099 |
- Steptoe/Morex(QxG) |
- AD_SCRI_137.CEL |
- |
- |
- OK |
- |
-
-
- | 77 |
- SM103 |
- 2907103 |
- Morex/Steptoe(IxE) |
- AD_SCRI_156.CEL |
- |
- |
- OK |
- |
-
-
- | 78 |
- SM104 |
- 2907104 |
- Steptoe/Morex(BxH) |
- AD_SCRI_70.CEL |
- |
- |
- ERROR |
- |
-
-
- | 79 |
- SM105 |
- 2907105 |
- Morex/Steptoe(IxE) |
- AD_SCRI_69.CEL |
- |
- |
- OK |
- |
-
-
- | 80 |
- SM110 |
- 2907110 |
- Morex/Steptoe(CxF) |
- AD_SCRI_75.CEL |
- |
- |
- ERROR |
- |
-
-
- | 81 |
- SM112 |
- 2907112 |
- Steptoe/Morex(BxF) |
- AD_SCRI_84.CEL |
- |
- |
- OK |
- |
-
-
- | 82 |
- SM116 |
- 2907116 |
- Morex/Steptoe(CxF) |
- AD_SCRI_117.CEL |
- 0521-20_SetA20.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 83 |
- SM120 |
- 2907120 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_138.CEL |
- |
- |
- OK |
- |
-
-
- | 84 |
- SM124 |
- 2907124 |
- Steptoe/Morex(BxF) |
- AD_SCRI_146.CEL |
- |
- |
- OK |
- |
-
-
- | 85 |
- SM125 |
- 2907125 |
- Morex/Steptoe(IxE) |
- AD_SCRI_43.CEL |
- |
- |
- OK |
- |
-
-
- | 86 |
- SM126 |
- 2907126 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_144_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 87 |
- SM127 |
- 2907127 |
- Steptoe/Morex(BxH) |
- AD_SCRI_129.CEL |
- |
- |
- OK |
- |
-
-
- | 88 |
- SM129 |
- 2907129 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_132.CEL |
- |
- |
- OK |
- |
-
-
- | 89 |
- SM130 |
- 2907130 |
- Morex/Steptoe(CxF) |
- AD_SCRI_101.CEL |
- 0521-21_SetA21.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 90 |
- SM131 |
- 2907131 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_102.CEL |
- |
- |
- OK |
- |
-
-
- | 91 |
- SM132 |
- 2907132 |
- Steptoe/Morex(QxG) |
- AD_SCRI_4_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 92 |
- SM133 |
- 2907133 |
- Morex/Steptoe(CxF) |
- AD_SCRI_157.CEL |
- |
- |
- OK |
- |
-
-
- | 93 |
- SM134 |
- 2907134 |
- Morex/Steptoe(IxE) |
- AD_SCRI_159.CEL |
- |
- |
- OK |
- |
-
-
- | 94 |
- SM135 |
- 2907135 |
- Steptoe/Morex(BxF) |
- AD_SCRI_72.CEL |
- 0521-22_SetA22.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 95 |
- SM136 |
- 2907136 |
- Steptoe/Morex(QxG) |
- AD_SCRI_123.CEL |
- 0521-23_SetA23.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 96 |
- SM137 |
- 2907137 |
- Steptoe/Morex(BxH) |
- AD_SCRI_39.CEL |
- |
- |
- OK |
- |
-
-
- | 97 |
- SM139 |
- 2907139 |
- Morex/Steptoe(CxF) |
- AD_SCRI_133.CEL |
- |
- |
- OK |
- |
-
-
- | 98 |
- SM140 |
- 2907140 |
- Morex/Steptoe(CxF) |
- AD_SCRI_134.CEL |
- 0521-24_SetA24.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 99 |
- SM141 |
- 2907141 |
- Steptoe/Morex(BxH) |
- AD_SCRI_136.CEL |
- 0521-25_SetA25.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 100 |
- SM142 |
- 2907142 |
- Morex/Steptoe(IxE) |
- AD_SCRI_6.CEL |
- |
- |
- OK |
- |
-
-
- | 101 |
- SM143 |
- 2907143 |
- Steptoe/Morex(BxH) |
- AD_SCRI_145.CEL |
- |
- |
- OK |
- |
-
-
- | 102 |
- SM144 |
- 2907144 |
- Steptoe/Morex(BxF) |
- AD_SCRI_103.CEL |
- |
- |
- OK |
- |
-
-
- | 103 |
- SM145 |
- 2907145 |
- Steptoe/Morex(QxG) |
- AD_SCRI_108.CEL |
- |
- |
- OK |
- |
-
-
- | 104 |
- SM146 |
- 2907146 |
- Morex/Steptoe(BxF) |
- AD_SCRI_91.CEL |
- 0521-26_SetA26.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 105 |
- SM147 |
- 2907147 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_139.CEL |
- |
- |
- OK |
- |
-
-
- | 106 |
- SM149 |
- 2907149 |
- Steptoe/Morex(BxF) |
- AD_SCRI_131.CEL |
- |
- |
- ERROR |
- |
-
-
- | 107 |
- SM150 |
- 2907150 |
- Morex/Steptoe(CxF) |
- AD_SCRI_37.CEL |
- |
- |
- OK |
- |
-
-
- | 108 |
- SM151 |
- 2907151 |
- Morex/Steptoe(IxE) |
- AD_SCRI_28.CEL |
- |
- |
- OK |
- |
-
-
- | 109 |
- SM152 |
- 2907152 |
- Steptoe/Morex(BxH) |
- AD_SCRI_9_redo.CEL |
- 0521-27_SetA27.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 110 |
- SM153 |
- 2907153 |
- Steptoe/Morex(BxH) |
- AD_SCRI_135.CEL |
- |
- |
- OK |
- |
-
-
- | 111 |
- SM154 |
- 2907154 |
- Steptoe/Morex(BxH) |
- AD_SCRI_114.CEL |
- |
- |
- OK |
- |
-
-
- | 112 |
- SM155 |
- 2907155 |
- Steptoe/Morex(BxH) |
- AD_SCRI_119.CEL |
- 0521-28_SetA28.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 113 |
- SM156 |
- 2907156 |
- Steptoe/Morex(BxH) |
- AD_SCRI_140.CEL |
- |
- |
- OK |
- |
-
-
- | 114 |
- SM157 |
- 2907157 |
- Morex/Steptoe(CxF) |
- AD_SCRI_106_redo.CEL |
- |
- |
- OK |
- |
-
-
- | 115 |
- SM158 |
- 2907158 |
- Morex/Steptoe(CxF) |
- AD_SCRI_65.CEL |
- |
- |
- OK |
- |
-
-
- | 116 |
- SM159 |
- 2907159 |
- Morex/Steptoe(IxE) |
- AD_SCRI_168.CEL |
- |
- |
- OK |
- |
-
-
- | 117 |
- SM160 |
- 2907160 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_47.CEL |
- 0521-29_SetA29.CEL |
- SMmini |
- OK |
- ERROR |
-
-
- | 118 |
- SM161 |
- 2907161 |
- Steptoe/Morex(BxH) |
- AD_SCRI_76.CEL |
- |
- |
- ERROR |
- |
-
-
- | 119 |
- SM162 |
- 2907162 |
- Morex/Steptoe(CxF) |
- AD_SCRI_147.CEL |
- |
- |
- OK |
- |
-
-
- | 120 |
- SM164 |
- 2907164 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_128.CEL |
- |
- |
- OK |
- |
-
-
- | 121 |
- SM165 |
- 2907165 |
- Steptoe/Morex(BxH) |
- AD_SCRI_143.CEL |
- |
- |
- OK |
- OK |
-
-
- | 122 |
- SM166 |
- 2907166 |
- Morex/Steptoe(CxF) |
- AD_SCRI_115.CEL |
- |
- |
- OK |
- |
-
-
- | 123 |
- SM167 |
- 2907167 |
- Steptoe/Morex(BxH) |
- AD_SCRI_127.CEL |
- 0521-30_SetA30.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 124 |
- SM168 |
- 2907168 |
- Steptoe/Morex(BxH) |
- AD_SCRI_130.CEL |
- |
- |
- OK |
- |
-
-
- | 125 |
- SM169 |
- 2907169 |
- Morex/Steptoe(CxF) |
- AD_SCRI_118.CEL |
- 0521-31_SetA31.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 126 |
- SM170 |
- 2907170 |
- Steptoe/Morex(BxF) |
- AD_SCRI_151.CEL |
- |
- |
- OK |
- |
-
-
- | 127 |
- SM171 |
- 2907171 |
- Steptoe/Morex(BxF) |
- AD_SCRI_165.CEL |
- |
- |
- ERROR |
- |
-
-
- | 128 |
- SM172 |
- 2907172 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_152.CEL |
- |
- |
- ERROR |
- |
-
-
- | 129 |
- SM173 |
- 2907173 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_104.CEL |
- 0521-32_SetA32.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 130 |
- SM174 |
- 2907174 |
- Steptoe/Morex(BxH) |
- AD_SCRI_154.CEL |
- |
- |
- OK |
- |
-
-
- | 131 |
- SM176 |
- 2907176 |
- Morex/Steptoe(CxF) |
- AD_SCRI_141.CEL |
- |
- |
- OK |
- |
-
-
- | 132 |
- SM177 |
- 2907177 |
- Morex/Steptoe(CxF) |
- AD_SCRI_111.CEL |
- 0521-33_SetA33.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 133 |
- SM179 |
- 2907179 |
- Morex/Steptoe(CxF) |
- AD_SCRI_166.CEL |
- |
- |
- OK |
- |
-
-
- | 134 |
- SM180 |
- 2907180 |
- Morex/Steptoe(IxE) |
- AD_SCRI_161.CEL |
- |
- |
- OK |
- |
-
-
- | 135 |
- SM181 |
- 2907181 |
- Morex/Steptoe(IxE) |
- AD_SCRI_162.CEL |
- |
- |
- OK |
- |
-
-
- | 136 |
- SM182 |
- 2907182 |
- Morex/Steptoe(CxF) |
- AD_SCRI_163.CEL |
- |
- |
- OK |
- |
-
-
- | 137 |
- SM183 |
- 2907183 |
- Morex/Steptoe(CxF) |
- AD_SCRI_164.CEL |
- |
- |
- OK |
- |
-
-
- | 138 |
- SM184 |
- 2907184 |
- Morex/Steptoe(IxE) |
- AD_SCRI_160.CEL |
- 0521-34_SetA34.CEL |
- SMmini |
- OK |
- OK |
-
-
- | 139 |
- SM185 |
- 2907185 |
- Morex/Steptoe(IxE) |
- AD_SCRI_167.CEL |
- |
- |
- OK |
- |
-
-
- | 140 |
- SM186 |
- 2907186 |
- Morex/Steptoe(IxE) |
- AD_SCRI_62.CEL |
- |
- |
- OK |
- |
-
-
- | 141 |
- SM187 |
- 2907187 |
- Morex/Steptoe(IxE) |
- AD_SCRI_61.CEL |
- |
- |
- OK |
- |
-
-
- | 142 |
- SM188 |
- 2907188 |
- Morex/Steptoe(CxF) |
- AD_SCRI_63.CEL |
- |
- |
- OK |
- |
-
-
- | 143 |
- SM189 |
- 2907189 |
- Steptoe/Morex(QxG) |
- AD_SCRI_80.CEL |
- |
- |
- OK |
- |
-
-
- | 144 |
- SM193 |
- 2907193 |
- Morex/Steptoe(IxE) |
- AD_SCRI_36.CEL |
- |
- |
- OK |
- |
-
-
- | 145 |
- SM194 |
- 2907194 |
- Steptoe/Morex(OxJ) |
- AD_SCRI_29.CEL |
- |
- |
- OK |
- |
-
-
- | 146 |
- SM196 |
- 2907196 |
- Steptoe/Morex(BxF) |
- AD_SCRI_26.CEL |
- |
- |
- OK |
- |
-
-
- | 147 |
- SM197 |
- 2907197 |
- Steptoe/Morex(BxF) |
- AD_SCRI_85.CEL |
- |
- |
- OK |
- |
-
-
- | 148 |
- SM198 |
- 2907198 |
- Morex/Steptoe(IxE) |
- AD_SCRI_8.CEL |
- |
- |
- OK |
- |
-
-
- | 149 |
- SM199 |
- 2907199 |
- Steptoe/Morex(BxF) |
- AD_SCRI_20.CEL |
- |
- |
- OK |
- |
-
-
- | 150 |
- SM200 |
- 2907200 |
- Morex/Steptoe(IxE) |
- AD_SCRI_38.CEL |
- 0521-35_SetA35.CEL |
- SMmini |
- OK |
- OK |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_17.CEL |
- 0521-36_SetA36.CEL |
- |
- |
- |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_66.CEL |
- 0521-37_SetA37.CEL |
- |
- |
- |
-
-
- | parent |
- Steptoe |
- |
- |
- AD_SCRI_68.CEL |
- 0521-38_SetA38.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_116.CEL |
- 0521-39_SetA39.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_14.CEL |
- 0521-40_SetA40.CEL |
- |
- |
- |
-
-
- | parent |
- Morex |
- |
- |
- AD_SCRI_67.CEL |
- 0521-41_SetA41.CEL |
- |
- |
- |
-
-
-
-
-
-
diff --git a/general/datasets/B30_K_1206_Rn/experiment-design.rtf b/general/datasets/B30_K_1206_Rn/experiment-design.rtf
deleted file mode 100644
index e743086..0000000
--- a/general/datasets/B30_K_1206_Rn/experiment-design.rtf
+++ /dev/null
@@ -1,62 +0,0 @@
-
-RNA Sample Processing:
-
-Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
-
-
-☠Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
-☠Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
-☠Incubate samples at 60oC for 10 minutes, vortexing three times.
-☠Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
-☠While centrifuging, label new set of 15 ml tubes
-☠Transfer supernatant to 15 ml centrifuge tube
-☠Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
-seconds, and incubate at room temperature for 5 minutes.
-☠Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
-☠While centrifuging, label new 15 ml tubes
-☠Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
-☠Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
-☠Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
-☠Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
-4000 rpm for 15 minutes @ 4oC.
-☠Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
-☠Air-dry the pellet for 10 minutes, inverted on a kimwipe.
-☠Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
-few times.
-☠Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
-☠Set water bath to 37oC.
-☠Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
-☠Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
-☠Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
-☠Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
-☠Label 15 ml tubes from the kit and place midi columns in them
-☠Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
-☠Discard the flow-through.
-☠Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
-incubate for 3 min
-☠Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
-☠Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
-gently, incubate for 3 min
-☠Centrifuge for 10 min at 3000 rpm, remove flow-through
-☠Centrifuge again for another 5 min.
-☠Label new 15 ml tubes from the kit.
-☠Transfer the RNA easy column to a new tube and pipet 250 ul volume of
-RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
-☠Centrifuge for 5 min at 3000 rpm.
-☠To the same tube add again 250 ul H2O, incubate for 1 min.
-☠Centrifuge for 5 min at 3000 rpm.
-☠Label two sets of 1.5 ml Eppendorf tubes.
-☠Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
-
-Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
-
-Replication and Sample Balance:
-
-3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
-
-Experimental Design and Batch Structure:
-
-
-
-The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs: E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
-
diff --git a/general/datasets/B30_K_1206_Rn/notes.rtf b/general/datasets/B30_K_1206_Rn/notes.rtf
deleted file mode 100644
index 46cff8f..0000000
--- a/general/datasets/B30_K_1206_Rn/notes.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Arnis Druka
-Genetics Programme
-Scottish Crop Research Institute
-Invergowrie, Dundee DD2 5DA
-Angus, Scotland, United Kingdom
-Tel +44 01382 562731
-Fax +44 01382 568587
-adruka@scri.sari.ac.uk
-
-
-
-This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
-
diff --git a/general/datasets/B30_K_1206_Rn/platform.rtf b/general/datasets/B30_K_1206_Rn/platform.rtf
deleted file mode 100644
index a935318..0000000
--- a/general/datasets/B30_K_1206_Rn/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
-
diff --git a/general/datasets/B30_K_1206_Rn/processing.rtf b/general/datasets/B30_K_1206_Rn/processing.rtf
deleted file mode 100644
index d8d039a..0000000
--- a/general/datasets/B30_K_1206_Rn/processing.rtf
+++ /dev/null
@@ -1,49 +0,0 @@
-
-
-
-
- |
- Types of the expression data-sets
- |
-
- Data processing description
- |
-
-
- Barley1 Embryo gcRMA SCRI (Dec 06)
- Barley1 Leaf gcRMA SCRI (Dec 06) |
-
-
-
- The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
-
-
- |
-
-
- Barley1 Embryo MAS 5.0 SCRI (Dec 06)
- Barley1 Leaf MAS 5.0 SCRI (Dec 06) |
-
-
-
- The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
-
-
- |
-
-
- Barley1 Embryo0 gcRMA SCRI (Apr 06)
- Barley1 Leaf gcRMAn SCRI (Dec 06) |
-
- The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
-
-
- - Values below 0.01 were set to 0.01.
- - Each measurement was divided by the 50.0th percentile of all measurements in that sample.
- - Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
-
- |
-
-
-
-
diff --git a/general/datasets/B30_K_1206_Rn/summary.rtf b/general/datasets/B30_K_1206_Rn/summary.rtf
deleted file mode 100644
index 67f4fab..0000000
--- a/general/datasets/B30_K_1206_Rn/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Barley1 Leaf MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
-
-
-The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip (GEO GPL1340).
-
diff --git a/general/datasets/B30_K_1206_Rn/tissue.rtf b/general/datasets/B30_K_1206_Rn/tissue.rtf
deleted file mode 100644
index a8351e8..0000000
--- a/general/datasets/B30_K_1206_Rn/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
-
-To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
-
-To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
-
-
-
diff --git a/general/datasets/B6BTBRF2Publish/acknowledgment.rtf b/general/datasets/B6BTBRF2Publish/acknowledgment.rtf
deleted file mode 100644
index 1405628..0000000
--- a/general/datasets/B6BTBRF2Publish/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This project was supported in part by NIH/NIDDK 5803701, NIH/NIDDK 66369-01 and American Diabetes Association 7-03-IG-01 to Alan D. Attie, USDA CSREES grants to the University of Wisconsin-Madison to Brian S. Yandell, and HHMI grant A-53-1200-4 to Christina Kendziorski.
diff --git a/general/datasets/B6BTBRF2Publish/summary.rtf b/general/datasets/B6BTBRF2Publish/summary.rtf
deleted file mode 100644
index ec934ba..0000000
--- a/general/datasets/B6BTBRF2Publish/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-The Phenotypes database of August 2005 provides quantitative trait data for 24 phenotypes from a set of 110 F2 animals generated by crossing strains C57BL/6J and BTBR. All F2s are homozygous for the obese (ob) allele of leptin (Lep) on Chr 6. Data were generated at the University of Wisconsin by Alan Attie and colleagues (Stoehr et al. 2000; Lan et al. 2003). This data release complement the liver transcriptome data described in the paper of Lan and colleagues (in submission, 2005). Traits include body weight, insulin and blood sugar levels, and rtPCR results. To review a complete list of the 24 phenotypes simply type in the wildcard character * in the ANY search field. This data set includes values for all 60 selected animals whose liver mRNA has been quantified using the Affymetrix M430A and B arrays, as well as an addition 50 F2 ob/ob animals from the same cross.
-
-The 110 F2-ob/ob mice were chosen from a larger mapping panel that we created to map diabetes related physiological phenotypes (Stoehr et al. 2000). All 110 of this subsetwere used to map mRNA abundance traits derived by quantitative real-time RT-PCR (Lan et al. 2003).
-
-
diff --git a/general/datasets/B6d2oncilm_0412/experiment-type.rtf b/general/datasets/B6d2oncilm_0412/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/B6d2oncilm_0412/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/BHHBF2Geno/summary.rtf b/general/datasets/BHHBF2Geno/summary.rtf
deleted file mode 100644
index 39d69d7..0000000
--- a/general/datasets/BHHBF2Geno/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-No information is available, please refer to the contact information above.
diff --git a/general/datasets/BRF2_M_0304_M/acknowledgment.rtf b/general/datasets/BRF2_M_0304_M/acknowledgment.rtf
deleted file mode 100644
index e67d66a..0000000
--- a/general/datasets/BRF2_M_0304_M/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
diff --git a/general/datasets/BRF2_M_0304_M/cases.rtf b/general/datasets/BRF2_M_0304_M/cases.rtf
deleted file mode 100644
index 3d9dd38..0000000
--- a/general/datasets/BRF2_M_0304_M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/BRF2_M_0304_M/experiment-design.rtf b/general/datasets/BRF2_M_0304_M/experiment-design.rtf
deleted file mode 100644
index 2829934..0000000
--- a/general/datasets/BRF2_M_0304_M/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Conventional F2 intercross.
diff --git a/general/datasets/BRF2_M_0304_M/notes.rtf b/general/datasets/BRF2_M_0304_M/notes.rtf
deleted file mode 100644
index c4a728d..0000000
--- a/general/datasets/BRF2_M_0304_M/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
-
-Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method developed by Zhang and colleagues (2003. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.
-
-Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.
diff --git a/general/datasets/BRF2_M_0304_M/platform.rtf b/general/datasets/BRF2_M_0304_M/platform.rtf
deleted file mode 100644
index ecb86bc..0000000
--- a/general/datasets/BRF2_M_0304_M/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/BRF2_M_0304_M/processing.rtf b/general/datasets/BRF2_M_0304_M/processing.rtf
deleted file mode 100644
index 002c868..0000000
--- a/general/datasets/BRF2_M_0304_M/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each probe signal.
- - Step 3: We computed the Z score for each signal within array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BRF2_M_0304_M/summary.rtf b/general/datasets/BRF2_M_0304_M/summary.rtf
deleted file mode 100644
index 8c926cd..0000000
--- a/general/datasets/BRF2_M_0304_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/BRF2_M_0304_M/tissue.rtf b/general/datasets/BRF2_M_0304_M/tissue.rtf
deleted file mode 100644
index 863b8e6..0000000
--- a/general/datasets/BRF2_M_0304_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
diff --git a/general/datasets/BRF2_M_0304_P/acknowledgment.rtf b/general/datasets/BRF2_M_0304_P/acknowledgment.rtf
deleted file mode 100644
index e67d66a..0000000
--- a/general/datasets/BRF2_M_0304_P/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
diff --git a/general/datasets/BRF2_M_0304_P/cases.rtf b/general/datasets/BRF2_M_0304_P/cases.rtf
deleted file mode 100644
index 3d9dd38..0000000
--- a/general/datasets/BRF2_M_0304_P/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/BRF2_M_0304_P/experiment-design.rtf b/general/datasets/BRF2_M_0304_P/experiment-design.rtf
deleted file mode 100644
index 2829934..0000000
--- a/general/datasets/BRF2_M_0304_P/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Conventional F2 intercross.
diff --git a/general/datasets/BRF2_M_0304_P/notes.rtf b/general/datasets/BRF2_M_0304_P/notes.rtf
deleted file mode 100644
index c4a728d..0000000
--- a/general/datasets/BRF2_M_0304_P/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
-
-Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method developed by Zhang and colleagues (2003. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.
-
-Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.
diff --git a/general/datasets/BRF2_M_0304_P/platform.rtf b/general/datasets/BRF2_M_0304_P/platform.rtf
deleted file mode 100644
index ecb86bc..0000000
--- a/general/datasets/BRF2_M_0304_P/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/BRF2_M_0304_P/processing.rtf b/general/datasets/BRF2_M_0304_P/processing.rtf
deleted file mode 100644
index 002c868..0000000
--- a/general/datasets/BRF2_M_0304_P/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each probe signal.
- - Step 3: We computed the Z score for each signal within array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BRF2_M_0304_P/summary.rtf b/general/datasets/BRF2_M_0304_P/summary.rtf
deleted file mode 100644
index 8c926cd..0000000
--- a/general/datasets/BRF2_M_0304_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/BRF2_M_0304_P/tissue.rtf b/general/datasets/BRF2_M_0304_P/tissue.rtf
deleted file mode 100644
index 863b8e6..0000000
--- a/general/datasets/BRF2_M_0304_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
diff --git a/general/datasets/BRF2_M_0304_R/acknowledgment.rtf b/general/datasets/BRF2_M_0304_R/acknowledgment.rtf
deleted file mode 100644
index e67d66a..0000000
--- a/general/datasets/BRF2_M_0304_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
diff --git a/general/datasets/BRF2_M_0304_R/cases.rtf b/general/datasets/BRF2_M_0304_R/cases.rtf
deleted file mode 100644
index 3d9dd38..0000000
--- a/general/datasets/BRF2_M_0304_R/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/BRF2_M_0304_R/experiment-design.rtf b/general/datasets/BRF2_M_0304_R/experiment-design.rtf
deleted file mode 100644
index 2829934..0000000
--- a/general/datasets/BRF2_M_0304_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Conventional F2 intercross.
diff --git a/general/datasets/BRF2_M_0304_R/notes.rtf b/general/datasets/BRF2_M_0304_R/notes.rtf
deleted file mode 100644
index c4a728d..0000000
--- a/general/datasets/BRF2_M_0304_R/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
-
-Data were processed using the Position-Dependent Nearest Neighbor (PDNN) method developed by Zhang and colleagues (2003. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.
-
-Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.
diff --git a/general/datasets/BRF2_M_0304_R/platform.rtf b/general/datasets/BRF2_M_0304_R/platform.rtf
deleted file mode 100644
index ecb86bc..0000000
--- a/general/datasets/BRF2_M_0304_R/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/BRF2_M_0304_R/processing.rtf b/general/datasets/BRF2_M_0304_R/processing.rtf
deleted file mode 100644
index 002c868..0000000
--- a/general/datasets/BRF2_M_0304_R/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each probe signal.
- - Step 3: We computed the Z score for each signal within array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BRF2_M_0304_R/summary.rtf b/general/datasets/BRF2_M_0304_R/summary.rtf
deleted file mode 100644
index 8c926cd..0000000
--- a/general/datasets/BRF2_M_0304_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This March 2004 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A microarrays. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/BRF2_M_0304_R/tissue.rtf b/general/datasets/BRF2_M_0304_R/tissue.rtf
deleted file mode 100644
index 863b8e6..0000000
--- a/general/datasets/BRF2_M_0304_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A array.
diff --git a/general/datasets/BRF2_M_0805_M/acknowledgment.rtf b/general/datasets/BRF2_M_0805_M/acknowledgment.rtf
deleted file mode 100644
index e7f05c1..0000000
--- a/general/datasets/BRF2_M_0805_M/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
-
diff --git a/general/datasets/BRF2_M_0805_M/cases.rtf b/general/datasets/BRF2_M_0805_M/cases.rtf
deleted file mode 100644
index 4f69ca9..0000000
--- a/general/datasets/BRF2_M_0805_M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/BRF2_M_0805_M/notes.rtf b/general/datasets/BRF2_M_0805_M/notes.rtf
deleted file mode 100644
index 7fafba3..0000000
--- a/general/datasets/BRF2_M_0805_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004, EJC June 21, 2005.
-
diff --git a/general/datasets/BRF2_M_0805_M/platform.rtf b/general/datasets/BRF2_M_0805_M/platform.rtf
deleted file mode 100644
index f0ee528..0000000
--- a/general/datasets/BRF2_M_0805_M/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/BRF2_M_0805_M/processing.rtf b/general/datasets/BRF2_M_0805_M/processing.rtf
deleted file mode 100644
index 8a23d84..0000000
--- a/general/datasets/BRF2_M_0805_M/processing.rtf
+++ /dev/null
@@ -1,26 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-
-About the marker set:
-
-
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
-
diff --git a/general/datasets/BRF2_M_0805_M/summary.rtf b/general/datasets/BRF2_M_0805_M/summary.rtf
deleted file mode 100644
index 6f477fe..0000000
--- a/general/datasets/BRF2_M_0805_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/BRF2_M_0805_M/tissue.rtf b/general/datasets/BRF2_M_0805_M/tissue.rtf
deleted file mode 100644
index ef85488..0000000
--- a/general/datasets/BRF2_M_0805_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
diff --git a/general/datasets/BRF2_M_0805_P/acknowledgment.rtf b/general/datasets/BRF2_M_0805_P/acknowledgment.rtf
deleted file mode 100644
index e7f05c1..0000000
--- a/general/datasets/BRF2_M_0805_P/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
-
diff --git a/general/datasets/BRF2_M_0805_P/cases.rtf b/general/datasets/BRF2_M_0805_P/cases.rtf
deleted file mode 100644
index 4f69ca9..0000000
--- a/general/datasets/BRF2_M_0805_P/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/BRF2_M_0805_P/notes.rtf b/general/datasets/BRF2_M_0805_P/notes.rtf
deleted file mode 100644
index 7fafba3..0000000
--- a/general/datasets/BRF2_M_0805_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004, EJC June 21, 2005.
-
diff --git a/general/datasets/BRF2_M_0805_P/platform.rtf b/general/datasets/BRF2_M_0805_P/platform.rtf
deleted file mode 100644
index f0ee528..0000000
--- a/general/datasets/BRF2_M_0805_P/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/BRF2_M_0805_P/processing.rtf b/general/datasets/BRF2_M_0805_P/processing.rtf
deleted file mode 100644
index 8a23d84..0000000
--- a/general/datasets/BRF2_M_0805_P/processing.rtf
+++ /dev/null
@@ -1,26 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-
-About the marker set:
-
-
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
-
diff --git a/general/datasets/BRF2_M_0805_P/summary.rtf b/general/datasets/BRF2_M_0805_P/summary.rtf
deleted file mode 100644
index 6f477fe..0000000
--- a/general/datasets/BRF2_M_0805_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/BRF2_M_0805_P/tissue.rtf b/general/datasets/BRF2_M_0805_P/tissue.rtf
deleted file mode 100644
index ef85488..0000000
--- a/general/datasets/BRF2_M_0805_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
diff --git a/general/datasets/BRF2_M_0805_R/acknowledgment.rtf b/general/datasets/BRF2_M_0805_R/acknowledgment.rtf
deleted file mode 100644
index e7f05c1..0000000
--- a/general/datasets/BRF2_M_0805_R/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
-
diff --git a/general/datasets/BRF2_M_0805_R/cases.rtf b/general/datasets/BRF2_M_0805_R/cases.rtf
deleted file mode 100644
index 4f69ca9..0000000
--- a/general/datasets/BRF2_M_0805_R/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/BRF2_M_0805_R/notes.rtf b/general/datasets/BRF2_M_0805_R/notes.rtf
deleted file mode 100644
index 7fafba3..0000000
--- a/general/datasets/BRF2_M_0805_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004, EJC June 21, 2005.
-
diff --git a/general/datasets/BRF2_M_0805_R/platform.rtf b/general/datasets/BRF2_M_0805_R/platform.rtf
deleted file mode 100644
index f0ee528..0000000
--- a/general/datasets/BRF2_M_0805_R/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/BRF2_M_0805_R/processing.rtf b/general/datasets/BRF2_M_0805_R/processing.rtf
deleted file mode 100644
index 8a23d84..0000000
--- a/general/datasets/BRF2_M_0805_R/processing.rtf
+++ /dev/null
@@ -1,26 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-
-About the marker set:
-
-
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
-
diff --git a/general/datasets/BRF2_M_0805_R/summary.rtf b/general/datasets/BRF2_M_0805_R/summary.rtf
deleted file mode 100644
index 6f477fe..0000000
--- a/general/datasets/BRF2_M_0805_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/BRF2_M_0805_R/tissue.rtf b/general/datasets/BRF2_M_0805_R/tissue.rtf
deleted file mode 100644
index ef85488..0000000
--- a/general/datasets/BRF2_M_0805_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
diff --git a/general/datasets/BR_M2_1106_R/acknowledgment.rtf b/general/datasets/BR_M2_1106_R/acknowledgment.rtf
deleted file mode 100644
index 0912bce..0000000
--- a/general/datasets/BR_M2_1106_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data was generated with funds from NIAAA for Gene Array Technology Center (AA013162) and from the NIAAA Integrated Neuroinformatics Resource for Alcoholism (AA013524).
-
diff --git a/general/datasets/BR_M2_1106_R/cases.rtf b/general/datasets/BR_M2_1106_R/cases.rtf
deleted file mode 100644
index 1d1f7d8..0000000
--- a/general/datasets/BR_M2_1106_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This data set includes estimates of gene expression for 50 genetically uniform lines of mice: C57BL/6J (B6 or simply B), DBA/2J (D2 or D), 30 BXD recombinant inbred (RI) strain derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations, and 18 other inbred strains of mice available from the Jackson Laboratory. All mice used were naïve males from 70-90 days old. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. Another significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-In this mRNA expression database we generally used stock obtained directly from The Jackson Laboratory between 2003 and 2005.
-
diff --git a/general/datasets/BR_M2_1106_R/notes.rtf b/general/datasets/BR_M2_1106_R/notes.rtf
deleted file mode 100644
index e379677..0000000
--- a/general/datasets/BR_M2_1106_R/notes.rtf
+++ /dev/null
@@ -1,2 +0,0 @@
-This text file originally generated by RWW, YHQ, August for UTHSC Brain mRNA U74Av2 (Aug05) RMA. Updated for UC Denver Whole Brain M430v2 BXD (Nov06) RMA Data by LMS, November 2006. Updated by RWW, Feb 2008.
-
diff --git a/general/datasets/BR_M2_1106_R/platform.rtf b/general/datasets/BR_M2_1106_R/platform.rtf
deleted file mode 100644
index bf888fd..0000000
--- a/general/datasets/BR_M2_1106_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix MOE430v2 GeneChip: The expression data were generated using 248 MOE430v2 arrays. The chromosomal locations of MOE430v2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6). This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
diff --git a/general/datasets/BR_M2_1106_R/processing.rtf b/general/datasets/BR_M2_1106_R/processing.rtf
deleted file mode 100644
index 96eb066..0000000
--- a/general/datasets/BR_M2_1106_R/processing.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-Probe set data: The expression data were processed by Laura Saba (UCDHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed within the rma function in R. This data set includes further normalization to produce final estimates of expression that can be compared directly to the other transforms.
-
-This includes an initial quantile normalization on the RMA normalized probe set data followed by a transformation to force an array average of 8 units and stabilized standard deviation of 2 units within each array. Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other methods of processing Affymetrix array data sets.
-
-
-Expression estimates (strain averages) range from a low of about 3.8 for probe set 1457109_x_at to a high of 15 for Gapdh (probe set 1418625_s_at). The mean expression of 8.0 actually represents a relatively low value of expression (roughly 250 on the original scale) because it is the average of all transcripts on the array, including those that are not expressed. Nonetheless, it is possible to obtain good signal down to very low values. For example, probe set 1437432_a_at (Trim12) has an average expression of 4.56 (extremely low), but it still is associated with a strong QTL (LRS of 45) precisely at the location of the parent gene (Chr 7 at 104 Mb). This demonstrates unequivocally that the small strain differences in expression of Trim12 measured by probe set 1437432_a_at is not noise but is generated by true allelic differences in Trim12 mRNA binding to the arrays.
diff --git a/general/datasets/BR_M2_1106_R/summary.rtf b/general/datasets/BR_M2_1106_R/summary.rtf
deleted file mode 100644
index c57e9ff..0000000
--- a/general/datasets/BR_M2_1106_R/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-A PhenoGen Informatics data set. Please cite: Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B (2006) Candidate genes and their regulatory elements: alcohol preference and tolerance. Mammalian Genome 17:669-688 Full Text PDF Version, Full Text HTML Version
-
-This November 2006 data freeze provides estimates of mRNA expression in whole brains of BXD recombinant inbred mice measured using Affymetrix MOE 430 version 2 micorarrays. Data were generated at the University of Colorado at Denver and Health Science Center (UCDHSC). Single whole brain samples were hybridized to 248 individual arrays. Data were processed using the RMA protocol followed by a secondary quantile normalization at the probe set level and a scale and location adjustment to ensure an average expression level of 8 units and a standard deviation of 2 units for easy comparison to other transforms.
-
-The PhenoGen Informatics web site provides additional analytic tools and transforms associated with these data.
diff --git a/general/datasets/BR_M2_1106_R/tissue.rtf b/general/datasets/BR_M2_1106_R/tissue.rtf
deleted file mode 100644
index 0989cd0..0000000
--- a/general/datasets/BR_M2_1106_R/tissue.rtf
+++ /dev/null
@@ -1,2751 +0,0 @@
-
-Naïve male mice were euthanized by CO2 exposure, and whole brains were removed and frozen on dry ice. Brains were stored at -70 deg C until used. The RNeasy Midi kit for lipid-rich tissues (Qiagen, Valencia, CA) was used to extract total RNA, and the RNeasy Mini kit (Qiagen) was used for cleanup. Biotin-labeled cRNA was obtained by in vitro transcription of the double-stranded cDNA that was originally synthesized from the total RNA. Each whole brain sample of biotin-labeled cRNA was fragmented and hybridized to a separate oligonucleotide array. After hybridization, the chips were stained with streptavidin-phycoerythrin conjugate and scanned using an Affymetrix GeneArray scanner.
-
-
-
-
-
-
- | Strain |
- Sample Number |
- Scale
- factor |
- Average
- background |
- Absent |
- Marginal |
- Present |
- Affy-bActin |
- Affy-GAPH |
-
-
- | BXD1 |
- 1 |
- 0.343 |
- 65.57 |
- 45.5% |
- 4.1% |
- 50.4% |
- 1.33 |
- 0.74 |
-
-
- | BXD1 |
- 2 |
- 0.362 |
- 68.26 |
- 46.9% |
- 4.5% |
- 48.6% |
- 1.30 |
- 0.76 |
-
-
- | BXD1 |
- 3 |
- 0.375 |
- 66.19 |
- 46.9% |
- 4.2% |
- 48.9% |
- 1.27 |
- 0.77 |
-
-
- | BXD1 |
- 4 |
- 0.408 |
- 57.16 |
- 45.0% |
- 4.0% |
- 51.1% |
- 1.27 |
- 0.80 |
-
-
- | BXD2 |
- 1 |
- 0.270 |
- 60.53 |
- 44.0% |
- 4.1% |
- 51.8% |
- 1.52 |
- 0.87 |
-
-
- | BXD2 |
- 2 |
- 0.280 |
- 67.57 |
- 45.0% |
- 4.2% |
- 50.8% |
- 1.31 |
- 0.75 |
-
-
- | BXD2 |
- 3 |
- 0.295 |
- 67.03 |
- 45.2% |
- 4.1% |
- 50.7% |
- 1.34 |
- 0.76 |
-
-
- | BXD2 |
- 4 |
- 0.209 |
- 99.86 |
- 50.0% |
- 4.7% |
- 45.3% |
- 1.24 |
- 0.73 |
-
-
- | BXD2 |
- 5 |
- 0.246 |
- 73.28 |
- 46.2% |
- 4.3% |
- 49.5% |
- 1.34 |
- 0.73 |
-
-
- | BXD5 |
- 1 |
- 0.249 |
- 75.34 |
- 47.3% |
- 4.4% |
- 48.3% |
- 1.34 |
- 0.73 |
-
-
- | BXD5 |
- 2 |
- 0.306 |
- 70.11 |
- 47.5% |
- 4.5% |
- 47.9% |
- 1.31 |
- 0.77 |
-
-
- | BXD5 |
- 3 |
- 0.265 |
- 64.80 |
- 44.8% |
- 4.3% |
- 50.9% |
- 1.33 |
- 0.74 |
-
-
- | BXD5 |
- 4 |
- 0.282 |
- 66.04 |
- 45.5% |
- 4.2% |
- 50.4% |
- 1.41 |
- 0.76 |
-
-
- | BXD5 |
- 5 |
- 0.216 |
- 71.87 |
- 46.0% |
- 3.9% |
- 50.1% |
- 3.07 |
- 1.01 |
-
-
- | BXD6 |
- 1 |
- 0.294 |
- 66.72 |
- 45.8% |
- 4.3% |
- 49.9% |
- 1.38 |
- 0.75 |
-
-
- | BXD6 |
- 2 |
- 0.304 |
- 62.83 |
- 45.8% |
- 4.2% |
- 50.0% |
- 1.25 |
- 0.72 |
-
-
- | BXD6 |
- 3 |
- 0.301 |
- 61.80 |
- 45.3% |
- 4.3% |
- 50.5% |
- 1.27 |
- 0.76 |
-
-
- | BXD6 |
- 5 |
- 0.273 |
- 67.04 |
- 44.4% |
- 4.2% |
- 51.4% |
- 1.32 |
- 0.76 |
-
-
- | BXD6 |
- 6 |
- 0.272 |
- 66.39 |
- 45.4% |
- 4.3% |
- 50.3% |
- 1.32 |
- 0.75 |
-
-
- | BXD8 |
- 1 |
- 0.207 |
- 81.90 |
- 44.0% |
- 3.9% |
- 52.1% |
- 1.33 |
- 0.74 |
-
-
- | BXD8 |
- 2 |
- 0.254 |
- 70.19 |
- 44.0% |
- 3.9% |
- 52.0% |
- 1.32 |
- 0.72 |
-
-
- | BXD8 |
- 3 |
- 0.300 |
- 72.61 |
- 46.0% |
- 4.0% |
- 50.0% |
- 1.30 |
- 0.74 |
-
-
- | BXD8 |
- 4 |
- 0.457 |
- 52.63 |
- 39.5% |
- 3.3% |
- 57.2% |
- 1.14 |
- 0.79 |
-
-
- | BXD8 |
- 5 |
- 0.381 |
- 55.09 |
- 41.2% |
- 3.4% |
- 55.4% |
- 1.12 |
- 0.79 |
-
-
- | BXD9 |
- 1 |
- 0.349 |
- 90.32 |
- 48.5% |
- 4.1% |
- 47.4% |
- 1.38 |
- 0.78 |
-
-
- | BXD9 |
- 2 |
- 0.241 |
- 86.66 |
- 51.2% |
- 4.8% |
- 44.0% |
- 1.38 |
- 0.75 |
-
-
- | BXD9 |
- 3 |
- 0.284 |
- 67.21 |
- 47.2% |
- 4.3% |
- 48.5% |
- 1.33 |
- 0.78 |
-
-
- | BXD9 |
- 4 |
- 0.303 |
- 64.47 |
- 46.9% |
- 4.5% |
- 48.6% |
- 1.32 |
- 0.77 |
-
-
- | BXD9 |
- 5 |
- 0.351 |
- 59.40 |
- 47.4% |
- 4.4% |
- 48.2% |
- 1.41 |
- 0.80 |
-
-
- | BXD9 |
- 6 |
- 0.312 |
- 63.41 |
- 46.3% |
- 4.4% |
- 49.4% |
- 1.39 |
- 0.76 |
-
-
- | BXD11 |
- 1 |
- 0.267 |
- 61.85 |
- 44.6% |
- 4.3% |
- 51.1% |
- 1.36 |
- 0.75 |
-
-
- | BXD11 |
- 2 |
- 0.317 |
- 63.76 |
- 45.3% |
- 4.3% |
- 50.4% |
- 1.29 |
- 0.79 |
-
-
- | BXD11 |
- 3 |
- 0.306 |
- 59.35 |
- 44.8% |
- 4.2% |
- 51.0% |
- 1.33 |
- 0.79 |
-
-
- | BXD11 |
- 4 |
- 0.223 |
- 98.84 |
- 51.1% |
- 4.6% |
- 44.3% |
- 1.32 |
- 0.73 |
-
-
- | BXD11 |
- 5 |
- 0.292 |
- 65.03 |
- 45.4% |
- 4.0% |
- 50.5% |
- 1.38 |
- 0.78 |
-
-
- | BXD12 |
- 1 |
- 0.357 |
- 54.50 |
- 42.5% |
- 3.7% |
- 53.8% |
- 1.15 |
- 0.76 |
-
-
- | BXD12 |
- 2 |
- 0.379 |
- 55.05 |
- 42.7% |
- 3.7% |
- 53.6% |
- 1.15 |
- 0.76 |
-
-
- | BXD12 |
- 3 |
- 0.347 |
- 56.34 |
- 43.2% |
- 3.9% |
- 52.9% |
- 1.17 |
- 0.74 |
-
-
- | BXD12 |
- 4 |
- 0.541 |
- 65.16 |
- 43.1% |
- 3.4% |
- 53.6% |
- 1.08 |
- 0.79 |
-
-
- | BXD12 |
- 5 |
- 0.178 |
- 96.04 |
- 43.4% |
- 4.0% |
- 52.7% |
- 1.29 |
- 0.74 |
-
-
- | BXD12 |
- 6 |
- 0.234 |
- 67.32 |
- 43.0% |
- 3.9% |
- 53.0% |
- 1.31 |
- 0.75 |
-
-
- | BXD12 |
- 7 |
- 0.255 |
- 68.41 |
- 42.7% |
- 4.2% |
- 53.2% |
- 1.50 |
- 0.76 |
-
-
- | BXD13 |
- 1 |
- 0.285 |
- 59.51 |
- 45.8% |
- 4.2% |
- 49.9% |
- 1.22 |
- 0.75 |
-
-
- | BXD13 |
- 2 |
- 0.275 |
- 67.19 |
- 44.9% |
- 4.2% |
- 50.9% |
- 1.29 |
- 0.76 |
-
-
- | BXD13 |
- 3 |
- 0.277 |
- 66.05 |
- 45.7% |
- 4.2% |
- 50.2% |
- 1.38 |
- 0.79 |
-
-
- | BXD13 |
- 4 |
- 0.214 |
- 82.73 |
- 48.6% |
- 4.5% |
- 46.9% |
- 1.40 |
- 0.78 |
-
-
- | BXD13 |
- 5 |
- 0.237 |
- 71.73 |
- 46.0% |
- 4.3% |
- 49.7% |
- 1.29 |
- 0.77 |
-
-
- | BXD13 |
- 6 |
- 0.308 |
- 57.58 |
- 47.2% |
- 4.2% |
- 48.6% |
- 1.33 |
- 0.74 |
-
-
- | BXD14 |
- 2 |
- 0.372 |
- 58.42 |
- 46.8% |
- 4.4% |
- 48.8% |
- 1.19 |
- 0.74 |
-
-
- | BXD14 |
- 3 |
- 0.354 |
- 57.39 |
- 45.0% |
- 4.2% |
- 50.8% |
- 1.20 |
- 0.72 |
-
-
- | BXD14 |
- 4 |
- 0.296 |
- 64.96 |
- 45.7% |
- 4.4% |
- 49.9% |
- 1.20 |
- 0.69 |
-
-
- | BXD14 |
- 5 |
- 0.257 |
- 66.46 |
- 44.9% |
- 4.4% |
- 50.8% |
- 1.24 |
- 0.72 |
-
-
- | BXD14 |
- 6 |
- 0.418 |
- 54.03 |
- 47.4% |
- 4.1% |
- 48.5% |
- 1.10 |
- 0.74 |
-
-
- | BXD15 |
- 1 |
- 0.396 |
- 58.77 |
- 43.6% |
- 3.9% |
- 52.5% |
- 1.33 |
- 0.78 |
-
-
- | BXD15 |
- 2 |
- 0.270 |
- 151.42 |
- 52.7% |
- 4.7% |
- 42.6% |
- 1.36 |
- 0.73 |
-
-
- | BXD15 |
- 3 |
- 0.366 |
- 70.26 |
- 44.7% |
- 3.9% |
- 51.4% |
- 1.29 |
- 0.79 |
-
-
- | BXD15 |
- 4 |
- 0.407 |
- 53.40 |
- 43.6% |
- 4.1% |
- 52.4% |
- 1.38 |
- 0.79 |
-
-
- | BXD16 |
- 1 |
- 0.388 |
- 48.98 |
- 43.7% |
- 4.1% |
- 52.2% |
- 1.41 |
- 0.79 |
-
-
- | BXD16 |
- 2 |
- 0.353 |
- 55.48 |
- 43.7% |
- 4.0% |
- 52.3% |
- 1.44 |
- 0.82 |
-
-
- | BXD16 |
- 3 |
- 0.339 |
- 61.60 |
- 45.3% |
- 4.2% |
- 50.5% |
- 1.42 |
- 0.80 |
-
-
- | BXD16 |
- 4 |
- 0.240 |
- 95.15 |
- 50.4% |
- 4.7% |
- 44.9% |
- 1.39 |
- 0.73 |
-
-
- | BXD16 |
- 5 |
- 0.270 |
- 70.63 |
- 46.3% |
- 4.3% |
- 49.4% |
- 1.45 |
- 0.75 |
-
-
- | BXD16 |
- 6 |
- 0.281 |
- 72.99 |
- 47.0% |
- 4.2% |
- 48.8% |
- 1.40 |
- 0.77 |
-
-
- | BXD18 |
- 1 |
- 0.384 |
- 59.78 |
- 45.4% |
- 4.0% |
- 50.6% |
- 1.12 |
- 0.71 |
-
-
- | BXD18 |
- 2 |
- 0.288 |
- 93.67 |
- 49.5% |
- 4.4% |
- 46.1% |
- 1.15 |
- 0.70 |
-
-
- | BXD18 |
- 3 |
- 0.286 |
- 89.64 |
- 45.2% |
- 4.1% |
- 50.8% |
- 1.27 |
- 0.71 |
-
-
- | BXD18 |
- 4 |
- 0.294 |
- 69.85 |
- 44.0% |
- 4.1% |
- 51.8% |
- 1.26 |
- 0.70 |
-
-
- | BXD18 |
- 5 |
- 0.417 |
- 59.80 |
- 47.0% |
- 4.3% |
- 48.7% |
- 1.15 |
- 0.72 |
-
-
- | BXD18 |
- 6 |
- 0.373 |
- 65.30 |
- 45.9% |
- 4.3% |
- 49.8% |
- 1.18 |
- 0.74 |
-
-
- | BXD19 |
- 1 |
- 0.364 |
- 59.35 |
- 46.7% |
- 4.2% |
- 49.1% |
- 1.27 |
- 0.73 |
-
-
- | BXD19 |
- 2 |
- 0.419 |
- 59.77 |
- 46.8% |
- 4.1% |
- 49.1% |
- 1.23 |
- 0.74 |
-
-
- | BXD19 |
- 3 |
- 0.303 |
- 62.66 |
- 46.0% |
- 4.4% |
- 49.6% |
- 1.30 |
- 0.74 |
-
-
- | BXD19 |
- 4 |
- 0.280 |
- 91.00 |
- 51.8% |
- 4.5% |
- 43.7% |
- 1.32 |
- 0.68 |
-
-
- | BXD19 |
- 5 |
- 0.303 |
- 66.18 |
- 47.1% |
- 4.5% |
- 48.4% |
- 1.33 |
- 0.72 |
-
-
- | BXD19 |
- 6 |
- 0.389 |
- 63.61 |
- 47.5% |
- 4.4% |
- 48.1% |
- 1.28 |
- 0.73 |
-
-
- | BXD21 |
- 1 |
- 0.350 |
- 75.93 |
- 44.9% |
- 3.9% |
- 51.3% |
- 1.29 |
- 0.77 |
-
-
- | BXD21 |
- 2 |
- 0.338 |
- 59.00 |
- 43.8% |
- 4.0% |
- 52.1% |
- 1.29 |
- 0.77 |
-
-
- | BXD21 |
- 3 |
- 0.304 |
- 59.94 |
- 44.9% |
- 4.0% |
- 51.2% |
- 1.44 |
- 0.77 |
-
-
- | BXD21 |
- 4 |
- 0.235 |
- 94.44 |
- 51.0% |
- 4.8% |
- 44.2% |
- 1.35 |
- 0.73 |
-
-
- | BXD21 |
- 5 |
- 0.310 |
- 64.22 |
- 46.9% |
- 4.2% |
- 48.9% |
- 1.42 |
- 0.77 |
-
-
- | BXD22 |
- 1 |
- 0.363 |
- 58.10 |
- 45.3% |
- 3.9% |
- 50.8% |
- 1.24 |
- 0.80 |
-
-
- | BXD22 |
- 2 |
- 0.385 |
- 55.58 |
- 44.5% |
- 4.0% |
- 51.5% |
- 1.28 |
- 0.80 |
-
-
- | BXD22 |
- 3 |
- 0.345 |
- 61.03 |
- 46.8% |
- 4.3% |
- 48.9% |
- 1.35 |
- 0.81 |
-
-
- | BXD22 |
- 4 |
- 0.242 |
- 85.36 |
- 53.6% |
- 4.8% |
- 41.6% |
- 1.35 |
- 0.75 |
-
-
- | BXD22 |
- 5 |
- 0.316 |
- 62.02 |
- 47.3% |
- 4.5% |
- 48.2% |
- 1.40 |
- 0.77 |
-
-
- | BXD22 |
- 6 |
- 0.325 |
- 66.38 |
- 47.5% |
- 4.3% |
- 48.2% |
- 1.29 |
- 0.78 |
-
-
- | BXD23 |
- 1 |
- 0.276 |
- 75.99 |
- 45.3% |
- 4.1% |
- 50.6% |
- 1.27 |
- 0.75 |
-
-
- | BXD23 |
- 2 |
- 0.333 |
- 81.76 |
- 47.9% |
- 4.0% |
- 48.1% |
- 1.28 |
- 0.78 |
-
-
- | BXD23 |
- 3 |
- 0.275 |
- 102.46 |
- 47.4% |
- 3.9% |
- 48.8% |
- 1.30 |
- 0.77 |
-
-
- | BXD23 |
- 4 |
- 0.178 |
- 115.83 |
- 50.2% |
- 4.7% |
- 45.2% |
- 1.38 |
- 0.73 |
-
-
- | BXD23 |
- 5 |
- 0.258 |
- 92.38 |
- 47.6% |
- 4.2% |
- 48.2% |
- 1.32 |
- 0.77 |
-
-
- | BXD23 |
- 6 |
- 0.256 |
- 88.23 |
- 46.3% |
- 4.1% |
- 49.5% |
- 1.31 |
- 0.74 |
-
-
- | BXD24 |
- 1 |
- 0.348 |
- 71.69 |
- 44.9% |
- 4.1% |
- 51.1% |
- 1.25 |
- 0.74 |
-
-
- | BXD24 |
- 2 |
- 0.324 |
- 74.05 |
- 44.3% |
- 4.0% |
- 51.7% |
- 1.23 |
- 0.80 |
-
-
- | BXD24 |
- 3 |
- 0.401 |
- 64.08 |
- 45.6% |
- 4.0% |
- 50.4% |
- 1.08 |
- 0.74 |
-
-
- | BXD24 |
- 4 |
- 0.246 |
- 82.84 |
- 45.7% |
- 4.3% |
- 50.0% |
- 1.20 |
- 0.75 |
-
-
- | BXD24 |
- 6 |
- 0.389 |
- 54.28 |
- 44.3% |
- 4.2% |
- 51.5% |
- 1.20 |
- 0.67 |
-
-
- | BXD27 |
- 1 |
- 0.507 |
- 50.08 |
- 43.6% |
- 3.9% |
- 52.5% |
- 1.48 |
- 0.81 |
-
-
- | BXD27 |
- 2 |
- 0.468 |
- 51.29 |
- 44.0% |
- 3.7% |
- 52.3% |
- 1.44 |
- 0.90 |
-
-
- | BXD27 |
- 3 |
- 0.526 |
- 49.67 |
- 43.5% |
- 3.9% |
- 52.6% |
- 1.29 |
- 0.94 |
-
-
- | BXD27 |
- 4 |
- 0.537 |
- 48.92 |
- 43.5% |
- 3.8% |
- 52.8% |
- 1.46 |
- 0.91 |
-
-
- | BXD28 |
- 1 |
- 0.284 |
- 51.58 |
- 44.6% |
- 4.2% |
- 51.2% |
- 1.26 |
- 0.80 |
-
-
- | BXD28 |
- 2 |
- 0.322 |
- 50.16 |
- 44.9% |
- 4.3% |
- 50.8% |
- 1.21 |
- 0.76 |
-
-
- | BXD28 |
- 3 |
- 0.397 |
- 50.97 |
- 45.9% |
- 4.2% |
- 49.9% |
- 1.14 |
- 0.78 |
-
-
- | BXD28 |
- 4 |
- 0.330 |
- 74.26 |
- 51.4% |
- 4.6% |
- 44.0% |
- 1.26 |
- 0.72 |
-
-
- | BXD28 |
- 5 |
- 0.284 |
- 52.34 |
- 44.3% |
- 4.4% |
- 51.3% |
- 1.32 |
- 0.73 |
-
-
- | BXD28 |
- 6 |
- 0.349 |
- 57.14 |
- 47.8% |
- 4.5% |
- 47.7% |
- 1.30 |
- 0.79 |
-
-
- | BXD29 |
- 1 |
- 0.422 |
- 58.68 |
- 44.0% |
- 3.7% |
- 52.3% |
- 1.42 |
- 0.86 |
-
-
- | BXD29 |
- 3 |
- 0.400 |
- 58.72 |
- 43.1% |
- 3.8% |
- 53.2% |
- 1.31 |
- 0.89 |
-
-
- | BXD29 |
- 5 |
- 0.365 |
- 61.79 |
- 46.9% |
- 4.3% |
- 48.8% |
- 1.38 |
- 0.91 |
-
-
- | BXD31 |
- 1 |
- 0.379 |
- 51.10 |
- 45.8% |
- 4.3% |
- 50.0% |
- 1.13 |
- 0.75 |
-
-
- | BXD31 |
- 2 |
- 0.333 |
- 48.64 |
- 43.7% |
- 4.1% |
- 52.2% |
- 1.22 |
- 0.71 |
-
-
- | BXD31 |
- 3 |
- 0.519 |
- 47.71 |
- 48.2% |
- 4.3% |
- 47.5% |
- 1.13 |
- 0.72 |
-
-
- | BXD31 |
- 4 |
- 0.243 |
- 75.24 |
- 48.6% |
- 4.8% |
- 46.6% |
- 1.23 |
- 0.71 |
-
-
- | BXD31 |
- 5 |
- 0.325 |
- 53.19 |
- 46.9% |
- 4.6% |
- 48.6% |
- 1.22 |
- 0.75 |
-
-
- | BXD31 |
- 6 |
- 0.320 |
- 46.98 |
- 44.5% |
- 4.3% |
- 51.2% |
- 1.24 |
- 0.74 |
-
-
- | BXD32 |
- 1 |
- 0.256 |
- 70.43 |
- 45.4% |
- 3.9% |
- 50.8% |
- 1.83 |
- 0.87 |
-
-
- | BXD32 |
- 2 |
- 0.288 |
- 67.44 |
- 44.5% |
- 4.1% |
- 51.4% |
- 1.34 |
- 0.77 |
-
-
- | BXD32 |
- 3 |
- 0.361 |
- 58.13 |
- 44.4% |
- 4.0% |
- 51.6% |
- 1.36 |
- 0.77 |
-
-
- | BXD32 |
- 4 |
- 0.367 |
- 61.39 |
- 44.7% |
- 4.1% |
- 51.2% |
- 1.40 |
- 0.78 |
-
-
- | BXD32 |
- 5 |
- 0.324 |
- 68.04 |
- 45.6% |
- 4.3% |
- 50.1% |
- 1.39 |
- 0.75 |
-
-
- | BXD32 |
- 6 |
- 0.266 |
- 95.49 |
- 50.8% |
- 4.5% |
- 44.6% |
- 1.41 |
- 0.73 |
-
-
- | BXD33 |
- 1 |
- 0.344 |
- 61.65 |
- 44.9% |
- 3.9% |
- 51.2% |
- 1.38 |
- 0.82 |
-
-
- | BXD33 |
- 2 |
- 0.356 |
- 61.04 |
- 44.7% |
- 4.1% |
- 51.2% |
- 1.44 |
- 0.79 |
-
-
- | BXD33 |
- 4 |
- 0.385 |
- 59.92 |
- 44.1% |
- 3.9% |
- 52.0% |
- 1.38 |
- 0.82 |
-
-
- | BXD34 |
- 1 |
- 0.297 |
- 91.13 |
- 52.1% |
- 4.6% |
- 43.3% |
- 1.34 |
- 0.70 |
-
-
- | BXD34 |
- 2 |
- 0.508 |
- 51.79 |
- 44.8% |
- 3.9% |
- 51.3% |
- 1.42 |
- 0.76 |
-
-
- | BXD34 |
- 3 |
- 0.284 |
- 85.33 |
- 50.7% |
- 4.6% |
- 44.7% |
- 1.51 |
- 0.72 |
-
-
- | BXD34 |
- 4 |
- 0.297 |
- 61.95 |
- 44.9% |
- 4.1% |
- 51.0% |
- 1.36 |
- 0.77 |
-
-
- | BXD34 |
- 5 |
- 0.516 |
- 56.02 |
- 46.3% |
- 4.0% |
- 49.7% |
- 1.33 |
- 0.74 |
-
-
- | BXD34 |
- 6 |
- 0.545 |
- 54.46 |
- 45.2% |
- 3.8% |
- 51.0% |
- 1.49 |
- 0.87 |
-
-
- | BXD36 |
- 1 |
- 0.435 |
- 62.74 |
- 48.1% |
- 4.0% |
- 47.8% |
- 1.36 |
- 0.73 |
-
-
- | BXD36 |
- 2 |
- 0.333 |
- 71.24 |
- 48.8% |
- 4.3% |
- 46.8% |
- 1.44 |
- 0.72 |
-
-
- | BXD36 |
- 3 |
- 0.320 |
- 72.97 |
- 48.3% |
- 4.3% |
- 47.4% |
- 1.38 |
- 0.74 |
-
-
- | BXD36 |
- 4 |
- 0.391 |
- 73.58 |
- 49.5% |
- 4.2% |
- 46.3% |
- 1.25 |
- 0.75 |
-
-
- | BXD38 |
- 1 |
- 0.303 |
- 87.68 |
- 39.2% |
- 3.3% |
- 57.5% |
- 1.08 |
- 0.82 |
-
-
- | BXD38 |
- 2 |
- 0.343 |
- 61.39 |
- 39.7% |
- 3.2% |
- 57.1% |
- 1.12 |
- 0.82 |
-
-
- | BXD38 |
- 3 |
- 0.453 |
- 67.19 |
- 41.2% |
- 3.4% |
- 55.4% |
- 1.11 |
- 0.83 |
-
-
- | BXD38 |
- 4 |
- 0.424 |
- 64.36 |
- 41.6% |
- 3.5% |
- 55.0% |
- 1.11 |
- 0.82 |
-
-
- | BXD39 |
- 1 |
- 0.357 |
- 64.36 |
- 47.3% |
- 4.3% |
- 48.3% |
- 1.33 |
- 0.78 |
-
-
- | BXD39 |
- 2 |
- 0.332 |
- 60.23 |
- 46.5% |
- 4.2% |
- 49.3% |
- 1.41 |
- 0.80 |
-
-
- | BXD39 |
- 3 |
- 0.331 |
- 65.27 |
- 46.2% |
- 4.2% |
- 49.6% |
- 1.32 |
- 0.75 |
-
-
- | BXD39 |
- 4 |
- 0.362 |
- 62.60 |
- 45.5% |
- 4.0% |
- 50.5% |
- 1.28 |
- 0.80 |
-
-
- | BXD39 |
- 5 |
- 0.347 |
- 58.97 |
- 46.1% |
- 4.3% |
- 49.7% |
- 1.29 |
- 0.79 |
-
-
- | BXD39 |
- 6 |
- 0.327 |
- 63.12 |
- 46.2% |
- 4.3% |
- 49.6% |
- 1.29 |
- 0.77 |
-
-
- | BXD40 |
- 1 |
- 0.371 |
- 60.01 |
- 45.2% |
- 4.1% |
- 50.7% |
- 1.32 |
- 0.77 |
-
-
- | BXD40 |
- 2 |
- 0.245 |
- 84.69 |
- 49.1% |
- 4.5% |
- 46.4% |
- 1.33 |
- 0.72 |
-
-
- | BXD40 |
- 3 |
- 0.324 |
- 64.17 |
- 46.8% |
- 4.3% |
- 48.8% |
- 1.34 |
- 0.73 |
-
-
- | BXD40 |
- 4 |
- 0.280 |
- 63.97 |
- 45.1% |
- 4.2% |
- 50.7% |
- 1.48 |
- 0.74 |
-
-
- | BXD40 |
- 5 |
- 0.271 |
- 69.40 |
- 45.9% |
- 4.3% |
- 49.8% |
- 1.33 |
- 0.74 |
-
-
- | BXD40 |
- 6 |
- 0.307 |
- 59.99 |
- 45.5% |
- 4.2% |
- 50.4% |
- 1.37 |
- 0.76 |
-
-
- | BXD42 |
- 1 |
- 0.424 |
- 53.91 |
- 45.1% |
- 4.1% |
- 50.8% |
- 1.54 |
- 0.83 |
-
-
- | BXD42 |
- 2 |
- 0.216 |
- 92.34 |
- 46.7% |
- 4.3% |
- 49.1% |
- 1.44 |
- 0.76 |
-
-
- | BXD42 |
- 3 |
- 0.249 |
- 84.52 |
- 45.7% |
- 4.1% |
- 50.2% |
- 1.52 |
- 0.80 |
-
-
- | BXD42 |
- 5 |
- 0.236 |
- 85.29 |
- 46.2% |
- 4.0% |
- 49.8% |
- 1.38 |
- 0.77 |
-
-
- | DBA/2J |
- 1 |
- 0.313 |
- 79.69 |
- 46.8% |
- 4.2% |
- 49.0% |
- 1.24 |
- 0.72 |
-
-
- | DBA/2J |
- 2 |
- 0.294 |
- 82.27 |
- 46.5% |
- 4.2% |
- 49.3% |
- 1.27 |
- 0.73 |
-
-
- | DBA/2J |
- 3 |
- 0.349 |
- 78.58 |
- 47.8% |
- 4.3% |
- 47.8% |
- 1.31 |
- 0.73 |
-
-
- | DBA/2J |
- 4 |
- 0.389 |
- 72.02 |
- 48.0% |
- 4.3% |
- 47.7% |
- 1.21 |
- 0.77 |
-
-
- | DBA/2J |
- 5 |
- 0.362 |
- 66.73 |
- 46.5% |
- 4.4% |
- 49.1% |
- 1.23 |
- 0.75 |
-
-
- | DBA/2J |
- 6 |
- 0.341 |
- 79.88 |
- 46.7% |
- 4.0% |
- 49.4% |
- 1.33 |
- 0.74 |
-
-
- | C57BL/6J |
- 1 |
- 0.294 |
- 82.84 |
- 46.7% |
- 4.1% |
- 49.2% |
- 1.23 |
- 0.76 |
-
-
- | C57BL/6J |
- 2 |
- 0.242 |
- 80.40 |
- 43.1% |
- 4.1% |
- 52.8% |
- 1.29 |
- 0.76 |
-
-
- | C57BL/6J |
- 3 |
- 0.250 |
- 110.90 |
- 47.8% |
- 4.0% |
- 48.2% |
- 1.32 |
- 0.76 |
-
-
- | C57BL/6J |
- 4 |
- 0.289 |
- 101.88 |
- 47.5% |
- 4.1% |
- 48.4% |
- 1.18 |
- 0.75 |
-
-
- | C57BL/6J |
- 5 |
- 0.299 |
- 114.59 |
- 48.7% |
- 4.1% |
- 47.3% |
- 1.13 |
- 0.74 |
-
-
- | C57BL/6J |
- 6 |
- 0.251 |
- 105.90 |
- 45.8% |
- 3.8% |
- 50.4% |
- 1.30 |
- 0.76 |
-
-
- | 129P3/J |
- 1 |
- 0.496 |
- 59.26 |
- 41.9% |
- 3.5% |
- 54.5% |
- 1.28 |
- 0.79 |
-
-
- | 129P3/J |
- 2 |
- 0.550 |
- 50.83 |
- 42.0% |
- 3.7% |
- 54.3% |
- 1.16 |
- 0.78 |
-
-
- | 129P3/J |
- 3 |
- 0.443 |
- 56.08 |
- 43.0% |
- 3.8% |
- 53.3% |
- 1.22 |
- 0.73 |
-
-
- | 129P3/J |
- 4 |
- 0.521 |
- 58.92 |
- 44.8% |
- 3.8% |
- 51.4% |
- 1.30 |
- 0.74 |
-
-
- | 129P3/J |
- 5 |
- 0.503 |
- 58.26 |
- 44.9% |
- 3.8% |
- 51.3% |
- 1.32 |
- 0.74 |
-
-
- | 129S1/SvImJ |
- 1 |
- 0.311 |
- 66.76 |
- 47.8% |
- 3.9% |
- 48.3% |
- 2.04 |
- 0.97 |
-
-
- | 129S1/SvImJ |
- 2 |
- 0.262 |
- 57.63 |
- 44.5% |
- 3.9% |
- 51.6% |
- 1.61 |
- 0.81 |
-
-
- | 129S1/SvImJ |
- 3 |
- 0.322 |
- 62.67 |
- 45.3% |
- 3.8% |
- 50.9% |
- 1.70 |
- 0.83 |
-
-
- | 129S1/SvImJ |
- 4 |
- 0.185 |
- 119.02 |
- 50.2% |
- 4.4% |
- 45.5% |
- 1.66 |
- 0.75 |
-
-
- | A/J |
- 1 |
- 0.453 |
- 51.85 |
- 42.6% |
- 3.6% |
- 53.8% |
- 1.20 |
- 0.73 |
-
-
- | A/J |
- 2 |
- 0.396 |
- 56.61 |
- 45.9% |
- 3.9% |
- 50.2% |
- 1.21 |
- 0.76 |
-
-
- | A/J |
- 3 |
- 0.421 |
- 62.34 |
- 47.0% |
- 4.1% |
- 48.8% |
- 1.29 |
- 0.72 |
-
-
- | A/J |
- 4 |
- 0.508 |
- 61.52 |
- 48.2% |
- 4.1% |
- 47.7% |
- 1.22 |
- 0.74 |
-
-
- | AKR/J |
- 1 |
- 0.331 |
- 54.70 |
- 41.7% |
- 3.9% |
- 54.4% |
- 1.22 |
- 0.74 |
-
-
- | AKR/J |
- 2 |
- 0.464 |
- 55.46 |
- 44.1% |
- 3.7% |
- 52.1% |
- 1.30 |
- 0.76 |
-
-
- | AKR/J |
- 4 |
- 0.444 |
- 53.62 |
- 47.6% |
- 4.0% |
- 48.4% |
- 1.23 |
- 0.71 |
-
-
- | AKR/J |
- 5 |
- 0.439 |
- 58.62 |
- 47.4% |
- 4.3% |
- 48.3% |
- 1.23 |
- 0.70 |
-
-
- | BALB/cByJ |
- 1 |
- 0.336 |
- 75.49 |
- 50.0% |
- 4.1% |
- 45.9% |
- 1.54 |
- 0.82 |
-
-
- | BALB/cByJ |
- 2 |
- 0.280 |
- 67.93 |
- 47.1% |
- 4.3% |
- 48.7% |
- 1.43 |
- 0.76 |
-
-
- | BALB/cByJ |
- 3 |
- 0.312 |
- 73.77 |
- 47.7% |
- 4.1% |
- 48.2% |
- 1.79 |
- 0.92 |
-
-
- | BALB/cByJ |
- 4 |
- 0.262 |
- 79.97 |
- 46.1% |
- 4.1% |
- 49.8% |
- 1.38 |
- 0.79 |
-
-
- | BALB/cByJ |
- 5 |
- 0.276 |
- 81.32 |
- 46.3% |
- 4.1% |
- 49.6% |
- 1.34 |
- 0.79 |
-
-
- | BALB/cJ |
- 1 |
- 0.591 |
- 54.25 |
- 43.2% |
- 3.5% |
- 53.3% |
- 1.15 |
- 0.80 |
-
-
- | BALB/cJ |
- 2 |
- 0.346 |
- 50.36 |
- 39.9% |
- 3.3% |
- 56.8% |
- 1.20 |
- 0.77 |
-
-
- | BALB/cJ |
- 3 |
- 0.333 |
- 52.79 |
- 40.4% |
- 3.7% |
- 55.9% |
- 1.25 |
- 0.77 |
-
-
- | BALB/cJ |
- 5 |
- 0.495 |
- 54.78 |
- 45.0% |
- 3.7% |
- 51.3% |
- 1.15 |
- 0.72 |
-
-
- | BTBR T+tf/J |
- 3 |
- 0.315 |
- 62.83 |
- 46.4% |
- 4.1% |
- 49.5% |
- 1.38 |
- 0.78 |
-
-
- | BTBR T+tf/J |
- 4 |
- 0.243 |
- 90.12 |
- 51.6% |
- 4.8% |
- 43.6% |
- 1.31 |
- 0.75 |
-
-
- | BTBR T+tf/J |
- 5 |
- 0.294 |
- 71.21 |
- 46.6% |
- 4.3% |
- 49.0% |
- 1.41 |
- 0.77 |
-
-
- | BTBR T+tf/J |
- 6 |
- 0.268 |
- 67.53 |
- 46.6% |
- 4.2% |
- 49.2% |
- 1.32 |
- 0.75 |
-
-
- | BTBR T+tf/J |
- 1 |
- 0.370 |
- 55.40 |
- 45.7% |
- 4.1% |
- 50.2% |
- 1.41 |
- 0.75 |
-
-
- | BTBR T+tf/J |
- 2 |
- 0.488 |
- 50.89 |
- 47.2% |
- 4.2% |
- 48.6% |
- 1.36 |
- 0.75 |
-
-
- | C3H/HeJ |
- 1 |
- 0.511 |
- 59.20 |
- 43.3% |
- 3.4% |
- 53.3% |
- 1.17 |
- 0.83 |
-
-
- | C3H/HeJ |
- 2 |
- 0.405 |
- 79.49 |
- 41.3% |
- 3.3% |
- 55.5% |
- 1.18 |
- 0.83 |
-
-
- | C3H/HeJ |
- 3 |
- 0.454 |
- 59.47 |
- 41.7% |
- 3.5% |
- 54.9% |
- 1.16 |
- 0.81 |
-
-
- | C3H/HeJ |
- 4 |
- 0.448 |
- 56.28 |
- 41.5% |
- 3.5% |
- 55.0% |
- 1.16 |
- 0.79 |
-
-
- | C3H/HeJ |
- 5 |
- 0.389 |
- 50.17 |
- 41.1% |
- 3.6% |
- 55.2% |
- 1.24 |
- 0.79 |
-
-
- | C58/J |
- 1 |
- 0.336 |
- 56.66 |
- 46.0% |
- 4.2% |
- 49.8% |
- 1.29 |
- 0.73 |
-
-
- | C58/J |
- 2 |
- 0.372 |
- 58.61 |
- 46.7% |
- 4.3% |
- 49.0% |
- 1.21 |
- 0.71 |
-
-
- | C58/J |
- 3 |
- 0.366 |
- 64.58 |
- 46.8% |
- 4.2% |
- 49.0% |
- 1.20 |
- 0.72 |
-
-
- | C58/J |
- 4 |
- 0.371 |
- 52.72 |
- 45.3% |
- 4.1% |
- 50.6% |
- 1.24 |
- 0.72 |
-
-
- | CAST/EiJ |
- 1 |
- 0.467 |
- 55.74 |
- 47.1% |
- 3.8% |
- 49.1% |
- 1.39 |
- 0.79 |
-
-
- | CAST/EiJ |
- 2 |
- 0.545 |
- 50.29 |
- 46.8% |
- 3.8% |
- 49.4% |
- 1.34 |
- 0.84 |
-
-
- | CAST/EiJ |
- 3 |
- 0.469 |
- 55.08 |
- 47.4% |
- 4.0% |
- 48.5% |
- 1.32 |
- 0.76 |
-
-
- | CAST/EiJ |
- 4 |
- 0.390 |
- 83.05 |
- 53.0% |
- 4.4% |
- 42.6% |
- 1.36 |
- 0.72 |
-
-
- | CBA/J |
- 1 |
- 0.292 |
- 67.25 |
- 44.9% |
- 4.0% |
- 51.2% |
- 1.22 |
- 0.76 |
-
-
- | CBA/J |
- 2 |
- 0.347 |
- 61.99 |
- 46.4% |
- 4.0% |
- 49.7% |
- 1.25 |
- 0.82 |
-
-
- | CBA/J |
- 3 |
- 0.305 |
- 62.16 |
- 46.3% |
- 4.3% |
- 49.4% |
- 1.31 |
- 0.75 |
-
-
- | CBA/J |
- 4 |
- 0.303 |
- 64.82 |
- 46.5% |
- 4.0% |
- 49.5% |
- 1.34 |
- 0.76 |
-
-
- | CBA/J |
- 5 |
- 0.313 |
- 64.15 |
- 45.3% |
- 4.1% |
- 50.7% |
- 1.37 |
- 0.78 |
-
-
- | CBA/J |
- 6 |
- 0.365 |
- 56.84 |
- 45.6% |
- 4.1% |
- 50.4% |
- 1.31 |
- 0.76 |
-
-
- | FVB/NJ |
- 1 |
- 0.497 |
- 63.99 |
- 44.2% |
- 3.5% |
- 52.3% |
- 1.33 |
- 0.79 |
-
-
- | FVB/NJ |
- 2 |
- 0.475 |
- 55.24 |
- 44.8% |
- 3.8% |
- 51.4% |
- 1.33 |
- 0.74 |
-
-
- | FVB/NJ |
- 3 |
- 0.527 |
- 56.07 |
- 42.6% |
- 3.5% |
- 53.9% |
- 1.31 |
- 0.86 |
-
-
- | FVB/NJ |
- 4 |
- 0.447 |
- 62.56 |
- 41.7% |
- 3.5% |
- 54.8% |
- 1.24 |
- 0.82 |
-
-
- | KK/HIJ |
- 1 |
- 0.309 |
- 93.54 |
- 49.6% |
- 4.3% |
- 46.1% |
- 1.57 |
- 0.74 |
-
-
- | KK/HIJ |
- 2 |
- 0.298 |
- 63.24 |
- 48.0% |
- 4.4% |
- 47.6% |
- 1.37 |
- 0.72 |
-
-
- | KK/HIJ |
- 4 |
- 0.223 |
- 93.03 |
- 44.7% |
- 4.0% |
- 51.3% |
- 1.39 |
- 0.74 |
-
-
- | KK/HIJ |
- 5 |
- 0.153 |
- 136.67 |
- 51.9% |
- 4.6% |
- 43.5% |
- 1.24 |
- 0.71 |
-
-
- | MOLF/EiJ |
- 1 |
- 0.339 |
- 67.11 |
- 49.1% |
- 4.3% |
- 46.6% |
- 1.55 |
- 0.83 |
-
-
- | MOLF/EiJ |
- 2 |
- 0.319 |
- 80.73 |
- 49.1% |
- 4.2% |
- 46.7% |
- 1.52 |
- 0.78 |
-
-
- | MOLF/EiJ |
- 3 |
- 0.380 |
- 69.03 |
- 49.1% |
- 4.2% |
- 46.7% |
- 1.29 |
- 0.82 |
-
-
- | MOLF/EiJ |
- 4 |
- 0.238 |
- 95.19 |
- 48.7% |
- 4.1% |
- 47.2% |
- 1.35 |
- 0.79 |
-
-
- | NOD/LtJ |
- 1 |
- 0.356 |
- 78.42 |
- 49.1% |
- 4.2% |
- 46.7% |
- 1.35 |
- 0.76 |
-
-
- | NOD/LtJ |
- 2 |
- 0.422 |
- 59.71 |
- 47.4% |
- 4.0% |
- 48.5% |
- 1.25 |
- 0.73 |
-
-
- | NOD/LtJ |
- 3 |
- 0.377 |
- 77.84 |
- 49.8% |
- 4.0% |
- 46.2% |
- 1.24 |
- 0.75 |
-
-
- | NOD/LtJ |
- 4 |
- 0.535 |
- 60.86 |
- 50.6% |
- 4.4% |
- 45.0% |
- 1.28 |
- 0.74 |
-
-
- | NOD/LtJ |
- 5 |
- 0.336 |
- 74.58 |
- 46.6% |
- 3.9% |
- 49.5% |
- 1.32 |
- 0.72 |
-
-
- | NZW/LacJ |
- 2 |
- 0.442 |
- 50.31 |
- 44.6% |
- 4.1% |
- 51.3% |
- 1.33 |
- 0.82 |
-
-
- | NZW/LacJ |
- 3 |
- 0.331 |
- 56.86 |
- 44.2% |
- 4.0% |
- 51.7% |
- 1.60 |
- 0.78 |
-
-
- | NZW/LacJ |
- 4 |
- 0.338 |
- 55.23 |
- 44.1% |
- 4.0% |
- 51.9% |
- 1.31 |
- 0.78 |
-
-
- | NZW/LacJ |
- 5 |
- 0.351 |
- 56.90 |
- 49.3% |
- 4.3% |
- 46.5% |
- 1.30 |
- 0.75 |
-
-
- | PWD/PhJ |
- 1 |
- 0.444 |
- 57.65 |
- 47.2% |
- 3.9% |
- 48.9% |
- 1.62 |
- 0.78 |
-
-
- | PWD/PhJ |
- 2 |
- 0.328 |
- 67.58 |
- 47.3% |
- 4.2% |
- 48.5% |
- 1.36 |
- 0.76 |
-
-
- | PWD/PhJ |
- 3 |
- 0.322 |
- 73.90 |
- 47.5% |
- 4.0% |
- 48.5% |
- 1.46 |
- 0.81 |
-
-
- | PWD/PhJ |
- 4 |
- 0.271 |
- 75.79 |
- 46.1% |
- 4.0% |
- 50.0% |
- 1.39 |
- 0.79 |
-
-
- | PWD/PhJ |
- 5 |
- 0.191 |
- 144.73 |
- 57.7% |
- 5.0% |
- 37.3% |
- 1.36 |
- 0.67 |
-
-
- | SJL/J |
- 1 |
- 0.528 |
- 54.58 |
- 41.1% |
- 3.4% |
- 55.4% |
- 1.16 |
- 0.80 |
-
-
- | SJL/J |
- 3 |
- 0.663 |
- 56.21 |
- 41.8% |
- 3.3% |
- 55.0% |
- 1.22 |
- 0.75 |
-
-
- | SJL/J |
- 4 |
- 0.646 |
- 52.96 |
- 40.5% |
- 3.2% |
- 56.3% |
- 1.13 |
- 0.81 |
-
-
- | SJL/J |
- 5 |
- 0.639 |
- 61.91 |
- 44.8% |
- 3.4% |
- 51.9% |
- 1.37 |
- 0.79 |
-
-
-
-
diff --git a/general/datasets/BR_U_0304_DPMMR/acknowledgment.rtf b/general/datasets/BR_U_0304_DPMMR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0304_DPMMR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0304_DPMMR/cases.rtf b/general/datasets/BR_U_0304_DPMMR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0304_DPMMR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0304_DPMMR/notes.rtf b/general/datasets/BR_U_0304_DPMMR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0304_DPMMR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0304_DPMMR/platform.rtf b/general/datasets/BR_U_0304_DPMMR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0304_DPMMR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0304_DPMMR/processing.rtf b/general/datasets/BR_U_0304_DPMMR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0304_DPMMR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0304_DPMMR/summary.rtf b/general/datasets/BR_U_0304_DPMMR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0304_DPMMR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0304_DPMMR/tissue.rtf b/general/datasets/BR_U_0304_DPMMR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0304_DPMMR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0304_DPMR/acknowledgment.rtf b/general/datasets/BR_U_0304_DPMR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0304_DPMR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0304_DPMR/cases.rtf b/general/datasets/BR_U_0304_DPMR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0304_DPMR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0304_DPMR/notes.rtf b/general/datasets/BR_U_0304_DPMR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0304_DPMR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0304_DPMR/platform.rtf b/general/datasets/BR_U_0304_DPMR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0304_DPMR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0304_DPMR/processing.rtf b/general/datasets/BR_U_0304_DPMR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0304_DPMR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0304_DPMR/summary.rtf b/general/datasets/BR_U_0304_DPMR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0304_DPMR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0304_DPMR/tissue.rtf b/general/datasets/BR_U_0304_DPMR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0304_DPMR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0304_R/acknowledgment.rtf b/general/datasets/BR_U_0304_R/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0304_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0304_R/cases.rtf b/general/datasets/BR_U_0304_R/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0304_R/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0304_R/notes.rtf b/general/datasets/BR_U_0304_R/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0304_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0304_R/platform.rtf b/general/datasets/BR_U_0304_R/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0304_R/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0304_R/processing.rtf b/general/datasets/BR_U_0304_R/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0304_R/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0304_R/summary.rtf b/general/datasets/BR_U_0304_R/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0304_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0304_R/tissue.rtf b/general/datasets/BR_U_0304_R/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0304_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0304_RR/acknowledgment.rtf b/general/datasets/BR_U_0304_RR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0304_RR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0304_RR/cases.rtf b/general/datasets/BR_U_0304_RR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0304_RR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0304_RR/notes.rtf b/general/datasets/BR_U_0304_RR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0304_RR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0304_RR/platform.rtf b/general/datasets/BR_U_0304_RR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0304_RR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0304_RR/processing.rtf b/general/datasets/BR_U_0304_RR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0304_RR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0304_RR/summary.rtf b/general/datasets/BR_U_0304_RR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0304_RR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0304_RR/tissue.rtf b/general/datasets/BR_U_0304_RR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0304_RR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0405_SS/acknowledgment.rtf b/general/datasets/BR_U_0405_SS/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0405_SS/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0405_SS/cases.rtf b/general/datasets/BR_U_0405_SS/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0405_SS/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0405_SS/notes.rtf b/general/datasets/BR_U_0405_SS/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0405_SS/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0405_SS/platform.rtf b/general/datasets/BR_U_0405_SS/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0405_SS/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0405_SS/processing.rtf b/general/datasets/BR_U_0405_SS/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0405_SS/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0405_SS/summary.rtf b/general/datasets/BR_U_0405_SS/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0405_SS/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0405_SS/tissue.rtf b/general/datasets/BR_U_0405_SS/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0405_SS/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0805_M/acknowledgment.rtf b/general/datasets/BR_U_0805_M/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0805_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0805_M/cases.rtf b/general/datasets/BR_U_0805_M/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0805_M/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0805_M/notes.rtf b/general/datasets/BR_U_0805_M/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0805_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0805_M/platform.rtf b/general/datasets/BR_U_0805_M/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0805_M/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0805_M/processing.rtf b/general/datasets/BR_U_0805_M/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0805_M/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0805_M/summary.rtf b/general/datasets/BR_U_0805_M/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0805_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0805_M/tissue.rtf b/general/datasets/BR_U_0805_M/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0805_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0805_P/acknowledgment.rtf b/general/datasets/BR_U_0805_P/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0805_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0805_P/cases.rtf b/general/datasets/BR_U_0805_P/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0805_P/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0805_P/notes.rtf b/general/datasets/BR_U_0805_P/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0805_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0805_P/platform.rtf b/general/datasets/BR_U_0805_P/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0805_P/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0805_P/processing.rtf b/general/datasets/BR_U_0805_P/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0805_P/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0805_P/summary.rtf b/general/datasets/BR_U_0805_P/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0805_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0805_P/tissue.rtf b/general/datasets/BR_U_0805_P/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0805_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0805_R/acknowledgment.rtf b/general/datasets/BR_U_0805_R/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_0805_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0805_R/cases.rtf b/general/datasets/BR_U_0805_R/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_0805_R/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_0805_R/notes.rtf b/general/datasets/BR_U_0805_R/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_0805_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_0805_R/platform.rtf b/general/datasets/BR_U_0805_R/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_0805_R/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_0805_R/processing.rtf b/general/datasets/BR_U_0805_R/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_0805_R/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_0805_R/summary.rtf b/general/datasets/BR_U_0805_R/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_0805_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0805_R/tissue.rtf b/general/datasets/BR_U_0805_R/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_0805_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0903_DPM/acknowledgment.rtf b/general/datasets/BR_U_0903_DPM/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/BR_U_0903_DPM/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0903_DPM/cases.rtf b/general/datasets/BR_U_0903_DPM/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/BR_U_0903_DPM/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/BR_U_0903_DPM/notes.rtf b/general/datasets/BR_U_0903_DPM/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/BR_U_0903_DPM/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/BR_U_0903_DPM/platform.rtf b/general/datasets/BR_U_0903_DPM/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/BR_U_0903_DPM/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BR_U_0903_DPM/processing.rtf b/general/datasets/BR_U_0903_DPM/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/BR_U_0903_DPM/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/BR_U_0903_DPM/summary.rtf b/general/datasets/BR_U_0903_DPM/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/BR_U_0903_DPM/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0903_DPM/tissue.rtf b/general/datasets/BR_U_0903_DPM/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/BR_U_0903_DPM/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0903_DPMM/acknowledgment.rtf b/general/datasets/BR_U_0903_DPMM/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/BR_U_0903_DPMM/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0903_DPMM/cases.rtf b/general/datasets/BR_U_0903_DPMM/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/BR_U_0903_DPMM/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/BR_U_0903_DPMM/notes.rtf b/general/datasets/BR_U_0903_DPMM/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/BR_U_0903_DPMM/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/BR_U_0903_DPMM/platform.rtf b/general/datasets/BR_U_0903_DPMM/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/BR_U_0903_DPMM/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BR_U_0903_DPMM/processing.rtf b/general/datasets/BR_U_0903_DPMM/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/BR_U_0903_DPMM/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/BR_U_0903_DPMM/summary.rtf b/general/datasets/BR_U_0903_DPMM/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/BR_U_0903_DPMM/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0903_DPMM/tissue.rtf b/general/datasets/BR_U_0903_DPMM/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/BR_U_0903_DPMM/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0903_M/acknowledgment.rtf b/general/datasets/BR_U_0903_M/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/BR_U_0903_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0903_M/cases.rtf b/general/datasets/BR_U_0903_M/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/BR_U_0903_M/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/BR_U_0903_M/notes.rtf b/general/datasets/BR_U_0903_M/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/BR_U_0903_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/BR_U_0903_M/platform.rtf b/general/datasets/BR_U_0903_M/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/BR_U_0903_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BR_U_0903_M/processing.rtf b/general/datasets/BR_U_0903_M/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/BR_U_0903_M/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/BR_U_0903_M/summary.rtf b/general/datasets/BR_U_0903_M/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/BR_U_0903_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0903_M/tissue.rtf b/general/datasets/BR_U_0903_M/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/BR_U_0903_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0903_P/acknowledgment.rtf b/general/datasets/BR_U_0903_P/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/BR_U_0903_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0903_P/cases.rtf b/general/datasets/BR_U_0903_P/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/BR_U_0903_P/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/BR_U_0903_P/notes.rtf b/general/datasets/BR_U_0903_P/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/BR_U_0903_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/BR_U_0903_P/platform.rtf b/general/datasets/BR_U_0903_P/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/BR_U_0903_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BR_U_0903_P/processing.rtf b/general/datasets/BR_U_0903_P/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/BR_U_0903_P/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/BR_U_0903_P/summary.rtf b/general/datasets/BR_U_0903_P/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/BR_U_0903_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0903_P/tissue.rtf b/general/datasets/BR_U_0903_P/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/BR_U_0903_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_0903_R/acknowledgment.rtf b/general/datasets/BR_U_0903_R/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/BR_U_0903_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_0903_R/cases.rtf b/general/datasets/BR_U_0903_R/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/BR_U_0903_R/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/BR_U_0903_R/notes.rtf b/general/datasets/BR_U_0903_R/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/BR_U_0903_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/BR_U_0903_R/platform.rtf b/general/datasets/BR_U_0903_R/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/BR_U_0903_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/BR_U_0903_R/processing.rtf b/general/datasets/BR_U_0903_R/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/BR_U_0903_R/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/BR_U_0903_R/summary.rtf b/general/datasets/BR_U_0903_R/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/BR_U_0903_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_0903_R/tissue.rtf b/general/datasets/BR_U_0903_R/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/BR_U_0903_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1105_P/acknowledgment.rtf b/general/datasets/BR_U_1105_P/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1105_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1105_P/cases.rtf b/general/datasets/BR_U_1105_P/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1105_P/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1105_P/notes.rtf b/general/datasets/BR_U_1105_P/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1105_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1105_P/platform.rtf b/general/datasets/BR_U_1105_P/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1105_P/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1105_P/processing.rtf b/general/datasets/BR_U_1105_P/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1105_P/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1105_P/summary.rtf b/general/datasets/BR_U_1105_P/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1105_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1105_P/tissue.rtf b/general/datasets/BR_U_1105_P/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1105_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1105_R/acknowledgment.rtf b/general/datasets/BR_U_1105_R/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1105_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1105_R/cases.rtf b/general/datasets/BR_U_1105_R/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1105_R/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1105_R/notes.rtf b/general/datasets/BR_U_1105_R/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1105_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1105_R/platform.rtf b/general/datasets/BR_U_1105_R/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1105_R/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1105_R/processing.rtf b/general/datasets/BR_U_1105_R/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1105_R/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1105_R/summary.rtf b/general/datasets/BR_U_1105_R/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1105_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1105_R/tissue.rtf b/general/datasets/BR_U_1105_R/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1105_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_DPM/acknowledgment.rtf b/general/datasets/BR_U_1203_DPM/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_DPM/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_DPM/cases.rtf b/general/datasets/BR_U_1203_DPM/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_DPM/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_DPM/notes.rtf b/general/datasets/BR_U_1203_DPM/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_DPM/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_DPM/platform.rtf b/general/datasets/BR_U_1203_DPM/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_DPM/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_DPM/processing.rtf b/general/datasets/BR_U_1203_DPM/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_DPM/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_DPM/summary.rtf b/general/datasets/BR_U_1203_DPM/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_DPM/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_DPM/tissue.rtf b/general/datasets/BR_U_1203_DPM/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_DPM/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_DPMM/acknowledgment.rtf b/general/datasets/BR_U_1203_DPMM/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_DPMM/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_DPMM/cases.rtf b/general/datasets/BR_U_1203_DPMM/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_DPMM/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_DPMM/notes.rtf b/general/datasets/BR_U_1203_DPMM/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_DPMM/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_DPMM/platform.rtf b/general/datasets/BR_U_1203_DPMM/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_DPMM/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_DPMM/processing.rtf b/general/datasets/BR_U_1203_DPMM/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_DPMM/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_DPMM/summary.rtf b/general/datasets/BR_U_1203_DPMM/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_DPMM/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_DPMM/tissue.rtf b/general/datasets/BR_U_1203_DPMM/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_DPMM/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_DPMMR/acknowledgment.rtf b/general/datasets/BR_U_1203_DPMMR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_DPMMR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_DPMMR/cases.rtf b/general/datasets/BR_U_1203_DPMMR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_DPMMR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_DPMMR/notes.rtf b/general/datasets/BR_U_1203_DPMMR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_DPMMR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_DPMMR/platform.rtf b/general/datasets/BR_U_1203_DPMMR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_DPMMR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_DPMMR/processing.rtf b/general/datasets/BR_U_1203_DPMMR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_DPMMR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_DPMMR/summary.rtf b/general/datasets/BR_U_1203_DPMMR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_DPMMR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_DPMMR/tissue.rtf b/general/datasets/BR_U_1203_DPMMR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_DPMMR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_DPMR/acknowledgment.rtf b/general/datasets/BR_U_1203_DPMR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_DPMR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_DPMR/cases.rtf b/general/datasets/BR_U_1203_DPMR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_DPMR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_DPMR/notes.rtf b/general/datasets/BR_U_1203_DPMR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_DPMR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_DPMR/platform.rtf b/general/datasets/BR_U_1203_DPMR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_DPMR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_DPMR/processing.rtf b/general/datasets/BR_U_1203_DPMR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_DPMR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_DPMR/summary.rtf b/general/datasets/BR_U_1203_DPMR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_DPMR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_DPMR/tissue.rtf b/general/datasets/BR_U_1203_DPMR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_DPMR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_H2/acknowledgment.rtf b/general/datasets/BR_U_1203_H2/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_H2/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_H2/cases.rtf b/general/datasets/BR_U_1203_H2/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_H2/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_H2/notes.rtf b/general/datasets/BR_U_1203_H2/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_H2/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_H2/platform.rtf b/general/datasets/BR_U_1203_H2/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_H2/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_H2/processing.rtf b/general/datasets/BR_U_1203_H2/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_H2/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_H2/summary.rtf b/general/datasets/BR_U_1203_H2/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_H2/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_H2/tissue.rtf b/general/datasets/BR_U_1203_H2/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_H2/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_M/acknowledgment.rtf b/general/datasets/BR_U_1203_M/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_M/cases.rtf b/general/datasets/BR_U_1203_M/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_M/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_M/notes.rtf b/general/datasets/BR_U_1203_M/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_M/platform.rtf b/general/datasets/BR_U_1203_M/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_M/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_M/processing.rtf b/general/datasets/BR_U_1203_M/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_M/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_M/summary.rtf b/general/datasets/BR_U_1203_M/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_M/tissue.rtf b/general/datasets/BR_U_1203_M/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_MR/acknowledgment.rtf b/general/datasets/BR_U_1203_MR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_MR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_MR/cases.rtf b/general/datasets/BR_U_1203_MR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_MR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_MR/notes.rtf b/general/datasets/BR_U_1203_MR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_MR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_MR/platform.rtf b/general/datasets/BR_U_1203_MR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_MR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_MR/processing.rtf b/general/datasets/BR_U_1203_MR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_MR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_MR/summary.rtf b/general/datasets/BR_U_1203_MR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_MR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_MR/tissue.rtf b/general/datasets/BR_U_1203_MR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_MR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_P/acknowledgment.rtf b/general/datasets/BR_U_1203_P/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_P/cases.rtf b/general/datasets/BR_U_1203_P/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_P/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_P/notes.rtf b/general/datasets/BR_U_1203_P/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_P/platform.rtf b/general/datasets/BR_U_1203_P/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_P/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_P/processing.rtf b/general/datasets/BR_U_1203_P/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_P/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_P/summary.rtf b/general/datasets/BR_U_1203_P/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_P/tissue.rtf b/general/datasets/BR_U_1203_P/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_PR/acknowledgment.rtf b/general/datasets/BR_U_1203_PR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_PR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_PR/cases.rtf b/general/datasets/BR_U_1203_PR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_PR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_PR/notes.rtf b/general/datasets/BR_U_1203_PR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_PR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_PR/platform.rtf b/general/datasets/BR_U_1203_PR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_PR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_PR/processing.rtf b/general/datasets/BR_U_1203_PR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_PR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_PR/summary.rtf b/general/datasets/BR_U_1203_PR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_PR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_PR/tissue.rtf b/general/datasets/BR_U_1203_PR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_PR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_R/acknowledgment.rtf b/general/datasets/BR_U_1203_R/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_R/cases.rtf b/general/datasets/BR_U_1203_R/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_R/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_R/notes.rtf b/general/datasets/BR_U_1203_R/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_R/platform.rtf b/general/datasets/BR_U_1203_R/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_R/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_R/processing.rtf b/general/datasets/BR_U_1203_R/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_R/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_R/summary.rtf b/general/datasets/BR_U_1203_R/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_R/tissue.rtf b/general/datasets/BR_U_1203_R/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BR_U_1203_RR/acknowledgment.rtf b/general/datasets/BR_U_1203_RR/acknowledgment.rtf
deleted file mode 100644
index b1a98cb..0000000
--- a/general/datasets/BR_U_1203_RR/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/BR_U_1203_RR/cases.rtf b/general/datasets/BR_U_1203_RR/cases.rtf
deleted file mode 100644
index 9076285..0000000
--- a/general/datasets/BR_U_1203_RR/cases.rtf
+++ /dev/null
@@ -1,232 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.
-
-
diff --git a/general/datasets/BR_U_1203_RR/notes.rtf b/general/datasets/BR_U_1203_RR/notes.rtf
deleted file mode 100644
index 1b8fd3d..0000000
--- a/general/datasets/BR_U_1203_RR/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, December 2003. Updated by RWW, October 29, 2004.
diff --git a/general/datasets/BR_U_1203_RR/platform.rtf b/general/datasets/BR_U_1203_RR/platform.rtf
deleted file mode 100644
index c6f6d68..0000000
--- a/general/datasets/BR_U_1203_RR/platform.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target) : Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
diff --git a/general/datasets/BR_U_1203_RR/processing.rtf b/general/datasets/BR_U_1203_RR/processing.rtf
deleted file mode 100644
index 2a34d5e..0000000
--- a/general/datasets/BR_U_1203_RR/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 97 arrays (all seven batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by seven batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all seven batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the seven batches is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 97 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
diff --git a/general/datasets/BR_U_1203_RR/summary.rtf b/general/datasets/BR_U_1203_RR/summary.rtf
deleted file mode 100644
index e2d448f..0000000
--- a/general/datasets/BR_U_1203_RR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/BR_U_1203_RR/tissue.rtf b/general/datasets/BR_U_1203_RR/tissue.rtf
deleted file mode 100644
index 1f09431..0000000
--- a/general/datasets/BR_U_1203_RR/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 97 such pooled samples were arrayed: 73 from females and 24 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/BXD_GLA_0911/experiment-design.rtf b/general/datasets/BXD_GLA_0911/experiment-design.rtf
deleted file mode 100644
index f01b888..0000000
--- a/general/datasets/BXD_GLA_0911/experiment-design.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-TEXT FROM GEO
-
-Genome-wide assessment of gene expression changes was performed in DBA/2J mice. The optic nerve head and retina from 40 DBA/2J eyes at 10.5 months of age were separately profiled. These eyes were selected as they encompassed a range of glaucoma severity. Two control groups were also included; 10 eyes from 10.5 months old D2-Gpnmb+ mice (age and strain matched, no glaucoma control) and 10 eyes from 4.5 months old DBA/2J mice (young, pre-glaucoma).
-
-In this study that was specifically designed to identify early stages of glaucoma in DBA/2J mice, we used genome-wide expression profiling and a series of computational methods. Our methods successfully subdivided eyes with no detectable glaucoma by conventional assays into molecularly defined stages of disease. These stages represent a temporally ordered sequence of glaucoma states. Using an array of tools, we then determined networks and biological processes that are altered at these early stages. Our strategy proved very sensitive, suggesting that similar approaches will be valuable for uncovering early processes in other complex, later-onset diseases. Early changes included upregulation of both the complement cascade and endothelin system, and so we tested the therapeutic value of separately inhibiting them. Mice with a mutation in the complement component 1a gene (C1qa) were robustly protected from glaucoma with the protection being among the greatest reported. Similarly, inhibition of the endothelin system was strongly protective. Since EDN2 is potently vasoconstrictive and was produced by microglial/macrophages, our data provide a novel link between these cell types and vascular dysfunction in glaucoma. Targeting early events such as the upregulation of the complement and endothelin pathways may provide effective new treatments for human glaucoma. (text above from GEO http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26299)
-
-
-
-
diff --git a/general/datasets/BXD_GLA_0911/summary.rtf b/general/datasets/BXD_GLA_0911/summary.rtf
deleted file mode 100644
index 09c8a43..0000000
--- a/general/datasets/BXD_GLA_0911/summary.rtf
+++ /dev/null
@@ -1,58 +0,0 @@
-This is an experimental glaucoma gene expression data set of retinal tissue entered into GeneNetwork by Dr. Eldon Geisert and Robert Williams in which BXD strains have been "highjacked" with experimental and control gene expression data generated by Drs Gareth Howell, Simon John, and colleagues at the Jackson Laboratory. These data were originally entered into GeneNetwork Sept 20, 2011.
-
-Please see the original paper by Howell et al (2011): http://www.jci.org/articles/view/44646 and GEO data at NCBI.
-
-Gareth R. Howell, Danilo G. Macalinao, Gregory L. Sousa, Michael Walden, Ileana Soto, Stephen C. Kneeland, Jessica M. Barbay, Benjamin L. King, Jeffrey K. Marchant, Matthew Hibbs, Beth Stevens, Ben A. Barres, Abbot F. Clark, Richard T. Libby, Simon S (2011) Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. J Clin Invest. 121:1429–1444
-
-Each strain corresponds to a particular retinal sample as shown below (note that we have not included ten "preglaucoma control" samples, see http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26299
-
-
- - BXD1 D2-Gpnmb+ control rep1 (retina)
- - BXD2 D2-Gpnmb+ control rep2 (retina)
- - BXD5 D2-Gpnmb+ control rep3 (retina)
- - BXD6 D2-Gpnmb+ control rep4 (retina)
- - BXD8 D2-Gpnmb+ control rep5 (retina)
- - BXD9 D2-Gpnmb+ control rep6 (retina)
- - BXD11 D2-Gpnmb+ control rep7 (retina)
- - BXD12 D2-Gpnmb+ control rep8 (retina)
- - BXD13 D2-Gpnmb+ control rep9 (retina)
- - BXD14 D2-Gpnmb+ control rep10 (retina)
- - BXD15 No or early 1 rep1 (retina)
- - BXD16 No or early 1 rep2 (retina)
- - BXD18 No or early 1 rep3 (retina)
- - BXD19 No or early 1 rep4 (retina)
- - BXD20 No or early 1 rep5 (retina)
- - BXD22 No or early 1 rep6 (retina)
- - BXD23 No or early 1 rep7 (retina)
- - BXD25 No or early 1 rep8 (retina)
- - BXD27 No or early 1 rep9 (retina)
- - BXD28 No or early 1 rep10 (retina)
- - BXD29 No or early 2 rep1 (retina)
- - BXD30 No or early 2 rep2 (retina)
- - BXD31 No or early 2 rep3 (retina)
- - BXD32 No or early 2 rep4 (retina)
- - BXD33 No or early 2 rep5 (retina)
- - BXD34 No or early 2 rep6 (retina)
- - BXD35 No or early 2 rep7 (retina)
- - BXD36 No or early 2 rep8 (retina)
- - BXD37 No or early 2 rep9 (retina)
- - BXD38 No or early 2 rep10 (retina)
- - BXD39 Moderate rep1 (retina)
- - BXD40 Moderate rep2 (retina)
- - BXD41 Moderate rep3 (retina)
- - BXD42 Moderate rep4 (retina)
- - BXD43 Moderate rep7 (retina)
- - BXD44 Moderate rep8 (retina)
- - BXD45 Moderate rep9 (retina)
- - BXD48 Moderate rep10 (retina)
- - BXD49 Severe rep1 (retina)
- - BXD50 Severe rep2 (retina)
- - BXD51 Severe rep3 (retina)
- - BXD52 Severe rep4 (retina)
- - BXD53 Severe rep5 (retina)
- - BXD54 Severe rep6 (retina)
- - BXD55 Severe rep7 (retina)
- - BXD56 Severe rep8 (retina)
- - BXD59 Severe rep9 (retina)
- - BXD60 Severe rep10 (retina)
-
diff --git a/general/datasets/Br_U_0303_M/acknowledgment.rtf b/general/datasets/Br_U_0303_M/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/Br_U_0303_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/Br_U_0303_M/cases.rtf b/general/datasets/Br_U_0303_M/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/Br_U_0303_M/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/Br_U_0303_M/notes.rtf b/general/datasets/Br_U_0303_M/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/Br_U_0303_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/Br_U_0303_M/platform.rtf b/general/datasets/Br_U_0303_M/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/Br_U_0303_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/Br_U_0303_M/processing.rtf b/general/datasets/Br_U_0303_M/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/Br_U_0303_M/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/Br_U_0303_M/summary.rtf b/general/datasets/Br_U_0303_M/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/Br_U_0303_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/Br_U_0303_M/tissue.rtf b/general/datasets/Br_U_0303_M/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/Br_U_0303_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/Br_U_0503_M/acknowledgment.rtf b/general/datasets/Br_U_0503_M/acknowledgment.rtf
deleted file mode 100644
index 5f21aed..0000000
--- a/general/datasets/Br_U_0503_M/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
-
diff --git a/general/datasets/Br_U_0503_M/cases.rtf b/general/datasets/Br_U_0503_M/cases.rtf
deleted file mode 100644
index bc98bcb..0000000
--- a/general/datasets/Br_U_0503_M/cases.rtf
+++ /dev/null
@@ -1,216 +0,0 @@
-The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males. All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.
-
-
-
-
-
-
-
-
- | Strain |
-
- Age
- |
- Strain |
-
- Age
- |
-
-
- |
- 8 Wks
- |
-
- 20 Wks
- |
-
- 52 Wks
- |
-
- 8 Wks
- |
-
- 20 Wks
- |
-
- 52 Wks
- |
-
-
- | C57BL/6J (B6) |
- ♂♂♂ |
- ♀ |
- ♀ |
- DBA/2J (D2) |
- ♀ |
- ♂♂♀ |
- |
-
-
- | B6D2F1 (F1) |
- ♀ ♀ |
- ♀ |
- |
- BXD1 |
- ♀♀ |
- |
- ♀ |
-
-
- | BXD2 |
- ♂ |
- ♀ |
- ♀ |
- BXD5 |
- ♂♀ |
- |
- |
-
-
- | BXD6 |
- ♀ |
- ♀ |
- ♀ |
- BXD8 |
- ♀ |
- ♂♀ |
- |
-
-
- | BXD9 |
- ♂ |
- ♀ |
- ♀ |
- BXD11 |
- ♀♀ |
- |
- ♀ |
-
-
- | BXD12 |
- |
- ♂♀ |
- ♀ |
- BXD13 |
- ♀ |
- |
- |
-
-
- | BXD14 |
- |
- ♀♀ |
- ♀ |
- BXD15 |
- ♀ |
- |
- ♀ |
-
-
- | BXD16 |
- ♀ |
- ♀♀ |
- |
- BXD18 |
- ♀ |
- ♂ |
- ♀ |
-
-
- | BXD19 |
- ♀ |
- ♀ |
- ♀ |
- BXD21 |
- ♀ |
- ♂♂ |
- |
-
-
- | BXD22 |
- ♀ |
- ♀♀ |
- |
- BXD24 |
- ♀♀ |
- |
- ♀ |
-
-
- | BXD25 |
- ♀♀ |
- ♀♀ |
- |
- BXD27 |
- |
- |
- ♀♀ |
-
-
- | BXD28 |
- ♀ |
- ♀ |
- ♀ |
- BXD29 |
- ♂ |
- |
- ♀ |
-
-
- | BXD31 |
- ♀♀ |
- ♀♀ |
- |
- BXD32 |
- ♀ |
- ♂♀ |
- ♀ |
-
-
- | BXD33 |
- ♂♀ |
- ♀ |
- |
- BXD34 |
- ♂♀ |
- ♀ |
- |
-
-
- | BXD39 |
- ♂♀ |
- ♂ |
- |
- BXD40 |
- ♂♂♀♀ |
- |
- |
-
-
- | BXD42 |
- ♂♂ ♀ |
- |
- |
- BXD67 |
- ♀ |
- |
- |
-
-
- | BXD68 (F9) |
- ♀ ♀ |
- |
- |
- |
- |
- |
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Br_U_0503_M/notes.rtf b/general/datasets/Br_U_0503_M/notes.rtf
deleted file mode 100644
index d198112..0000000
--- a/general/datasets/Br_U_0503_M/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Information about this text file:
-
-
-This text file originally generated by RWW, EJC, and YHQ, May 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/Br_U_0503_M/platform.rtf b/general/datasets/Br_U_0503_M/platform.rtf
deleted file mode 100644
index 04f8269..0000000
--- a/general/datasets/Br_U_0503_M/platform.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/Br_U_0503_M/processing.rtf b/general/datasets/Br_U_0503_M/processing.rtf
deleted file mode 100644
index e763fc9..0000000
--- a/general/datasets/Br_U_0503_M/processing.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by MAS 5 are the 75% quantiles from a set of 36 pixel values per cell (the pixel with the 12th highest value represents the whole cell).
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains. We have not corrected for variance introduced by sex, age, or a sex-by-age interaction. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the .TXT file: These .TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a 2-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers were initially determined by BLAT analysis using the Mouse Genome Sequencing Consortium OCT 2003 Assembly (see http://genome.ucsc.edu/). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/Br_U_0503_M/summary.rtf b/general/datasets/Br_U_0503_M/summary.rtf
deleted file mode 100644
index 2d69c8a..0000000
--- a/general/datasets/Br_U_0503_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This May 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004). Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 33 strains were hybridized in small pools (n=3) to 97 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, these MAS 5 transforms do not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/Br_U_0503_M/tissue.rtf b/general/datasets/Br_U_0503_M/tissue.rtf
deleted file mode 100644
index 045e2a2..0000000
--- a/general/datasets/Br_U_0503_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 97 arrays were used: 74 were female pools and 23 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
diff --git a/general/datasets/Br_U_0603_M/acknowledgment.rtf b/general/datasets/Br_U_0603_M/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/Br_U_0603_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/Br_U_0603_M/cases.rtf b/general/datasets/Br_U_0603_M/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/Br_U_0603_M/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/Br_U_0603_M/notes.rtf b/general/datasets/Br_U_0603_M/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/Br_U_0603_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/Br_U_0603_M/platform.rtf b/general/datasets/Br_U_0603_M/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/Br_U_0603_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/Br_U_0603_M/processing.rtf b/general/datasets/Br_U_0603_M/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/Br_U_0603_M/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/Br_U_0603_M/summary.rtf b/general/datasets/Br_U_0603_M/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/Br_U_0603_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/Br_U_0603_M/tissue.rtf b/general/datasets/Br_U_0603_M/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/Br_U_0603_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/Br_U_0803_M/acknowledgment.rtf b/general/datasets/Br_U_0803_M/acknowledgment.rtf
deleted file mode 100644
index 1efbf49..0000000
--- a/general/datasets/Br_U_0803_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.
diff --git a/general/datasets/Br_U_0803_M/cases.rtf b/general/datasets/Br_U_0803_M/cases.rtf
deleted file mode 100644
index 38a782c..0000000
--- a/general/datasets/Br_U_0803_M/cases.rtf
+++ /dev/null
@@ -1,230 +0,0 @@
-This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Only two of these incipient strains are included in the current database (BXD67 and BXD68).
-
-In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice. Note that this table includes six arrays dropped from the December 2003 data sets (BXD6, n=2; BXD12, BXD16, BXD40, and BXD67, n=1 each).
-
-
diff --git a/general/datasets/Br_U_0803_M/notes.rtf b/general/datasets/Br_U_0803_M/notes.rtf
deleted file mode 100644
index 68a18e4..0000000
--- a/general/datasets/Br_U_0803_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, EJC, and YHQ, August 2003. Updated by RWW, October 30, 2004.
diff --git a/general/datasets/Br_U_0803_M/platform.rtf b/general/datasets/Br_U_0803_M/platform.rtf
deleted file mode 100644
index e8ac283..0000000
--- a/general/datasets/Br_U_0803_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix U74Av2 GeneChip: The expression data were generated using 100 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/Br_U_0803_M/processing.rtf b/general/datasets/Br_U_0803_M/processing.rtf
deleted file mode 100644
index 9b386b5..0000000
--- a/general/datasets/Br_U_0803_M/processing.rtf
+++ /dev/null
@@ -1,27 +0,0 @@
-Probe (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal intensity.
- - Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: Probe set estimates of expression were initially generated using the standard Affymetrix MAS 5 algorithm. The CHP values were then processed following precisely the same six steps listed above to normalize expression and stabilize the variance of all 106 arrays. The mean expression within each array is therefore 8 units with a standard deviation of 2 units. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the background noise level. While a value of 8 unit is nominally the average expression, this average includes all those transcripts with negligible expression in the brain that would often be eliminated from subsequent analysis (so-called "absent" and "marginal" calls in the CHP file).
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/Br_U_0803_M/summary.rtf b/general/datasets/Br_U_0803_M/summary.rtf
deleted file mode 100644
index 7826a5c..0000000
--- a/general/datasets/Br_U_0803_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2003 freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This is data set includes six arrays which are of marginal quality. New users are encouraged to use one of the more recent data sets (December 2003 or March 2004) from which these six arrays have been excluded. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 300 brain samples from 35 strains were hybridized in small pools (n=3) to 106 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, the MAS 5 transform does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).
diff --git a/general/datasets/Br_U_0803_M/tissue.rtf b/general/datasets/Br_U_0803_M/tissue.rtf
deleted file mode 100644
index 6961982..0000000
--- a/general/datasets/Br_U_0803_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 100 such pooled samples were arrayed: 74 from females and 26 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.
diff --git a/general/datasets/Br_u_0303_m/experiment-type.rtf b/general/datasets/Br_u_0303_m/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Br_u_0303_m/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Br_u_0503_m/experiment-type.rtf b/general/datasets/Br_u_0503_m/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Br_u_0503_m/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Br_u_0603_m/experiment-type.rtf b/general/datasets/Br_u_0603_m/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Br_u_0603_m/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Br_u_0803_m/experiment-type.rtf b/general/datasets/Br_u_0803_m/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Br_u_0803_m/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Br_u_0903_p/experiment-type.rtf b/general/datasets/Br_u_0903_p/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Br_u_0903_p/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/CANDLE_NB_0711/acknowledgment.rtf b/general/datasets/CANDLE_NB_0711/acknowledgment.rtf
deleted file mode 100644
index ea399b5..0000000
--- a/general/datasets/CANDLE_NB_0711/acknowledgment.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Data Owner: Dr. Robert W. Williams, Dr. Ron Adkins, UTHSC Department of Pediatrics
-
-Expression data generated by the UTHSC Molecular Resources Center with funding from the Center for Integrative and Translational Genomics
-
-Data processing by Drs. Ron Adkins and Julia Krushkal. Data entry into GeneNetwork by Arthur Centeno and Robert W. Williams.
-
-
- - background subtraction (using Illumina's GenomeStudio)
- - VST transform (using lumi in Bioconductor)
- - quantile normalization (also using lumi)
- - [any outliers that did not pass QC were removed using sample clustering, MA plots, boxplots, etc.] correction for batch effects using COMBAT
-
-
-Please refer to information provided by Drs. Williams or Adkins with the data that specifies exactly which of these steps (or all of them) were included in the final data set that he provided to you.
diff --git a/general/datasets/CANDLE_NB_0711/cases.rtf b/general/datasets/CANDLE_NB_0711/cases.rtf
deleted file mode 100644
index c7fe664..0000000
--- a/general/datasets/CANDLE_NB_0711/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-A subset of neonatal cord blood samples from the CANDLE cohort.
diff --git a/general/datasets/CANDLE_NB_0711/summary.rtf b/general/datasets/CANDLE_NB_0711/summary.rtf
deleted file mode 100644
index df02b8b..0000000
--- a/general/datasets/CANDLE_NB_0711/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-The CANDLE Study is a large multidisciplinary study of early child development that involves genetic, genomic, environmental, and large-scale behavioral evaluation of children and their families from the second trimester of development through to 4 years of age. The full study involves more than 1000 children and their mothers and fathers.
-
-For information on genomic and genetic studies related to CANDLE, please contact: Dr. Robert W. Williams (rwilliams@uthsc.edu). These data were originally generated by Drs. Ronald M. Adkins and Julia Krushkal at UTHSC.
-
-For information on the composition of neonatal cord blood, please see the review article by Jose N Tolosa and colleagues (2010).
-
-For information on the overall design of CANDLE, please contact: Dr. Frances A. Tylavsky (ftylavsk at uthsc.edu).
-
-Summary from The Urban Child Institute: "The primary goal of the CANDLE study is to study factors that affect brain development in young children. To this end, the current study will test specific hypotheses regarding factors that may negatively influence cognitive development in children. Participants in this cohort study will include 1,500 mother-child dyads, recruited during the second trimester of pregnancy and followed from birth to age 3. Data on a wide range of possible influences on children's cognitive outcomes will be collected from numerous sources, including questionnaires, interviews, psychosocial assessments, medical chart abstraction, environmental samples from the child's home environment, blood and urine samples from the mother, cord blood, and placental tissue. The primary outcomes of the current study are those associated with a poor cognitive outcome in the child. Outcomes will be measured using standardized cognitive assessments conducted at 12 months, 24 months, and 36 months of age. Epidemiological, clinical, and laboratory-based research may be undertaken using data from the project, with sub-studies including, but not limited to, molecular genetics, environmental exposure assessments, and micronutrient deficiency analyses. Results of this cohort study may provide information that will ultimately lead to improvements in the health, development, and well-being of children in Shelby County, Tennessee through interventions and policy enforcement and/or development. Full participant recruitment and complete data collection began in November 2006."
diff --git a/general/datasets/CANDLE_NB_0711/tissue.rtf b/general/datasets/CANDLE_NB_0711/tissue.rtf
deleted file mode 100644
index 736f786..0000000
--- a/general/datasets/CANDLE_NB_0711/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Neonatal cord blood.
diff --git a/general/datasets/CB_M_0104_M/acknowledgment.rtf b/general/datasets/CB_M_0104_M/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_0104_M/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_0104_M/cases.rtf b/general/datasets/CB_M_0104_M/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_0104_M/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_0104_M/notes.rtf b/general/datasets/CB_M_0104_M/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_0104_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_0104_M/platform.rtf b/general/datasets/CB_M_0104_M/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_0104_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_0104_M/processing.rtf b/general/datasets/CB_M_0104_M/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_0104_M/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_0104_M/summary.rtf b/general/datasets/CB_M_0104_M/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_0104_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_0104_M/tissue.rtf b/general/datasets/CB_M_0104_M/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_0104_M/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_0104_P/acknowledgment.rtf b/general/datasets/CB_M_0104_P/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_0104_P/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_0104_P/cases.rtf b/general/datasets/CB_M_0104_P/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_0104_P/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_0104_P/notes.rtf b/general/datasets/CB_M_0104_P/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_0104_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_0104_P/platform.rtf b/general/datasets/CB_M_0104_P/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_0104_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_0104_P/processing.rtf b/general/datasets/CB_M_0104_P/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_0104_P/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_0104_P/summary.rtf b/general/datasets/CB_M_0104_P/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_0104_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_0104_P/tissue.rtf b/general/datasets/CB_M_0104_P/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_0104_P/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_0104_R/acknowledgment.rtf b/general/datasets/CB_M_0104_R/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_0104_R/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_0104_R/cases.rtf b/general/datasets/CB_M_0104_R/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_0104_R/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_0104_R/notes.rtf b/general/datasets/CB_M_0104_R/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_0104_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_0104_R/platform.rtf b/general/datasets/CB_M_0104_R/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_0104_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_0104_R/processing.rtf b/general/datasets/CB_M_0104_R/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_0104_R/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_0104_R/summary.rtf b/general/datasets/CB_M_0104_R/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_0104_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_0104_R/tissue.rtf b/general/datasets/CB_M_0104_R/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_0104_R/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_0204_P/acknowledgment.rtf b/general/datasets/CB_M_0204_P/acknowledgment.rtf
deleted file mode 100644
index 7b62a11..0000000
--- a/general/datasets/CB_M_0204_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data for the microarrays were generously provided by support from NIAAA INIA grants to RWW and Thomas Sutter. Support for sample acquistion and WebQTL have been provided by NIMH Human Brain Project, and the Dunavant Chair of Excellence, University of Tennessee Health Science Center. All arrays were processed at the University of Memphis by Dr. Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/CB_M_0204_P/cases.rtf b/general/datasets/CB_M_0204_P/cases.rtf
deleted file mode 100644
index 9dc5cbe..0000000
--- a/general/datasets/CB_M_0204_P/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B) and DBA/2J (D). Both B and D strains have been almost fully sequence (8x coverage for B by a public consortium and approximately 1.5x coverage for D by Celera).
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
diff --git a/general/datasets/CB_M_0204_P/notes.rtf b/general/datasets/CB_M_0204_P/notes.rtf
deleted file mode 100644
index f3ea488..0000000
--- a/general/datasets/CB_M_0204_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004.
diff --git a/general/datasets/CB_M_0204_P/platform.rtf b/general/datasets/CB_M_0204_P/platform.rtf
deleted file mode 100644
index 51cbff2..0000000
--- a/general/datasets/CB_M_0204_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 430A and 430B GeneChip Set: Expression data were generated using 430AB array pairs. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on either the Verify UCSC and Verify Ensembl links in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/CB_M_0204_P/processing.rtf b/general/datasets/CB_M_0204_P/processing.rtf
deleted file mode 100644
index 4663b88..0000000
--- a/general/datasets/CB_M_0204_P/processing.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: We corrected for technical variance introduced by two batches. Means separated by the first batch for each gene are corrected same as means of the second batch.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-
-
-
-Probe set data: The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
-
-PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
-
-When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
-
-
-About the array probe sets names:
-
-
-Most probe sets on the mouse 430A and 430B arrays consist of a total of 22 probes, divided into 11 perfect match(PM) probes and 11 mismatch (MM) controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, several suffix characters that highlight design features, a a final A or B character to specify the array pair member. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene.
-
diff --git a/general/datasets/CB_M_0204_P/summary.rtf b/general/datasets/CB_M_0204_P/summary.rtf
deleted file mode 100644
index c32676a..0000000
--- a/general/datasets/CB_M_0204_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This October 2004 data freeze provides initial estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix M430AB microarrays. In contast to the U74Av2 array, this new data set provides broader coverage (~45,000 transcripts) but does not include replicates or as many strains (25 vs 35). Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Data were processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
diff --git a/general/datasets/CB_M_0204_P/tissue.rtf b/general/datasets/CB_M_0204_P/tissue.rtf
deleted file mode 100644
index cac878a..0000000
--- a/general/datasets/CB_M_0204_P/tissue.rtf
+++ /dev/null
@@ -1,261 +0,0 @@
-The data set consists of a single batch of Affymetrix mouse expression 430A and 430B GeneChip array pairs. Each AB pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter and colleagues at the University of Memphis. Before running the main batch of 30 pairs of array, we ran four "test" samples (one male and one female pool from each of the two parental strains, C57BL/6J and DBA/2J). The main set of 30 array pairs includes the same four samples (in other words we have four technical replicates), two F1 hybrid sample (each run two times for a within-batch technical replication), and 22 BXD strains. The data set therefore consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. We should note that the four technical replicates between batches were eventually combined with a correction for a highly significant batch effect. This was done at both the probe and probe set levels to "align" the test batch values with the two main batches. (The ratio of the probe average in the four test arrays to the average of the same probe in the four corresponding main batch arrays was used as a correction factor.) The F1 within-batch technical replicates were simply averaged. In the next batch we will reverse the sex of the BXD samples to achieve a balance with at least 22 BXD strains with one male and one female sample each.
-
-The table below lists the arrays by strain, sex, age, sample identifier, and data results were obtained from the Bioanalytical Core at the University of Memphis. Each array was hybridized to a pool of mRNA from three mice.
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Date |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F2 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F2 |
- Jan04 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F2 |
- Jan03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F2 |
- Jan04 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F1 |
- Nov03 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F2 |
- Jan04 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F1 |
- Nov03 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F2 |
- Jan04 |
-
-
- | BXD1 |
- F |
- 95 |
- 895-F1 |
- Jan04 |
-
-
- | BXD5 |
- M |
- 71 |
- 728-F1 |
- Jan04 |
-
-
- | BXD6 |
- M |
- 92 |
- 902-F1 |
- Jan04 |
-
-
- | BXD8 |
- F |
- 72 |
- S167-F1 |
- Jan04 |
-
-
- | BXD9 |
- M |
- 86 |
- 909-F1 |
- Jan04 |
-
-
- | BXD12 |
- M |
- 64 |
- 897-F1 |
- Jan04 |
-
-
- | BXD13 |
- F |
- 86 |
- 748-F1 |
- Jan04 |
-
-
- | BXD14 |
- M |
- 91 |
- 912-F1 |
- Jan04 |
-
-
- | BXD18 |
- F |
- 108 |
- 771-F1 |
- Jan04 |
-
-
- | BXD19 |
- F |
- 56 |
- S236-F1 |
- Jan04 |
-
-
- | BXD21 |
- F |
- 67 |
- 740-F1 |
- Jan04 |
-
-
- | BXD23 |
- F |
- 88 |
- 815-F1 |
- Jan04 |
-
-
- | BXD24 |
- M |
- 71 |
- 913-F1 |
- Jan04 |
-
-
- | BXD25 |
- F |
- 74 |
- S373-F1 |
- Jan04 |
-
-
- | BXD28 |
- F |
- 79 |
- 910-F1 |
- Jan04 |
-
-
- | BXD29 |
- F |
- 76 |
- 693-F1 |
- Jan04 |
-
-
- | BXD32 |
- F |
- 93 |
- 898-F1 |
- Jan04 |
-
-
- | BXD33 |
- M |
- 77 |
- 915-F1 |
- Jan04 |
-
-
- | BXD34 |
- M |
- 72 |
- 916-F1 |
- Jan04 |
-
-
- | BXD36 |
- M |
- 77 |
- 926-F1 |
- Jan04 |
-
-
- | BXD38 |
- M |
- 69 |
- 731-F1 |
- Jan04 |
-
-
- | BXD42 |
- M |
- 97 |
- 936-F1 |
- Jan04 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/CB_M_0204_R/acknowledgment.rtf b/general/datasets/CB_M_0204_R/acknowledgment.rtf
deleted file mode 100644
index 7b62a11..0000000
--- a/general/datasets/CB_M_0204_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data for the microarrays were generously provided by support from NIAAA INIA grants to RWW and Thomas Sutter. Support for sample acquistion and WebQTL have been provided by NIMH Human Brain Project, and the Dunavant Chair of Excellence, University of Tennessee Health Science Center. All arrays were processed at the University of Memphis by Dr. Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/CB_M_0204_R/cases.rtf b/general/datasets/CB_M_0204_R/cases.rtf
deleted file mode 100644
index 9dc5cbe..0000000
--- a/general/datasets/CB_M_0204_R/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B) and DBA/2J (D). Both B and D strains have been almost fully sequence (8x coverage for B by a public consortium and approximately 1.5x coverage for D by Celera).
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
diff --git a/general/datasets/CB_M_0204_R/notes.rtf b/general/datasets/CB_M_0204_R/notes.rtf
deleted file mode 100644
index f3ea488..0000000
--- a/general/datasets/CB_M_0204_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004.
diff --git a/general/datasets/CB_M_0204_R/platform.rtf b/general/datasets/CB_M_0204_R/platform.rtf
deleted file mode 100644
index 51cbff2..0000000
--- a/general/datasets/CB_M_0204_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 430A and 430B GeneChip Set: Expression data were generated using 430AB array pairs. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on either the Verify UCSC and Verify Ensembl links in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/CB_M_0204_R/processing.rtf b/general/datasets/CB_M_0204_R/processing.rtf
deleted file mode 100644
index 4663b88..0000000
--- a/general/datasets/CB_M_0204_R/processing.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: We corrected for technical variance introduced by two batches. Means separated by the first batch for each gene are corrected same as means of the second batch.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-
-
-
-Probe set data: The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
-
-PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
-
-When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
-
-
-About the array probe sets names:
-
-
-Most probe sets on the mouse 430A and 430B arrays consist of a total of 22 probes, divided into 11 perfect match(PM) probes and 11 mismatch (MM) controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, several suffix characters that highlight design features, a a final A or B character to specify the array pair member. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene.
-
diff --git a/general/datasets/CB_M_0204_R/summary.rtf b/general/datasets/CB_M_0204_R/summary.rtf
deleted file mode 100644
index c32676a..0000000
--- a/general/datasets/CB_M_0204_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This October 2004 data freeze provides initial estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix M430AB microarrays. In contast to the U74Av2 array, this new data set provides broader coverage (~45,000 transcripts) but does not include replicates or as many strains (25 vs 35). Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Data were processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
diff --git a/general/datasets/CB_M_0204_R/tissue.rtf b/general/datasets/CB_M_0204_R/tissue.rtf
deleted file mode 100644
index cac878a..0000000
--- a/general/datasets/CB_M_0204_R/tissue.rtf
+++ /dev/null
@@ -1,261 +0,0 @@
-The data set consists of a single batch of Affymetrix mouse expression 430A and 430B GeneChip array pairs. Each AB pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter and colleagues at the University of Memphis. Before running the main batch of 30 pairs of array, we ran four "test" samples (one male and one female pool from each of the two parental strains, C57BL/6J and DBA/2J). The main set of 30 array pairs includes the same four samples (in other words we have four technical replicates), two F1 hybrid sample (each run two times for a within-batch technical replication), and 22 BXD strains. The data set therefore consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. We should note that the four technical replicates between batches were eventually combined with a correction for a highly significant batch effect. This was done at both the probe and probe set levels to "align" the test batch values with the two main batches. (The ratio of the probe average in the four test arrays to the average of the same probe in the four corresponding main batch arrays was used as a correction factor.) The F1 within-batch technical replicates were simply averaged. In the next batch we will reverse the sex of the BXD samples to achieve a balance with at least 22 BXD strains with one male and one female sample each.
-
-The table below lists the arrays by strain, sex, age, sample identifier, and data results were obtained from the Bioanalytical Core at the University of Memphis. Each array was hybridized to a pool of mRNA from three mice.
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Date |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F2 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F2 |
- Jan04 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F2 |
- Jan03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F2 |
- Jan04 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F1 |
- Nov03 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F2 |
- Jan04 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F1 |
- Nov03 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F2 |
- Jan04 |
-
-
- | BXD1 |
- F |
- 95 |
- 895-F1 |
- Jan04 |
-
-
- | BXD5 |
- M |
- 71 |
- 728-F1 |
- Jan04 |
-
-
- | BXD6 |
- M |
- 92 |
- 902-F1 |
- Jan04 |
-
-
- | BXD8 |
- F |
- 72 |
- S167-F1 |
- Jan04 |
-
-
- | BXD9 |
- M |
- 86 |
- 909-F1 |
- Jan04 |
-
-
- | BXD12 |
- M |
- 64 |
- 897-F1 |
- Jan04 |
-
-
- | BXD13 |
- F |
- 86 |
- 748-F1 |
- Jan04 |
-
-
- | BXD14 |
- M |
- 91 |
- 912-F1 |
- Jan04 |
-
-
- | BXD18 |
- F |
- 108 |
- 771-F1 |
- Jan04 |
-
-
- | BXD19 |
- F |
- 56 |
- S236-F1 |
- Jan04 |
-
-
- | BXD21 |
- F |
- 67 |
- 740-F1 |
- Jan04 |
-
-
- | BXD23 |
- F |
- 88 |
- 815-F1 |
- Jan04 |
-
-
- | BXD24 |
- M |
- 71 |
- 913-F1 |
- Jan04 |
-
-
- | BXD25 |
- F |
- 74 |
- S373-F1 |
- Jan04 |
-
-
- | BXD28 |
- F |
- 79 |
- 910-F1 |
- Jan04 |
-
-
- | BXD29 |
- F |
- 76 |
- 693-F1 |
- Jan04 |
-
-
- | BXD32 |
- F |
- 93 |
- 898-F1 |
- Jan04 |
-
-
- | BXD33 |
- M |
- 77 |
- 915-F1 |
- Jan04 |
-
-
- | BXD34 |
- M |
- 72 |
- 916-F1 |
- Jan04 |
-
-
- | BXD36 |
- M |
- 77 |
- 926-F1 |
- Jan04 |
-
-
- | BXD38 |
- M |
- 69 |
- 731-F1 |
- Jan04 |
-
-
- | BXD42 |
- M |
- 97 |
- 936-F1 |
- Jan04 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/CB_M_0305_M/acknowledgment.rtf b/general/datasets/CB_M_0305_M/acknowledgment.rtf
deleted file mode 100644
index 4fa1990..0000000
--- a/general/datasets/CB_M_0305_M/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed by members of the UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - Jim Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_0305_M/cases.rtf b/general/datasets/CB_M_0305_M/cases.rtf
deleted file mode 100644
index 7c1e52c..0000000
--- a/general/datasets/CB_M_0305_M/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. All BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTLs genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
-
-
-Most BXD animals were generated in-house at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and Hui-Chen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).
-
diff --git a/general/datasets/CB_M_0305_M/notes.rtf b/general/datasets/CB_M_0305_M/notes.rtf
deleted file mode 100644
index 73487ea..0000000
--- a/general/datasets/CB_M_0305_M/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
-
-This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.
diff --git a/general/datasets/CB_M_0305_M/platform.rtf b/general/datasets/CB_M_0305_M/platform.rtf
deleted file mode 100644
index 39256be..0000000
--- a/general/datasets/CB_M_0305_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/CB_M_0305_M/processing.rtf b/general/datasets/CB_M_0305_M/processing.rtf
deleted file mode 100644
index f7b4668..0000000
--- a/general/datasets/CB_M_0305_M/processing.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by three large batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all three batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the three batches is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/CB_M_0305_M/summary.rtf b/general/datasets/CB_M_0305_M/summary.rtf
deleted file mode 100644
index 34c7e0d..0000000
--- a/general/datasets/CB_M_0305_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This March 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 48 lines of mice including 45 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and F1 hybrids. Data were generated by a consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430A and B arrays. This particular data set was processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/CB_M_0305_M/tissue.rtf b/general/datasets/CB_M_0305_M/tissue.rtf
deleted file mode 100644
index e803a45..0000000
--- a/general/datasets/CB_M_0305_M/tissue.rtf
+++ /dev/null
@@ -1,1370 +0,0 @@
-
-The March 2005 data set consists of a total of 102 array pairs (Affymetrix 430A and 430B) from 49 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. Two sets of technical replicates (BXD14 n = 2; BXD29 n = 3) were combined before generating group means; giving a total of 101 biologically independent data sets. The two reciprocal F1s (D2B6F1 and B6D2F1) were combined to give a single F1 mean estimate of gene expression. 430A and 430B arrays were processed in three large batches. The first batch (May03 data) consists of 17 samples from 17 strains balanced by sex (8M and 9F). The second batch consists of 29 samples, and includes biological replicates, 2 technical replicates, and data for 9 new strains. The third batch consists of 56 samples, and also includes biological replicates, 2 technical replicates, and data for 15 additional strains.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from both sexes for each strain. Six of 48 genotypes are still represented by single samples: BXD5, BXD13, BXD20, BXD23, BXD27 are female-only strains, whereas BXD25, BXD77, BXD90 are male-only. Ten strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 1M), B6D2F1 (1F 2M), BXD2 (2F 1M), BXD11 (2F 1M), BXD28 (2F 1M), BXD40 (2F 1M), BXD51 (1F 2M), BXD60 (1F 2M), BXD92 (2F 1M).
-
-The age range of samples is relatively narrow. Only 18 samples were taken from animals older than 99 days and only two samples are older than 7 months of age. BXD11 includes an extra (third) 441-day-old female sample and the BXD28 includes an extra 427-day-old sample.
-
-RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The table below summarizes information on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
-
- SampleName
- |
-
- BatchID
- |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 116 |
-
- R0773C
- |
-
- 2
- |
- UAB |
-
-
- | 2 |
- C57BL/6J |
- M |
- 109 |
-
- R0054C
- |
-
- 1
- |
- JAX |
-
-
- | 3 |
- C57BL/6J |
- M |
- 71 |
-
- R1450C
- |
-
- 3
- |
- UTM DG |
-
-
- | 4 |
- DBA/2J |
- F |
- 71 |
-
- R0175C
- |
-
- 1
- |
- UAB |
-
-
- | 5 |
- DBA/2J |
- F |
- 91 |
-
- R0782C
- |
-
- 2
- |
- UAB |
-
-
- | 6 |
- DBA/2J |
- M |
- 62 |
-
- R1121C
- |
-
- 3
- |
- UTM RW |
-
-
- | 7 |
- B6D2F1 |
- F |
- 60 |
-
- R1115C
- |
-
- 3
- |
- UTM RW |
-
-
- | 8 |
- B6D2F1 |
- M |
- 94 |
-
- R0347C
- |
-
- 1
- |
- JAX |
-
-
- | 9 |
- B6D2F1 |
- M |
- 127 |
-
- R0766C
- |
-
- 2
- |
- UTM JB |
-
-
- | 10 |
- D2B6F1 |
- F |
- 57 |
-
- R1067C
- |
-
- 3
- |
- UTM RW |
-
-
- | 11 |
- D2B6F1 |
- M |
- 60 |
-
- R1387C
- |
-
- 3
- |
- UTM RW |
-
-
- | 12 |
- BXD1 |
- F |
- 57 |
-
- R0813C
- |
-
- 2
- |
- UAB |
-
-
- | 13 |
- BXD1 |
- M |
- 181 |
-
- R1151C
- |
-
- 3
- |
- UTM JB |
-
-
- | 14 |
- BXD2 |
- F |
- 142 |
-
- R0751C
- |
-
- 1
- |
- UAB |
-
-
- | 15 |
- BXD2 |
- F |
- 78 |
-
- R0774C
- |
-
- 2
- |
- UAB |
-
-
- | 16 |
- BXD2 |
- M |
- 61 |
-
- R1503C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 17 |
- BXD5 |
- F |
- 56 |
-
- R0802C
- |
-
- 2
- |
- UMemphis |
-
-
-
- | 18 |
- BXD6 |
- F |
- 92 |
-
- R0719C
- |
-
- 1
- |
- UMemphis |
-
-
- | 19 |
- BXD6 |
- M |
- 92 |
-
- R0720C
- |
-
- 3
- |
- UMemphis |
-
-
- | 20 |
- BXD8 |
- F |
- 72 |
-
- R0173C
- |
-
- 1
- |
- UAB |
-
-
- | 21 |
- BXD8 |
- M |
- 59 |
-
- R1484C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 22 |
- BXD9 |
- F |
- 86 |
-
- R0736C
- |
-
- 3
- |
- UMemphis |
-
-
- | 23 |
- BXD9 |
- M |
- 86 |
-
- R0737C
- |
-
- 1
- |
- UMemphis |
-
-
- | 24 |
- BXD11 |
- F |
- 441 |
-
- R0200C
- |
-
- 1
- |
- UAB |
-
-
- | 25 |
- BXD11 |
- F |
- 97 |
-
- R0791C
- |
-
- 3
- |
- UAB |
-
-
- | 26 |
- BXD11 |
- M |
- 92 |
-
- R0790C
- |
-
- 2
- |
- UMemphis |
-
-
- | 27 |
- BXD12 |
- F |
- 130 |
-
- R0776C
- |
-
- 2
- |
- UAB |
-
-
- | 28 |
- BXD12 |
- M |
- 64 |
-
- R0756C
- |
-
- 2
- |
- UMemphis |
-
-
- | 29 |
- BXD13 |
- F |
- 86 |
-
- R1144C
- |
-
- 3
- |
- UMemphis |
-
-
- | 30 |
- BXD14 |
- F |
- 190 |
-
- R0794C
- |
-
- 2
- |
- UAB |
-
-
- | 31 |
- BXD14 |
- F |
- 190 |
-
- R0794C
- |
-
- 3
- |
- UAB |
-
-
- | 32 |
- BXD14 |
- M |
- 91 |
-
- R0758C
- |
-
- 2
- |
- UMemphis |
-
-
- | 33 |
- BXD14 |
- M |
- 65 |
-
- R1130C
- |
-
- 3
- |
- UTM RW |
-
-
-
- | 34 |
- BXD15 |
- F |
- 60 |
-
- R1491C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 35 |
- BXD15 |
- M |
- 61 |
-
- R1499C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 36 |
- BXD16 |
- F |
- 163 |
-
- R0750C
- |
-
- 1
- |
- UAB |
-
-
- | 37 |
- BXD16 |
- M |
- 61 |
-
- R1572C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 38 |
- BXD19 |
- F |
- 61 |
-
- R0772C
- |
-
- 2
- |
- UAB |
-
-
- | 39 |
- BXD19 |
- M |
- 157 |
-
- R1230C
- |
-
- 3
- |
- UTM JB |
-
-
- | 40 |
- BXD20 |
- F |
- 59 |
-
- R1488C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 41 |
- BXD21 |
- F |
- 116 |
-
- R0711C
- |
-
- 1
- |
- UAB |
-
-
- | 42 |
- BXD21 |
- M |
- 64 |
-
- R0803C
- |
-
- 2
- |
- UMemphis |
-
-
- | 43 |
- BXD22 |
- F |
- 65 |
-
- R0174C
- |
-
- 1
- |
- UAB |
-
-
- | 44 |
- BXD22 |
- M |
- 59 |
-
- R1489C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 45 |
- BXD23 |
- F |
- 88 |
-
- R0814C
- |
-
- 2
- |
- UAB |
-
-
- | 46 |
- BXD24 |
- F |
- 71 |
-
- R0805C
- |
-
- 2
- |
- UMemphis |
-
-
- | 47 |
- BXD24 |
- M |
- 71 |
-
- R0759C
- |
-
- 2
- |
- UMemphis |
-
-
- | 48 |
- BXD25 |
- M |
- 90 |
-
- R0429C
- |
-
- 1
- |
- UTM RW |
-
-
- | 49 |
- BXD27 |
- F |
- 60 |
-
- R1496C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 50 |
- BXD28 |
- F |
- 113 |
-
- R0785C
- |
-
- 2
- |
- UTM RW |
-
-
- | 51 |
- BXD28 |
- M |
- 79 |
-
- R0739C
- |
-
- 3
- |
- UMemphis |
-
-
- | 52 |
- BXD29 |
- F |
- 82 |
-
- R0777C
- |
-
- 2
- |
- UAB |
-
-
- | 53 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 1
- |
- UMemphis |
-
-
- | 54 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 2
- |
- UMemphis |
-
-
- | 55 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 3
- |
- UMemphis |
-
-
- | 56 |
- BXD31 |
- F |
- 142 |
-
- R0816C
- |
-
- 2
- |
- UAB |
-
-
- | 57 |
- BXD31 |
- M |
- 61 |
-
- R1142C
- |
-
- 3
- |
- UTM RW |
-
-
- | 58 |
- BXD32 |
- F |
- 62 |
-
- R0778C
- |
-
- 2
- |
- UAB |
-
-
- | 59 |
- BXD32 |
- M |
- 218 |
-
- R0786C
- |
-
- 2
- |
- UAB |
-
-
- | 60 |
- BXD33 |
- F |
- 184 |
-
- R0793C
- |
-
- 2
- |
- UAB |
-
-
- | 61 |
- BXD33 |
- M |
- 124 |
-
- R0715C
- |
-
- 1
- |
- UAB |
-
-
- | 62 |
- BXD34 |
- F |
- 56 |
-
- R0725C
- |
-
- 1
- |
- UMemphis |
-
-
- | 63 |
- BXD34 |
- M |
- 91 |
-
- R0789C
- |
-
- 2
- |
- UMemphis |
-
-
-
- | 64 |
- BXD36 |
- F |
- 64 |
-
- R1667C
- |
-
- 3
- |
- UTM RW |
-
-
- | 65 |
- BXD36 |
- M |
- 61 |
-
- R1212C
- |
-
- 3
- |
- UMemphis |
-
-
- | 66 |
- BXD38 |
- F |
- 55 |
-
- R0781C
- |
-
- 2
- |
- UAB |
-
-
- | 67 |
- BXD38 |
- M |
- 65 |
-
- R0761C
- |
-
- 2
- |
- UMemphis |
-
-
- | 68 |
- BXD39 |
- F |
- 59 |
-
- R1490C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 69 |
- BXD39 |
- M |
- 165 |
-
- R0723C
- |
-
- 1
- |
- UAB |
-
-
- | 70 |
- BXD40 |
- F |
- 56 |
-
- R0718C
- |
-
- 2
- |
- UMemphis |
-
-
- | 71 |
- BXD40 |
- M |
- 73 |
-
- R0812C
- |
-
- 2
- |
- UMemphis |
-
-
- | 72 |
- BXD42 |
- F |
- 100 |
-
- R0799C
- |
-
- 2
- |
- UAB |
-
-
- | 73 |
- BXD42 |
- M |
- 97 |
-
- R0709C
- |
-
- 1
- |
- UMemphis |
-
-
- | 74 |
- BXD43 |
- F |
- 61 |
-
- R1200C
- |
-
- 3
- |
- UTM RW |
-
-
- | 75 |
- BXD43 |
- M |
- 63 |
-
- R1182C
- |
-
- 3
- |
- UTM RW |
-
-
- | 76 |
- BXD44 |
- F |
- 61 |
-
- R1188C
- |
-
- 3
- |
- UTM RW |
-
-
- | 77 |
- BXD44 |
- M |
- 58 |
-
- R1073C
- |
-
- 3
- |
- UTM RW |
-
-
- | 78 |
- BXD45 |
- F |
- 63 |
-
- R1404C
- |
-
- 3
- |
- UTM RW |
-
-
- | 79 |
- BXD45 |
- M |
- 93 |
-
- R1506C
- |
-
- 3
- |
- UTM RW |
-
-
- | 80 |
- BXD48 |
- F |
- 64 |
-
- R1158C
- |
-
- 3
- |
- UTM RW |
-
-
- | 81 |
- BXD48 |
- M |
- 65 |
-
- R1165C
- |
-
- 3
- |
- UTM RW |
-
-
- | 82 |
- BXD51 |
- F |
- 66 |
-
- R1666C
- |
-
- 3
- |
- UTM RW |
-
-
- | 83 |
- BXD51 |
- M |
- 62 |
-
- R1180C
- |
-
- 3
- |
- UTM RW |
-
-
- | 84 |
- BXD51 |
- M |
- 79 |
-
- R1671C
- |
-
- 3
- |
- UTM RW |
-
-
- | 85 |
- BXD60 |
- F |
- 64 |
-
- R1160C
- |
-
- 3
- |
- UTM RW |
-
-
- | 86 |
- BXD60 |
- M |
- 61 |
-
- R1103C
- |
-
- 3
- |
- UTM RW |
-
-
- | 87 |
- BXD60 |
- M |
- 99 |
-
- R1669C
- |
-
- 3
- |
- UTM RW |
-
-
- | 88 |
- BXD62 |
- M |
- 61 |
-
- R1149C
- |
-
- 3
- |
- UTM RW |
-
-
- | 89 |
- BXD62 |
- M |
- 60 |
-
- R1668C
- |
-
- 3
- |
- UTM RW |
-
-
- | 90 |
- BXD69 |
- F |
- 60 |
-
- R1440C
- |
-
- 3
- |
- UTM RW |
-
-
- | 91 |
- BXD69 |
- M |
- 64 |
-
- R1197C
- |
-
- 3
- |
- UTM RW |
-
-
- | 92 |
- BXD73 |
- F |
- 60 |
-
- R1276C
- |
-
- 3
- |
- UTM RW |
-
-
- | 93 |
- BXD73 |
- M |
- 77 |
-
- R1665C
- |
-
- 3
- |
- UTM RW |
-
-
- | 94 |
- BXD77 |
- M |
- 62 |
-
- R1424C
- |
-
- 3
- |
- UTM RW |
-
-
- | 95 |
- BXD85 |
- F |
- 79 |
-
- R1486C
- |
-
- 3
- |
- UTM RW |
-
-
- | 96 |
- BXD85 |
- M |
- 79 |
-
- R1487C
- |
-
- 3
- |
- UTM RW |
-
-
- | 97 |
- BXD86 |
- F |
- 58 |
-
- R1408C
- |
-
- 3
- |
- UTM RW |
-
-
- | 98 |
- BXD86 |
- M |
- 58 |
-
- R1412C
- |
-
- 3
- |
- UTM RW |
-
-
- | 99 |
- BXD90 |
- M |
- 74 |
-
- R1664C
- |
-
- 3
- |
- UTM RW |
-
-
- | 100 |
- BXD92 |
- F |
- 62 |
-
- R1391C
- |
-
- 3
- |
- UTM RW |
-
-
- | 101 |
- BXD92 |
- F |
- 63 |
-
- R1670C
- |
-
- 3
- |
- UTM RW |
-
-
- | 102 |
- BXD92 |
- M |
- 59 |
-
- R1308C
- |
-
- 3
- |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_0305_P/acknowledgment.rtf b/general/datasets/CB_M_0305_P/acknowledgment.rtf
deleted file mode 100644
index 4fa1990..0000000
--- a/general/datasets/CB_M_0305_P/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed by members of the UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - Jim Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_0305_P/cases.rtf b/general/datasets/CB_M_0305_P/cases.rtf
deleted file mode 100644
index 7c1e52c..0000000
--- a/general/datasets/CB_M_0305_P/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. All BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTLs genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
-
-
-Most BXD animals were generated in-house at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and Hui-Chen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).
-
diff --git a/general/datasets/CB_M_0305_P/notes.rtf b/general/datasets/CB_M_0305_P/notes.rtf
deleted file mode 100644
index 73487ea..0000000
--- a/general/datasets/CB_M_0305_P/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
-
-This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.
diff --git a/general/datasets/CB_M_0305_P/platform.rtf b/general/datasets/CB_M_0305_P/platform.rtf
deleted file mode 100644
index 39256be..0000000
--- a/general/datasets/CB_M_0305_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/CB_M_0305_P/processing.rtf b/general/datasets/CB_M_0305_P/processing.rtf
deleted file mode 100644
index f7b4668..0000000
--- a/general/datasets/CB_M_0305_P/processing.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by three large batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all three batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the three batches is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/CB_M_0305_P/summary.rtf b/general/datasets/CB_M_0305_P/summary.rtf
deleted file mode 100644
index 34c7e0d..0000000
--- a/general/datasets/CB_M_0305_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This March 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 48 lines of mice including 45 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and F1 hybrids. Data were generated by a consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430A and B arrays. This particular data set was processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/CB_M_0305_P/tissue.rtf b/general/datasets/CB_M_0305_P/tissue.rtf
deleted file mode 100644
index e803a45..0000000
--- a/general/datasets/CB_M_0305_P/tissue.rtf
+++ /dev/null
@@ -1,1370 +0,0 @@
-
-The March 2005 data set consists of a total of 102 array pairs (Affymetrix 430A and 430B) from 49 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. Two sets of technical replicates (BXD14 n = 2; BXD29 n = 3) were combined before generating group means; giving a total of 101 biologically independent data sets. The two reciprocal F1s (D2B6F1 and B6D2F1) were combined to give a single F1 mean estimate of gene expression. 430A and 430B arrays were processed in three large batches. The first batch (May03 data) consists of 17 samples from 17 strains balanced by sex (8M and 9F). The second batch consists of 29 samples, and includes biological replicates, 2 technical replicates, and data for 9 new strains. The third batch consists of 56 samples, and also includes biological replicates, 2 technical replicates, and data for 15 additional strains.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from both sexes for each strain. Six of 48 genotypes are still represented by single samples: BXD5, BXD13, BXD20, BXD23, BXD27 are female-only strains, whereas BXD25, BXD77, BXD90 are male-only. Ten strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 1M), B6D2F1 (1F 2M), BXD2 (2F 1M), BXD11 (2F 1M), BXD28 (2F 1M), BXD40 (2F 1M), BXD51 (1F 2M), BXD60 (1F 2M), BXD92 (2F 1M).
-
-The age range of samples is relatively narrow. Only 18 samples were taken from animals older than 99 days and only two samples are older than 7 months of age. BXD11 includes an extra (third) 441-day-old female sample and the BXD28 includes an extra 427-day-old sample.
-
-RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The table below summarizes information on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
-
- SampleName
- |
-
- BatchID
- |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 116 |
-
- R0773C
- |
-
- 2
- |
- UAB |
-
-
- | 2 |
- C57BL/6J |
- M |
- 109 |
-
- R0054C
- |
-
- 1
- |
- JAX |
-
-
- | 3 |
- C57BL/6J |
- M |
- 71 |
-
- R1450C
- |
-
- 3
- |
- UTM DG |
-
-
- | 4 |
- DBA/2J |
- F |
- 71 |
-
- R0175C
- |
-
- 1
- |
- UAB |
-
-
- | 5 |
- DBA/2J |
- F |
- 91 |
-
- R0782C
- |
-
- 2
- |
- UAB |
-
-
- | 6 |
- DBA/2J |
- M |
- 62 |
-
- R1121C
- |
-
- 3
- |
- UTM RW |
-
-
- | 7 |
- B6D2F1 |
- F |
- 60 |
-
- R1115C
- |
-
- 3
- |
- UTM RW |
-
-
- | 8 |
- B6D2F1 |
- M |
- 94 |
-
- R0347C
- |
-
- 1
- |
- JAX |
-
-
- | 9 |
- B6D2F1 |
- M |
- 127 |
-
- R0766C
- |
-
- 2
- |
- UTM JB |
-
-
- | 10 |
- D2B6F1 |
- F |
- 57 |
-
- R1067C
- |
-
- 3
- |
- UTM RW |
-
-
- | 11 |
- D2B6F1 |
- M |
- 60 |
-
- R1387C
- |
-
- 3
- |
- UTM RW |
-
-
- | 12 |
- BXD1 |
- F |
- 57 |
-
- R0813C
- |
-
- 2
- |
- UAB |
-
-
- | 13 |
- BXD1 |
- M |
- 181 |
-
- R1151C
- |
-
- 3
- |
- UTM JB |
-
-
- | 14 |
- BXD2 |
- F |
- 142 |
-
- R0751C
- |
-
- 1
- |
- UAB |
-
-
- | 15 |
- BXD2 |
- F |
- 78 |
-
- R0774C
- |
-
- 2
- |
- UAB |
-
-
- | 16 |
- BXD2 |
- M |
- 61 |
-
- R1503C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 17 |
- BXD5 |
- F |
- 56 |
-
- R0802C
- |
-
- 2
- |
- UMemphis |
-
-
-
- | 18 |
- BXD6 |
- F |
- 92 |
-
- R0719C
- |
-
- 1
- |
- UMemphis |
-
-
- | 19 |
- BXD6 |
- M |
- 92 |
-
- R0720C
- |
-
- 3
- |
- UMemphis |
-
-
- | 20 |
- BXD8 |
- F |
- 72 |
-
- R0173C
- |
-
- 1
- |
- UAB |
-
-
- | 21 |
- BXD8 |
- M |
- 59 |
-
- R1484C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 22 |
- BXD9 |
- F |
- 86 |
-
- R0736C
- |
-
- 3
- |
- UMemphis |
-
-
- | 23 |
- BXD9 |
- M |
- 86 |
-
- R0737C
- |
-
- 1
- |
- UMemphis |
-
-
- | 24 |
- BXD11 |
- F |
- 441 |
-
- R0200C
- |
-
- 1
- |
- UAB |
-
-
- | 25 |
- BXD11 |
- F |
- 97 |
-
- R0791C
- |
-
- 3
- |
- UAB |
-
-
- | 26 |
- BXD11 |
- M |
- 92 |
-
- R0790C
- |
-
- 2
- |
- UMemphis |
-
-
- | 27 |
- BXD12 |
- F |
- 130 |
-
- R0776C
- |
-
- 2
- |
- UAB |
-
-
- | 28 |
- BXD12 |
- M |
- 64 |
-
- R0756C
- |
-
- 2
- |
- UMemphis |
-
-
- | 29 |
- BXD13 |
- F |
- 86 |
-
- R1144C
- |
-
- 3
- |
- UMemphis |
-
-
- | 30 |
- BXD14 |
- F |
- 190 |
-
- R0794C
- |
-
- 2
- |
- UAB |
-
-
- | 31 |
- BXD14 |
- F |
- 190 |
-
- R0794C
- |
-
- 3
- |
- UAB |
-
-
- | 32 |
- BXD14 |
- M |
- 91 |
-
- R0758C
- |
-
- 2
- |
- UMemphis |
-
-
- | 33 |
- BXD14 |
- M |
- 65 |
-
- R1130C
- |
-
- 3
- |
- UTM RW |
-
-
-
- | 34 |
- BXD15 |
- F |
- 60 |
-
- R1491C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 35 |
- BXD15 |
- M |
- 61 |
-
- R1499C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 36 |
- BXD16 |
- F |
- 163 |
-
- R0750C
- |
-
- 1
- |
- UAB |
-
-
- | 37 |
- BXD16 |
- M |
- 61 |
-
- R1572C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 38 |
- BXD19 |
- F |
- 61 |
-
- R0772C
- |
-
- 2
- |
- UAB |
-
-
- | 39 |
- BXD19 |
- M |
- 157 |
-
- R1230C
- |
-
- 3
- |
- UTM JB |
-
-
- | 40 |
- BXD20 |
- F |
- 59 |
-
- R1488C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 41 |
- BXD21 |
- F |
- 116 |
-
- R0711C
- |
-
- 1
- |
- UAB |
-
-
- | 42 |
- BXD21 |
- M |
- 64 |
-
- R0803C
- |
-
- 2
- |
- UMemphis |
-
-
- | 43 |
- BXD22 |
- F |
- 65 |
-
- R0174C
- |
-
- 1
- |
- UAB |
-
-
- | 44 |
- BXD22 |
- M |
- 59 |
-
- R1489C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 45 |
- BXD23 |
- F |
- 88 |
-
- R0814C
- |
-
- 2
- |
- UAB |
-
-
- | 46 |
- BXD24 |
- F |
- 71 |
-
- R0805C
- |
-
- 2
- |
- UMemphis |
-
-
- | 47 |
- BXD24 |
- M |
- 71 |
-
- R0759C
- |
-
- 2
- |
- UMemphis |
-
-
- | 48 |
- BXD25 |
- M |
- 90 |
-
- R0429C
- |
-
- 1
- |
- UTM RW |
-
-
- | 49 |
- BXD27 |
- F |
- 60 |
-
- R1496C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 50 |
- BXD28 |
- F |
- 113 |
-
- R0785C
- |
-
- 2
- |
- UTM RW |
-
-
- | 51 |
- BXD28 |
- M |
- 79 |
-
- R0739C
- |
-
- 3
- |
- UMemphis |
-
-
- | 52 |
- BXD29 |
- F |
- 82 |
-
- R0777C
- |
-
- 2
- |
- UAB |
-
-
- | 53 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 1
- |
- UMemphis |
-
-
- | 54 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 2
- |
- UMemphis |
-
-
- | 55 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 3
- |
- UMemphis |
-
-
- | 56 |
- BXD31 |
- F |
- 142 |
-
- R0816C
- |
-
- 2
- |
- UAB |
-
-
- | 57 |
- BXD31 |
- M |
- 61 |
-
- R1142C
- |
-
- 3
- |
- UTM RW |
-
-
- | 58 |
- BXD32 |
- F |
- 62 |
-
- R0778C
- |
-
- 2
- |
- UAB |
-
-
- | 59 |
- BXD32 |
- M |
- 218 |
-
- R0786C
- |
-
- 2
- |
- UAB |
-
-
- | 60 |
- BXD33 |
- F |
- 184 |
-
- R0793C
- |
-
- 2
- |
- UAB |
-
-
- | 61 |
- BXD33 |
- M |
- 124 |
-
- R0715C
- |
-
- 1
- |
- UAB |
-
-
- | 62 |
- BXD34 |
- F |
- 56 |
-
- R0725C
- |
-
- 1
- |
- UMemphis |
-
-
- | 63 |
- BXD34 |
- M |
- 91 |
-
- R0789C
- |
-
- 2
- |
- UMemphis |
-
-
-
- | 64 |
- BXD36 |
- F |
- 64 |
-
- R1667C
- |
-
- 3
- |
- UTM RW |
-
-
- | 65 |
- BXD36 |
- M |
- 61 |
-
- R1212C
- |
-
- 3
- |
- UMemphis |
-
-
- | 66 |
- BXD38 |
- F |
- 55 |
-
- R0781C
- |
-
- 2
- |
- UAB |
-
-
- | 67 |
- BXD38 |
- M |
- 65 |
-
- R0761C
- |
-
- 2
- |
- UMemphis |
-
-
- | 68 |
- BXD39 |
- F |
- 59 |
-
- R1490C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 69 |
- BXD39 |
- M |
- 165 |
-
- R0723C
- |
-
- 1
- |
- UAB |
-
-
- | 70 |
- BXD40 |
- F |
- 56 |
-
- R0718C
- |
-
- 2
- |
- UMemphis |
-
-
- | 71 |
- BXD40 |
- M |
- 73 |
-
- R0812C
- |
-
- 2
- |
- UMemphis |
-
-
- | 72 |
- BXD42 |
- F |
- 100 |
-
- R0799C
- |
-
- 2
- |
- UAB |
-
-
- | 73 |
- BXD42 |
- M |
- 97 |
-
- R0709C
- |
-
- 1
- |
- UMemphis |
-
-
- | 74 |
- BXD43 |
- F |
- 61 |
-
- R1200C
- |
-
- 3
- |
- UTM RW |
-
-
- | 75 |
- BXD43 |
- M |
- 63 |
-
- R1182C
- |
-
- 3
- |
- UTM RW |
-
-
- | 76 |
- BXD44 |
- F |
- 61 |
-
- R1188C
- |
-
- 3
- |
- UTM RW |
-
-
- | 77 |
- BXD44 |
- M |
- 58 |
-
- R1073C
- |
-
- 3
- |
- UTM RW |
-
-
- | 78 |
- BXD45 |
- F |
- 63 |
-
- R1404C
- |
-
- 3
- |
- UTM RW |
-
-
- | 79 |
- BXD45 |
- M |
- 93 |
-
- R1506C
- |
-
- 3
- |
- UTM RW |
-
-
- | 80 |
- BXD48 |
- F |
- 64 |
-
- R1158C
- |
-
- 3
- |
- UTM RW |
-
-
- | 81 |
- BXD48 |
- M |
- 65 |
-
- R1165C
- |
-
- 3
- |
- UTM RW |
-
-
- | 82 |
- BXD51 |
- F |
- 66 |
-
- R1666C
- |
-
- 3
- |
- UTM RW |
-
-
- | 83 |
- BXD51 |
- M |
- 62 |
-
- R1180C
- |
-
- 3
- |
- UTM RW |
-
-
- | 84 |
- BXD51 |
- M |
- 79 |
-
- R1671C
- |
-
- 3
- |
- UTM RW |
-
-
- | 85 |
- BXD60 |
- F |
- 64 |
-
- R1160C
- |
-
- 3
- |
- UTM RW |
-
-
- | 86 |
- BXD60 |
- M |
- 61 |
-
- R1103C
- |
-
- 3
- |
- UTM RW |
-
-
- | 87 |
- BXD60 |
- M |
- 99 |
-
- R1669C
- |
-
- 3
- |
- UTM RW |
-
-
- | 88 |
- BXD62 |
- M |
- 61 |
-
- R1149C
- |
-
- 3
- |
- UTM RW |
-
-
- | 89 |
- BXD62 |
- M |
- 60 |
-
- R1668C
- |
-
- 3
- |
- UTM RW |
-
-
- | 90 |
- BXD69 |
- F |
- 60 |
-
- R1440C
- |
-
- 3
- |
- UTM RW |
-
-
- | 91 |
- BXD69 |
- M |
- 64 |
-
- R1197C
- |
-
- 3
- |
- UTM RW |
-
-
- | 92 |
- BXD73 |
- F |
- 60 |
-
- R1276C
- |
-
- 3
- |
- UTM RW |
-
-
- | 93 |
- BXD73 |
- M |
- 77 |
-
- R1665C
- |
-
- 3
- |
- UTM RW |
-
-
- | 94 |
- BXD77 |
- M |
- 62 |
-
- R1424C
- |
-
- 3
- |
- UTM RW |
-
-
- | 95 |
- BXD85 |
- F |
- 79 |
-
- R1486C
- |
-
- 3
- |
- UTM RW |
-
-
- | 96 |
- BXD85 |
- M |
- 79 |
-
- R1487C
- |
-
- 3
- |
- UTM RW |
-
-
- | 97 |
- BXD86 |
- F |
- 58 |
-
- R1408C
- |
-
- 3
- |
- UTM RW |
-
-
- | 98 |
- BXD86 |
- M |
- 58 |
-
- R1412C
- |
-
- 3
- |
- UTM RW |
-
-
- | 99 |
- BXD90 |
- M |
- 74 |
-
- R1664C
- |
-
- 3
- |
- UTM RW |
-
-
- | 100 |
- BXD92 |
- F |
- 62 |
-
- R1391C
- |
-
- 3
- |
- UTM RW |
-
-
- | 101 |
- BXD92 |
- F |
- 63 |
-
- R1670C
- |
-
- 3
- |
- UTM RW |
-
-
- | 102 |
- BXD92 |
- M |
- 59 |
-
- R1308C
- |
-
- 3
- |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_0305_R/acknowledgment.rtf b/general/datasets/CB_M_0305_R/acknowledgment.rtf
deleted file mode 100644
index 4fa1990..0000000
--- a/general/datasets/CB_M_0305_R/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed by members of the UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - Jim Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_0305_R/cases.rtf b/general/datasets/CB_M_0305_R/cases.rtf
deleted file mode 100644
index 7c1e52c..0000000
--- a/general/datasets/CB_M_0305_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. All BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTLs genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
-
-
-Most BXD animals were generated in-house at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and Hui-Chen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).
-
diff --git a/general/datasets/CB_M_0305_R/notes.rtf b/general/datasets/CB_M_0305_R/notes.rtf
deleted file mode 100644
index 73487ea..0000000
--- a/general/datasets/CB_M_0305_R/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
-
-This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.
diff --git a/general/datasets/CB_M_0305_R/platform.rtf b/general/datasets/CB_M_0305_R/platform.rtf
deleted file mode 100644
index 39256be..0000000
--- a/general/datasets/CB_M_0305_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/CB_M_0305_R/processing.rtf b/general/datasets/CB_M_0305_R/processing.rtf
deleted file mode 100644
index f7b4668..0000000
--- a/general/datasets/CB_M_0305_R/processing.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We corrected for technical variance introduced by three large batches at the probe level. To do this we determined the ratio of the batch mean to the mean of all three batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each of the three batches is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/CB_M_0305_R/summary.rtf b/general/datasets/CB_M_0305_R/summary.rtf
deleted file mode 100644
index 34c7e0d..0000000
--- a/general/datasets/CB_M_0305_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This March 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 48 lines of mice including 45 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and F1 hybrids. Data were generated by a consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430A and B arrays. This particular data set was processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/CB_M_0305_R/tissue.rtf b/general/datasets/CB_M_0305_R/tissue.rtf
deleted file mode 100644
index e803a45..0000000
--- a/general/datasets/CB_M_0305_R/tissue.rtf
+++ /dev/null
@@ -1,1370 +0,0 @@
-
-The March 2005 data set consists of a total of 102 array pairs (Affymetrix 430A and 430B) from 49 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. Two sets of technical replicates (BXD14 n = 2; BXD29 n = 3) were combined before generating group means; giving a total of 101 biologically independent data sets. The two reciprocal F1s (D2B6F1 and B6D2F1) were combined to give a single F1 mean estimate of gene expression. 430A and 430B arrays were processed in three large batches. The first batch (May03 data) consists of 17 samples from 17 strains balanced by sex (8M and 9F). The second batch consists of 29 samples, and includes biological replicates, 2 technical replicates, and data for 9 new strains. The third batch consists of 56 samples, and also includes biological replicates, 2 technical replicates, and data for 15 additional strains.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from both sexes for each strain. Six of 48 genotypes are still represented by single samples: BXD5, BXD13, BXD20, BXD23, BXD27 are female-only strains, whereas BXD25, BXD77, BXD90 are male-only. Ten strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 1M), B6D2F1 (1F 2M), BXD2 (2F 1M), BXD11 (2F 1M), BXD28 (2F 1M), BXD40 (2F 1M), BXD51 (1F 2M), BXD60 (1F 2M), BXD92 (2F 1M).
-
-The age range of samples is relatively narrow. Only 18 samples were taken from animals older than 99 days and only two samples are older than 7 months of age. BXD11 includes an extra (third) 441-day-old female sample and the BXD28 includes an extra 427-day-old sample.
-
-RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The table below summarizes information on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
-
- SampleName
- |
-
- BatchID
- |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 116 |
-
- R0773C
- |
-
- 2
- |
- UAB |
-
-
- | 2 |
- C57BL/6J |
- M |
- 109 |
-
- R0054C
- |
-
- 1
- |
- JAX |
-
-
- | 3 |
- C57BL/6J |
- M |
- 71 |
-
- R1450C
- |
-
- 3
- |
- UTM DG |
-
-
- | 4 |
- DBA/2J |
- F |
- 71 |
-
- R0175C
- |
-
- 1
- |
- UAB |
-
-
- | 5 |
- DBA/2J |
- F |
- 91 |
-
- R0782C
- |
-
- 2
- |
- UAB |
-
-
- | 6 |
- DBA/2J |
- M |
- 62 |
-
- R1121C
- |
-
- 3
- |
- UTM RW |
-
-
- | 7 |
- B6D2F1 |
- F |
- 60 |
-
- R1115C
- |
-
- 3
- |
- UTM RW |
-
-
- | 8 |
- B6D2F1 |
- M |
- 94 |
-
- R0347C
- |
-
- 1
- |
- JAX |
-
-
- | 9 |
- B6D2F1 |
- M |
- 127 |
-
- R0766C
- |
-
- 2
- |
- UTM JB |
-
-
- | 10 |
- D2B6F1 |
- F |
- 57 |
-
- R1067C
- |
-
- 3
- |
- UTM RW |
-
-
- | 11 |
- D2B6F1 |
- M |
- 60 |
-
- R1387C
- |
-
- 3
- |
- UTM RW |
-
-
- | 12 |
- BXD1 |
- F |
- 57 |
-
- R0813C
- |
-
- 2
- |
- UAB |
-
-
- | 13 |
- BXD1 |
- M |
- 181 |
-
- R1151C
- |
-
- 3
- |
- UTM JB |
-
-
- | 14 |
- BXD2 |
- F |
- 142 |
-
- R0751C
- |
-
- 1
- |
- UAB |
-
-
- | 15 |
- BXD2 |
- F |
- 78 |
-
- R0774C
- |
-
- 2
- |
- UAB |
-
-
- | 16 |
- BXD2 |
- M |
- 61 |
-
- R1503C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 17 |
- BXD5 |
- F |
- 56 |
-
- R0802C
- |
-
- 2
- |
- UMemphis |
-
-
-
- | 18 |
- BXD6 |
- F |
- 92 |
-
- R0719C
- |
-
- 1
- |
- UMemphis |
-
-
- | 19 |
- BXD6 |
- M |
- 92 |
-
- R0720C
- |
-
- 3
- |
- UMemphis |
-
-
- | 20 |
- BXD8 |
- F |
- 72 |
-
- R0173C
- |
-
- 1
- |
- UAB |
-
-
- | 21 |
- BXD8 |
- M |
- 59 |
-
- R1484C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 22 |
- BXD9 |
- F |
- 86 |
-
- R0736C
- |
-
- 3
- |
- UMemphis |
-
-
- | 23 |
- BXD9 |
- M |
- 86 |
-
- R0737C
- |
-
- 1
- |
- UMemphis |
-
-
- | 24 |
- BXD11 |
- F |
- 441 |
-
- R0200C
- |
-
- 1
- |
- UAB |
-
-
- | 25 |
- BXD11 |
- F |
- 97 |
-
- R0791C
- |
-
- 3
- |
- UAB |
-
-
- | 26 |
- BXD11 |
- M |
- 92 |
-
- R0790C
- |
-
- 2
- |
- UMemphis |
-
-
- | 27 |
- BXD12 |
- F |
- 130 |
-
- R0776C
- |
-
- 2
- |
- UAB |
-
-
- | 28 |
- BXD12 |
- M |
- 64 |
-
- R0756C
- |
-
- 2
- |
- UMemphis |
-
-
- | 29 |
- BXD13 |
- F |
- 86 |
-
- R1144C
- |
-
- 3
- |
- UMemphis |
-
-
- | 30 |
- BXD14 |
- F |
- 190 |
-
- R0794C
- |
-
- 2
- |
- UAB |
-
-
- | 31 |
- BXD14 |
- F |
- 190 |
-
- R0794C
- |
-
- 3
- |
- UAB |
-
-
- | 32 |
- BXD14 |
- M |
- 91 |
-
- R0758C
- |
-
- 2
- |
- UMemphis |
-
-
- | 33 |
- BXD14 |
- M |
- 65 |
-
- R1130C
- |
-
- 3
- |
- UTM RW |
-
-
-
- | 34 |
- BXD15 |
- F |
- 60 |
-
- R1491C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 35 |
- BXD15 |
- M |
- 61 |
-
- R1499C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 36 |
- BXD16 |
- F |
- 163 |
-
- R0750C
- |
-
- 1
- |
- UAB |
-
-
- | 37 |
- BXD16 |
- M |
- 61 |
-
- R1572C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 38 |
- BXD19 |
- F |
- 61 |
-
- R0772C
- |
-
- 2
- |
- UAB |
-
-
- | 39 |
- BXD19 |
- M |
- 157 |
-
- R1230C
- |
-
- 3
- |
- UTM JB |
-
-
- | 40 |
- BXD20 |
- F |
- 59 |
-
- R1488C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 41 |
- BXD21 |
- F |
- 116 |
-
- R0711C
- |
-
- 1
- |
- UAB |
-
-
- | 42 |
- BXD21 |
- M |
- 64 |
-
- R0803C
- |
-
- 2
- |
- UMemphis |
-
-
- | 43 |
- BXD22 |
- F |
- 65 |
-
- R0174C
- |
-
- 1
- |
- UAB |
-
-
- | 44 |
- BXD22 |
- M |
- 59 |
-
- R1489C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 45 |
- BXD23 |
- F |
- 88 |
-
- R0814C
- |
-
- 2
- |
- UAB |
-
-
- | 46 |
- BXD24 |
- F |
- 71 |
-
- R0805C
- |
-
- 2
- |
- UMemphis |
-
-
- | 47 |
- BXD24 |
- M |
- 71 |
-
- R0759C
- |
-
- 2
- |
- UMemphis |
-
-
- | 48 |
- BXD25 |
- M |
- 90 |
-
- R0429C
- |
-
- 1
- |
- UTM RW |
-
-
- | 49 |
- BXD27 |
- F |
- 60 |
-
- R1496C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 50 |
- BXD28 |
- F |
- 113 |
-
- R0785C
- |
-
- 2
- |
- UTM RW |
-
-
- | 51 |
- BXD28 |
- M |
- 79 |
-
- R0739C
- |
-
- 3
- |
- UMemphis |
-
-
- | 52 |
- BXD29 |
- F |
- 82 |
-
- R0777C
- |
-
- 2
- |
- UAB |
-
-
- | 53 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 1
- |
- UMemphis |
-
-
- | 54 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 2
- |
- UMemphis |
-
-
- | 55 |
- BXD29 |
- M |
- 76 |
-
- R0714C
- |
-
- 3
- |
- UMemphis |
-
-
- | 56 |
- BXD31 |
- F |
- 142 |
-
- R0816C
- |
-
- 2
- |
- UAB |
-
-
- | 57 |
- BXD31 |
- M |
- 61 |
-
- R1142C
- |
-
- 3
- |
- UTM RW |
-
-
- | 58 |
- BXD32 |
- F |
- 62 |
-
- R0778C
- |
-
- 2
- |
- UAB |
-
-
- | 59 |
- BXD32 |
- M |
- 218 |
-
- R0786C
- |
-
- 2
- |
- UAB |
-
-
- | 60 |
- BXD33 |
- F |
- 184 |
-
- R0793C
- |
-
- 2
- |
- UAB |
-
-
- | 61 |
- BXD33 |
- M |
- 124 |
-
- R0715C
- |
-
- 1
- |
- UAB |
-
-
- | 62 |
- BXD34 |
- F |
- 56 |
-
- R0725C
- |
-
- 1
- |
- UMemphis |
-
-
- | 63 |
- BXD34 |
- M |
- 91 |
-
- R0789C
- |
-
- 2
- |
- UMemphis |
-
-
-
- | 64 |
- BXD36 |
- F |
- 64 |
-
- R1667C
- |
-
- 3
- |
- UTM RW |
-
-
- | 65 |
- BXD36 |
- M |
- 61 |
-
- R1212C
- |
-
- 3
- |
- UMemphis |
-
-
- | 66 |
- BXD38 |
- F |
- 55 |
-
- R0781C
- |
-
- 2
- |
- UAB |
-
-
- | 67 |
- BXD38 |
- M |
- 65 |
-
- R0761C
- |
-
- 2
- |
- UMemphis |
-
-
- | 68 |
- BXD39 |
- F |
- 59 |
-
- R1490C
- |
-
- 3
- |
- HarvardU GR |
-
-
- | 69 |
- BXD39 |
- M |
- 165 |
-
- R0723C
- |
-
- 1
- |
- UAB |
-
-
- | 70 |
- BXD40 |
- F |
- 56 |
-
- R0718C
- |
-
- 2
- |
- UMemphis |
-
-
- | 71 |
- BXD40 |
- M |
- 73 |
-
- R0812C
- |
-
- 2
- |
- UMemphis |
-
-
- | 72 |
- BXD42 |
- F |
- 100 |
-
- R0799C
- |
-
- 2
- |
- UAB |
-
-
- | 73 |
- BXD42 |
- M |
- 97 |
-
- R0709C
- |
-
- 1
- |
- UMemphis |
-
-
- | 74 |
- BXD43 |
- F |
- 61 |
-
- R1200C
- |
-
- 3
- |
- UTM RW |
-
-
- | 75 |
- BXD43 |
- M |
- 63 |
-
- R1182C
- |
-
- 3
- |
- UTM RW |
-
-
- | 76 |
- BXD44 |
- F |
- 61 |
-
- R1188C
- |
-
- 3
- |
- UTM RW |
-
-
- | 77 |
- BXD44 |
- M |
- 58 |
-
- R1073C
- |
-
- 3
- |
- UTM RW |
-
-
- | 78 |
- BXD45 |
- F |
- 63 |
-
- R1404C
- |
-
- 3
- |
- UTM RW |
-
-
- | 79 |
- BXD45 |
- M |
- 93 |
-
- R1506C
- |
-
- 3
- |
- UTM RW |
-
-
- | 80 |
- BXD48 |
- F |
- 64 |
-
- R1158C
- |
-
- 3
- |
- UTM RW |
-
-
- | 81 |
- BXD48 |
- M |
- 65 |
-
- R1165C
- |
-
- 3
- |
- UTM RW |
-
-
- | 82 |
- BXD51 |
- F |
- 66 |
-
- R1666C
- |
-
- 3
- |
- UTM RW |
-
-
- | 83 |
- BXD51 |
- M |
- 62 |
-
- R1180C
- |
-
- 3
- |
- UTM RW |
-
-
- | 84 |
- BXD51 |
- M |
- 79 |
-
- R1671C
- |
-
- 3
- |
- UTM RW |
-
-
- | 85 |
- BXD60 |
- F |
- 64 |
-
- R1160C
- |
-
- 3
- |
- UTM RW |
-
-
- | 86 |
- BXD60 |
- M |
- 61 |
-
- R1103C
- |
-
- 3
- |
- UTM RW |
-
-
- | 87 |
- BXD60 |
- M |
- 99 |
-
- R1669C
- |
-
- 3
- |
- UTM RW |
-
-
- | 88 |
- BXD62 |
- M |
- 61 |
-
- R1149C
- |
-
- 3
- |
- UTM RW |
-
-
- | 89 |
- BXD62 |
- M |
- 60 |
-
- R1668C
- |
-
- 3
- |
- UTM RW |
-
-
- | 90 |
- BXD69 |
- F |
- 60 |
-
- R1440C
- |
-
- 3
- |
- UTM RW |
-
-
- | 91 |
- BXD69 |
- M |
- 64 |
-
- R1197C
- |
-
- 3
- |
- UTM RW |
-
-
- | 92 |
- BXD73 |
- F |
- 60 |
-
- R1276C
- |
-
- 3
- |
- UTM RW |
-
-
- | 93 |
- BXD73 |
- M |
- 77 |
-
- R1665C
- |
-
- 3
- |
- UTM RW |
-
-
- | 94 |
- BXD77 |
- M |
- 62 |
-
- R1424C
- |
-
- 3
- |
- UTM RW |
-
-
- | 95 |
- BXD85 |
- F |
- 79 |
-
- R1486C
- |
-
- 3
- |
- UTM RW |
-
-
- | 96 |
- BXD85 |
- M |
- 79 |
-
- R1487C
- |
-
- 3
- |
- UTM RW |
-
-
- | 97 |
- BXD86 |
- F |
- 58 |
-
- R1408C
- |
-
- 3
- |
- UTM RW |
-
-
- | 98 |
- BXD86 |
- M |
- 58 |
-
- R1412C
- |
-
- 3
- |
- UTM RW |
-
-
- | 99 |
- BXD90 |
- M |
- 74 |
-
- R1664C
- |
-
- 3
- |
- UTM RW |
-
-
- | 100 |
- BXD92 |
- F |
- 62 |
-
- R1391C
- |
-
- 3
- |
- UTM RW |
-
-
- | 101 |
- BXD92 |
- F |
- 63 |
-
- R1670C
- |
-
- 3
- |
- UTM RW |
-
-
- | 102 |
- BXD92 |
- M |
- 59 |
-
- R1308C
- |
-
- 3
- |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_1003_M/acknowledgment.rtf b/general/datasets/CB_M_1003_M/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_1003_M/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_1003_M/cases.rtf b/general/datasets/CB_M_1003_M/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_1003_M/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_1003_M/notes.rtf b/general/datasets/CB_M_1003_M/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_1003_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_1003_M/platform.rtf b/general/datasets/CB_M_1003_M/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_1003_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_1003_M/processing.rtf b/general/datasets/CB_M_1003_M/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_1003_M/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_1003_M/summary.rtf b/general/datasets/CB_M_1003_M/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_1003_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_1003_M/tissue.rtf b/general/datasets/CB_M_1003_M/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_1003_M/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_1004_M/acknowledgment.rtf b/general/datasets/CB_M_1004_M/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_1004_M/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_1004_M/cases.rtf b/general/datasets/CB_M_1004_M/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_1004_M/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_1004_M/notes.rtf b/general/datasets/CB_M_1004_M/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_1004_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_1004_M/platform.rtf b/general/datasets/CB_M_1004_M/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_1004_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_1004_M/processing.rtf b/general/datasets/CB_M_1004_M/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_1004_M/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_1004_M/summary.rtf b/general/datasets/CB_M_1004_M/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_1004_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_1004_M/tissue.rtf b/general/datasets/CB_M_1004_M/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_1004_M/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_1004_P/acknowledgment.rtf b/general/datasets/CB_M_1004_P/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_1004_P/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_1004_P/cases.rtf b/general/datasets/CB_M_1004_P/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_1004_P/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_1004_P/notes.rtf b/general/datasets/CB_M_1004_P/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_1004_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_1004_P/platform.rtf b/general/datasets/CB_M_1004_P/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_1004_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_1004_P/processing.rtf b/general/datasets/CB_M_1004_P/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_1004_P/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_1004_P/summary.rtf b/general/datasets/CB_M_1004_P/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_1004_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_1004_P/tissue.rtf b/general/datasets/CB_M_1004_P/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_1004_P/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/CB_M_1004_R/acknowledgment.rtf b/general/datasets/CB_M_1004_R/acknowledgment.rtf
deleted file mode 100644
index b048bb0..0000000
--- a/general/datasets/CB_M_1004_R/acknowledgment.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:
-
- - Tom Curran
- - Dan Goldowitz
- - Kristin Hamre
- - Lu Lu
- - Peter McKinnon
- - James Morgan
- - Clayton Naeve
- - Richard Smeyne
- - Robert W. Williams
- - The Center of Genomics and Bioinformatics at UTHSC
- - The Hartwell Center at SJCRH
-
-
diff --git a/general/datasets/CB_M_1004_R/cases.rtf b/general/datasets/CB_M_1004_R/cases.rtf
deleted file mode 100644
index f5e6bdf..0000000
--- a/general/datasets/CB_M_1004_R/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems). Chromosomes of the two parental strains have been recombined and fixed randomly in the many different BXD strains. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine.
-
-
-In this mRNA expression data set we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.
-
-
-The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXD67, BXD68, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be 45 of these BXD strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/CB_M_1004_R/notes.rtf b/general/datasets/CB_M_1004_R/notes.rtf
deleted file mode 100644
index 5d4ac24..0000000
--- a/general/datasets/CB_M_1004_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and YHQ, September 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/CB_M_1004_R/platform.rtf b/general/datasets/CB_M_1004_R/platform.rtf
deleted file mode 100644
index 188038b..0000000
--- a/general/datasets/CB_M_1004_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix Mouse Expression 430 GeneChip set: The expression data were generated using 430A and 430B arrays. Chromosomal positions of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
diff --git a/general/datasets/CB_M_1004_R/processing.rtf b/general/datasets/CB_M_1004_R/processing.rtf
deleted file mode 100644
index cdfa27a..0000000
--- a/general/datasets/CB_M_1004_R/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added a constant offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell signal level.
- - Step 3: We computed the Z scores for each cell within its array.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets that have identical sequences. These 100 probe sets and 2200 probes provide a good way to adjust expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array (the A array contains the more commonly expressed transcripts). To bring the two arrays into numerical alignment, we regressed Z scores of the common set of 2200 probes to obtain linear regression corrections to rescale the 430B arrays to values that match the 430A array. This involved multiplying all 430B Z scores by the slope of the regression and adding a very small offset (the regression intercept). The result of this adjustment is that the mean of the 430A array expression is fixed at a value of 8, whereas that of the 430B chip is typically 7.
- - Step 6b: We recentered the entire combined set of 430A and 430B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: No batch correction was applied.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have only a very modest number of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that this data set does not provide any correction for variance introduced by differences in sex, age, tissue source, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-Probe set data from the CHP file: These CHP files were generated using MAS 5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a 2-fold difference in expression level. Expression levels below 5 are close to the noise level.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/CB_M_1004_R/summary.rtf b/general/datasets/CB_M_1004_R/summary.rtf
deleted file mode 100644
index 8a59cc3..0000000
--- a/general/datasets/CB_M_1004_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This October 2003 freeze provides estimates of mRNA expression in cerebellum of 26 adult BXD recombinant inbred strains, as well as C57BL/6J, DBA/2J, and their F1 hybrid, measured using the Affymetrix M430A and B microarrays. Data were generated by a small consortium of investigators at St. Jude Children's Research Hospital (SJ) and the University of Tennessee Health Science Center (UT). Data were processed using the Microarray Suite 5 (<a data-cke-saved-href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" href="http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf" _blank"="" class="fs14">MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run in two large batches with careful consideration to balancing samples by sex and age. Eighteen strains have been profiled using two or three independent samples. All other strains were sampled once.
-
diff --git a/general/datasets/CB_M_1004_R/tissue.rtf b/general/datasets/CB_M_1004_R/tissue.rtf
deleted file mode 100644
index 4f8e5ed..0000000
--- a/general/datasets/CB_M_1004_R/tissue.rtf
+++ /dev/null
@@ -1,376 +0,0 @@
-
-The October 2003 data set was processed in two large batches. The first batch (the May 2003 data set) consists of 20 pooled samples from 20 strains run on pairs of Affymetrix 430A and 430B arrays (40 arrays total). The second batch consists of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of whole cerebellum taken from three adult animals of the same age and sex. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-RNA was extracted at UTHSC by Zhiping Jia and Hongtao Zhai.
-
-All samples were subsequently processed at the Hartwell Center Affymetrix laboratory at SJCRH by Jay Morris.
-
-
-The January04 data were processed in two large batches. The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years.
-
-The table below summarizes informaton on strain, sex, age, sample name, and batch number.
-
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Batch |
-
-
- | B6D2F1 |
- M |
- 127 |
- 766-C1 |
- 2 |
-
-
- | B6D2F1 |
- M |
- 94 |
- S347-1C1 |
- 1 |
-
-
- | C57BL/6J |
- F |
- 116 |
- 773-C1 |
- 2 |
-
-
- | C57BL/6J |
- M |
- 109 |
- S054-1C2 |
- 1 |
-
-
- | DBA/2J |
- F |
- 71 |
- S175-1C1 |
- 1 |
-
-
- | DBA/2J |
- F |
- 91 |
- 782-C1 |
- 2 |
-
-
- | BXD1 |
- F |
- 57 |
- 813-C1 |
- 2 |
-
-
- | BXD2 |
- F |
- 142 |
- 751-C1 |
- 1 |
-
-
- | BXD2 |
- F |
- 78 |
- 774-C1 |
- 2 |
-
-
- | BXD5 |
- F |
- 56 |
- 802-C1 |
- 2 |
-
-
- | BXD5 |
- M |
- 71 |
- 752-C1 |
- 1 |
-
-
- | BXD6 |
- F |
- 92 |
- 719-C1 |
- 1 |
-
-
- | BXD8 |
- F |
- 72 |
- S173-1C1 |
- 1 |
-
-
- | BXD9 |
- M |
- 86 |
- 737-C1 |
- 1 |
-
-
- | BXD11 |
- F |
- 441 |
- S200-1C1 |
- 1 |
-
-
- | BXD11 |
- M |
- 92 |
- 790-C1 |
- 2 |
-
-
- | BXD12 |
- F |
- 130 |
- 776-C1 |
- 2 |
-
-
- | BXD12 |
- M |
- 64 |
- 756-C1 |
- 2 |
-
-
- | BXD14 |
- F |
- 190 |
- 794-C1 |
- 2 |
-
-
- | BXD14 |
- M |
- 91 |
- 758-C1 |
- 2 |
-
-
- | BXD16 |
- F |
- 163 |
- 750-C1 |
- 1 |
-
-
- | BXD19 |
- F |
- 61 |
- 772-C1 |
- 2 |
-
-
- | BXD21 |
- F |
- 116 |
- 711-C1 |
- 1 |
-
-
- | BXD21 |
- M |
- 64 |
- 803-C1 |
- 2 |
-
-
- | BXD22 |
- F |
- 65 |
- S174-1C1 |
- 1 |
-
-
- | BXD23 |
- F |
- 88 |
- 814-C1 |
- 2 |
-
-
- | BXD24 |
- F |
- 71 |
- 805-C1 |
- 2 |
-
-
- | BXD24 |
- M |
- 71 |
- 759-C1 |
- 2 |
-
-
- | BXD25 |
- M |
- 90 |
- S429-1C1 |
- 1 |
-
-
- | BXD28 |
- F |
- 113 |
- 785-C1 |
- 2 |
-
-
- | BXD28 |
- F |
- 427 |
- S203-1C1 |
- 1 |
-
-
- | BXD29 |
- F |
- 82 |
- 777-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 2 |
-
-
- | BXD29 |
- M |
- 76 |
- 714-C1 |
- 1 |
-
-
- | BXD31 |
- F |
- 142 |
- 816-C1 |
- 2 |
-
-
- | BXD32 |
- F |
- 62 |
- 778-C1 |
- 2 |
-
-
- | BXD32 |
- M |
- 218 |
- 786-C1 |
- 2 |
-
-
- | BXD33 |
- F |
- 184 |
- 793-C1 |
- 2 |
-
-
- | BXD33 |
- M |
- 124 |
- 715-C1 |
- 1 |
-
-
- | BXD34 |
- F |
- 56 |
- 725-C1 |
- 1 |
-
-
- | BXD34 |
- M |
- 91 |
- 789-C1 |
- 2 |
-
-
- | BXD38 |
- F |
- 55 |
- 781-C1 |
- 2 |
-
-
- | BXD38 |
- M |
- 65 |
- 761-C1 |
- 2 |
-
-
- | BXD39 |
- M |
- 165 |
- 723-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 1 |
-
-
- | BXD40 |
- F |
- 56 |
- 718-C1 |
- 2 |
-
-
- | BXD40 |
- M |
- 73 |
- 812-C1 |
- 2 |
-
-
- | BXD42 |
- F |
- 100 |
- 799-C1 |
- 2 |
-
-
- | BXD42 |
- M |
- 97 |
- 709-C1 |
- 1 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/DBA2J-ONH-1212/experiment-design.rtf b/general/datasets/DBA2J-ONH-1212/experiment-design.rtf
deleted file mode 100644
index f01b888..0000000
--- a/general/datasets/DBA2J-ONH-1212/experiment-design.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-TEXT FROM GEO
-
-Genome-wide assessment of gene expression changes was performed in DBA/2J mice. The optic nerve head and retina from 40 DBA/2J eyes at 10.5 months of age were separately profiled. These eyes were selected as they encompassed a range of glaucoma severity. Two control groups were also included; 10 eyes from 10.5 months old D2-Gpnmb+ mice (age and strain matched, no glaucoma control) and 10 eyes from 4.5 months old DBA/2J mice (young, pre-glaucoma).
-
-In this study that was specifically designed to identify early stages of glaucoma in DBA/2J mice, we used genome-wide expression profiling and a series of computational methods. Our methods successfully subdivided eyes with no detectable glaucoma by conventional assays into molecularly defined stages of disease. These stages represent a temporally ordered sequence of glaucoma states. Using an array of tools, we then determined networks and biological processes that are altered at these early stages. Our strategy proved very sensitive, suggesting that similar approaches will be valuable for uncovering early processes in other complex, later-onset diseases. Early changes included upregulation of both the complement cascade and endothelin system, and so we tested the therapeutic value of separately inhibiting them. Mice with a mutation in the complement component 1a gene (C1qa) were robustly protected from glaucoma with the protection being among the greatest reported. Similarly, inhibition of the endothelin system was strongly protective. Since EDN2 is potently vasoconstrictive and was produced by microglial/macrophages, our data provide a novel link between these cell types and vascular dysfunction in glaucoma. Targeting early events such as the upregulation of the complement and endothelin pathways may provide effective new treatments for human glaucoma. (text above from GEO http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26299)
-
-
-
-
diff --git a/general/datasets/DBA2J-ONH-1212/summary.rtf b/general/datasets/DBA2J-ONH-1212/summary.rtf
deleted file mode 100644
index 09c8a43..0000000
--- a/general/datasets/DBA2J-ONH-1212/summary.rtf
+++ /dev/null
@@ -1,58 +0,0 @@
-This is an experimental glaucoma gene expression data set of retinal tissue entered into GeneNetwork by Dr. Eldon Geisert and Robert Williams in which BXD strains have been "highjacked" with experimental and control gene expression data generated by Drs Gareth Howell, Simon John, and colleagues at the Jackson Laboratory. These data were originally entered into GeneNetwork Sept 20, 2011.
-
-Please see the original paper by Howell et al (2011): http://www.jci.org/articles/view/44646 and GEO data at NCBI.
-
-Gareth R. Howell, Danilo G. Macalinao, Gregory L. Sousa, Michael Walden, Ileana Soto, Stephen C. Kneeland, Jessica M. Barbay, Benjamin L. King, Jeffrey K. Marchant, Matthew Hibbs, Beth Stevens, Ben A. Barres, Abbot F. Clark, Richard T. Libby, Simon S (2011) Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. J Clin Invest. 121:1429–1444
-
-Each strain corresponds to a particular retinal sample as shown below (note that we have not included ten "preglaucoma control" samples, see http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26299
-
-
- - BXD1 D2-Gpnmb+ control rep1 (retina)
- - BXD2 D2-Gpnmb+ control rep2 (retina)
- - BXD5 D2-Gpnmb+ control rep3 (retina)
- - BXD6 D2-Gpnmb+ control rep4 (retina)
- - BXD8 D2-Gpnmb+ control rep5 (retina)
- - BXD9 D2-Gpnmb+ control rep6 (retina)
- - BXD11 D2-Gpnmb+ control rep7 (retina)
- - BXD12 D2-Gpnmb+ control rep8 (retina)
- - BXD13 D2-Gpnmb+ control rep9 (retina)
- - BXD14 D2-Gpnmb+ control rep10 (retina)
- - BXD15 No or early 1 rep1 (retina)
- - BXD16 No or early 1 rep2 (retina)
- - BXD18 No or early 1 rep3 (retina)
- - BXD19 No or early 1 rep4 (retina)
- - BXD20 No or early 1 rep5 (retina)
- - BXD22 No or early 1 rep6 (retina)
- - BXD23 No or early 1 rep7 (retina)
- - BXD25 No or early 1 rep8 (retina)
- - BXD27 No or early 1 rep9 (retina)
- - BXD28 No or early 1 rep10 (retina)
- - BXD29 No or early 2 rep1 (retina)
- - BXD30 No or early 2 rep2 (retina)
- - BXD31 No or early 2 rep3 (retina)
- - BXD32 No or early 2 rep4 (retina)
- - BXD33 No or early 2 rep5 (retina)
- - BXD34 No or early 2 rep6 (retina)
- - BXD35 No or early 2 rep7 (retina)
- - BXD36 No or early 2 rep8 (retina)
- - BXD37 No or early 2 rep9 (retina)
- - BXD38 No or early 2 rep10 (retina)
- - BXD39 Moderate rep1 (retina)
- - BXD40 Moderate rep2 (retina)
- - BXD41 Moderate rep3 (retina)
- - BXD42 Moderate rep4 (retina)
- - BXD43 Moderate rep7 (retina)
- - BXD44 Moderate rep8 (retina)
- - BXD45 Moderate rep9 (retina)
- - BXD48 Moderate rep10 (retina)
- - BXD49 Severe rep1 (retina)
- - BXD50 Severe rep2 (retina)
- - BXD51 Severe rep3 (retina)
- - BXD52 Severe rep4 (retina)
- - BXD53 Severe rep5 (retina)
- - BXD54 Severe rep6 (retina)
- - BXD55 Severe rep7 (retina)
- - BXD56 Severe rep8 (retina)
- - BXD59 Severe rep9 (retina)
- - BXD60 Severe rep10 (retina)
-
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/cases.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/cases.rtf
deleted file mode 100644
index 70216c8..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About the strains used to generate this set of data
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/experiment-design.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/experiment-design.rtf
deleted file mode 100644
index 616db01..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/summary.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/summary.rtf
deleted file mode 100644
index 70d7451..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data generated by Dr. Glenn D. Rosen and colleagues
-
-The Neocortex Developmental data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-Some of these data were used in
-Gaglani SM, Lu L, Williams RW, Rosen GD (2009) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 Full Text HTML Version, Full Text PDF Version
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the Striatal Developmental Transcriptome data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Developmental data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. ABOUT THE NEOCORTEX
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/tissue.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/tissue.rtf
deleted file mode 100644
index 51f6e74..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1110/tissue.rtf
+++ /dev/null
@@ -1,536 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected neocortical tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn D. Rosen and colleagues.
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 2 |
- 5384138018_F |
- 236 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 3 |
- 5384138058_A |
- 239 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 2 |
- 5384138018_C |
- 168 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 1 |
- 5448576044_F |
- 167 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 7 |
- 5384138020_A |
- 273 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 4 |
- 5452241022_C |
- 267 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 3 |
- 5384138048_A |
- 107 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 4 |
- 5452241007_A |
- 108 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 6 |
- 5384138009_A |
- 113 |
-
-
- | 10 |
- BXD8 |
- P3 |
- 7 |
- 5384138021_C |
- 115 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 5 |
- 5452241004_F |
- 289 |
-
-
- | 12 |
- BXD9 |
- P3 |
- 4 |
- 5452241022_D |
- 288 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 8 |
- 5237939010_A |
- 117 |
-
-
- | 14 |
- BXD11 |
- P3 |
- 1 |
- 5448576044_D |
- 120 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 6 |
- 5384138009_B |
- 130 |
-
-
- | 16 |
- BXD12 |
- P3 |
- 7 |
- 5384138021_B |
- 132 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 7 |
- 5384138020_F |
- 161 |
-
-
- | 18 |
- BXD13 |
- P3 |
- 5 |
- 5452241004_C |
- 164 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 5 |
- 5452241004_B |
- 158 |
-
-
- | 20 |
- BXD14 |
- P3 |
- 6 |
- 5452241033_D |
- 424 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 3 |
- 5452241008_C |
- 437 |
-
-
- | 22 |
- BXD15 |
- P3 |
- 4 |
- 5452241023_D |
- 438 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 3 |
- 5384138048_D |
- 170 |
-
-
- | 24 |
- BXD16 |
- P3 |
- 4 |
- 5452241007_D |
- 172 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 8 |
- 5448576010_A |
- 390 |
-
-
- | 26 |
- BXD18 |
- P3 |
- 1 |
- 5448576045_E |
- 392 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 8 |
- 5237939010_E |
- 210 |
-
-
- | 28 |
- BXD19 |
- P3 |
- 1 |
- 5448576045_A |
- 211 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 5 |
- 5452241017_B |
- 439 |
-
-
- | 30 |
- BXD20 |
- P3 |
- 6 |
- 5452241033_E |
- 441 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 7 |
- 5384138021_F |
- 341 |
-
-
- | 32 |
- BXD21 |
- P3 |
- 6 |
- 5384138053_F |
- 315 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 8 |
- 5237939012_B |
- 251 |
-
-
- | 34 |
- BXD24a |
- P3 |
- 7 |
- 5384138020_B |
- 250 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 8 |
- 5237939012_D |
- 298 |
-
-
- | 36 |
- BXD27 |
- P3 |
- 1 |
- 5448576045_C |
- 300 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 2 |
- 5384138049_B |
- 550 |
-
-
- | 38 |
- BXD28 |
- P3 |
- 1 |
- 5448576029_F |
- 548 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 2 |
- 5384138047_F |
- 502 |
-
-
- | 40 |
- BXD29 |
- P3 |
- 1 |
- 5448576029_D |
- 501 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 5 |
- 5452241024_D |
- 579 |
-
-
- | 42 |
- BXD31 |
- P3 |
- 6 |
- 5452241035_D |
- 582 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_F |
- 407 |
-
-
- | 44 |
- BXD32 |
- P3 |
- 6 |
- 5452241033_C |
- 408 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 8 |
- 5237939012_F |
- 345 |
-
-
- | 46 |
- BXD34 |
- P3 |
- 4 |
- 5452241022_F |
- 355 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 7 |
- 5384138016_A |
- 429 |
-
-
- | 48 |
- BXD36 |
- P3 |
- 8 |
- 5448576010_D |
- 430 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 2 |
- 5384138041_F |
- 327 |
-
-
- | 50 |
- BXD38 |
- P3 |
- 3 |
- 5384138058_E |
- 328 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 7 |
- 5384138016_E |
- 515 |
-
-
- | 52 |
- BXD39 |
- P3 |
- 5 |
- 5452241024_A |
- 518 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 2 |
- 5384138041_C |
- 373 |
-
-
- | 54 |
- BXD40 |
- P3 |
- 3 |
- 5452241008_A |
- 375 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 3 |
- 5452241008_E |
- 485 |
-
-
- | 56 |
- BXD42 |
- P3 |
- 4 |
- 5452241023_F |
- 486 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 5 |
- 5452241024_F |
- 621 |
-
-
- | 58 |
- BXD51 |
- P3 |
- 6 |
- 5452241035_F |
- 622 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 4 |
- 5452241031_C |
- 554 |
-
-
- | 60 |
- BXD61 |
- P3 |
- 3 |
- 5452241034_A |
- 552 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 2 |
- 5384138049_D |
- 590 |
-
-
- | 62 |
- BXD70 |
- P3 |
- 1 |
- 5448576044_B |
- 589 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 2 |
- 5384138049_E |
- 603 |
-
-
- | 64 |
- BXD73 |
- P3 |
- 8 |
- 5448576011_E |
- 605 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/cases.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/cases.rtf
deleted file mode 100644
index 70216c8..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About the strains used to generate this set of data
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/experiment-design.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/experiment-design.rtf
deleted file mode 100644
index 616db01..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/summary.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/summary.rtf
deleted file mode 100644
index 70d7451..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data generated by Dr. Glenn D. Rosen and colleagues
-
-The Neocortex Developmental data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-Some of these data were used in
-Gaglani SM, Lu L, Williams RW, Rosen GD (2009) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 Full Text HTML Version, Full Text PDF Version
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the Striatal Developmental Transcriptome data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Developmental data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. ABOUT THE NEOCORTEX
diff --git a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/tissue.rtf b/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/tissue.rtf
deleted file mode 100644
index 51f6e74..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P14RInv_1111/tissue.rtf
+++ /dev/null
@@ -1,536 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected neocortical tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn D. Rosen and colleagues.
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 2 |
- 5384138018_F |
- 236 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 3 |
- 5384138058_A |
- 239 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 2 |
- 5384138018_C |
- 168 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 1 |
- 5448576044_F |
- 167 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 7 |
- 5384138020_A |
- 273 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 4 |
- 5452241022_C |
- 267 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 3 |
- 5384138048_A |
- 107 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 4 |
- 5452241007_A |
- 108 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 6 |
- 5384138009_A |
- 113 |
-
-
- | 10 |
- BXD8 |
- P3 |
- 7 |
- 5384138021_C |
- 115 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 5 |
- 5452241004_F |
- 289 |
-
-
- | 12 |
- BXD9 |
- P3 |
- 4 |
- 5452241022_D |
- 288 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 8 |
- 5237939010_A |
- 117 |
-
-
- | 14 |
- BXD11 |
- P3 |
- 1 |
- 5448576044_D |
- 120 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 6 |
- 5384138009_B |
- 130 |
-
-
- | 16 |
- BXD12 |
- P3 |
- 7 |
- 5384138021_B |
- 132 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 7 |
- 5384138020_F |
- 161 |
-
-
- | 18 |
- BXD13 |
- P3 |
- 5 |
- 5452241004_C |
- 164 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 5 |
- 5452241004_B |
- 158 |
-
-
- | 20 |
- BXD14 |
- P3 |
- 6 |
- 5452241033_D |
- 424 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 3 |
- 5452241008_C |
- 437 |
-
-
- | 22 |
- BXD15 |
- P3 |
- 4 |
- 5452241023_D |
- 438 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 3 |
- 5384138048_D |
- 170 |
-
-
- | 24 |
- BXD16 |
- P3 |
- 4 |
- 5452241007_D |
- 172 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 8 |
- 5448576010_A |
- 390 |
-
-
- | 26 |
- BXD18 |
- P3 |
- 1 |
- 5448576045_E |
- 392 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 8 |
- 5237939010_E |
- 210 |
-
-
- | 28 |
- BXD19 |
- P3 |
- 1 |
- 5448576045_A |
- 211 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 5 |
- 5452241017_B |
- 439 |
-
-
- | 30 |
- BXD20 |
- P3 |
- 6 |
- 5452241033_E |
- 441 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 7 |
- 5384138021_F |
- 341 |
-
-
- | 32 |
- BXD21 |
- P3 |
- 6 |
- 5384138053_F |
- 315 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 8 |
- 5237939012_B |
- 251 |
-
-
- | 34 |
- BXD24a |
- P3 |
- 7 |
- 5384138020_B |
- 250 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 8 |
- 5237939012_D |
- 298 |
-
-
- | 36 |
- BXD27 |
- P3 |
- 1 |
- 5448576045_C |
- 300 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 2 |
- 5384138049_B |
- 550 |
-
-
- | 38 |
- BXD28 |
- P3 |
- 1 |
- 5448576029_F |
- 548 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 2 |
- 5384138047_F |
- 502 |
-
-
- | 40 |
- BXD29 |
- P3 |
- 1 |
- 5448576029_D |
- 501 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 5 |
- 5452241024_D |
- 579 |
-
-
- | 42 |
- BXD31 |
- P3 |
- 6 |
- 5452241035_D |
- 582 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_F |
- 407 |
-
-
- | 44 |
- BXD32 |
- P3 |
- 6 |
- 5452241033_C |
- 408 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 8 |
- 5237939012_F |
- 345 |
-
-
- | 46 |
- BXD34 |
- P3 |
- 4 |
- 5452241022_F |
- 355 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 7 |
- 5384138016_A |
- 429 |
-
-
- | 48 |
- BXD36 |
- P3 |
- 8 |
- 5448576010_D |
- 430 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 2 |
- 5384138041_F |
- 327 |
-
-
- | 50 |
- BXD38 |
- P3 |
- 3 |
- 5384138058_E |
- 328 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 7 |
- 5384138016_E |
- 515 |
-
-
- | 52 |
- BXD39 |
- P3 |
- 5 |
- 5452241024_A |
- 518 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 2 |
- 5384138041_C |
- 373 |
-
-
- | 54 |
- BXD40 |
- P3 |
- 3 |
- 5452241008_A |
- 375 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 3 |
- 5452241008_E |
- 485 |
-
-
- | 56 |
- BXD42 |
- P3 |
- 4 |
- 5452241023_F |
- 486 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 5 |
- 5452241024_F |
- 621 |
-
-
- | 58 |
- BXD51 |
- P3 |
- 6 |
- 5452241035_F |
- 622 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 4 |
- 5452241031_C |
- 554 |
-
-
- | 60 |
- BXD61 |
- P3 |
- 3 |
- 5452241034_A |
- 552 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 2 |
- 5384138049_D |
- 590 |
-
-
- | 62 |
- BXD70 |
- P3 |
- 1 |
- 5448576044_B |
- 589 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 2 |
- 5384138049_E |
- 603 |
-
-
- | 64 |
- BXD73 |
- P3 |
- 8 |
- 5448576011_E |
- 605 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/cases.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/cases.rtf
deleted file mode 100644
index 70216c8..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About the strains used to generate this set of data
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/experiment-design.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/experiment-design.rtf
deleted file mode 100644
index 616db01..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/summary.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/summary.rtf
deleted file mode 100644
index 70d7451..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data generated by Dr. Glenn D. Rosen and colleagues
-
-The Neocortex Developmental data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-Some of these data were used in
-Gaglani SM, Lu L, Williams RW, Rosen GD (2009) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 Full Text HTML Version, Full Text PDF Version
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the Striatal Developmental Transcriptome data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Developmental data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. ABOUT THE NEOCORTEX
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/tissue.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/tissue.rtf
deleted file mode 100644
index 51f6e74..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1110/tissue.rtf
+++ /dev/null
@@ -1,536 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected neocortical tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn D. Rosen and colleagues.
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 2 |
- 5384138018_F |
- 236 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 3 |
- 5384138058_A |
- 239 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 2 |
- 5384138018_C |
- 168 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 1 |
- 5448576044_F |
- 167 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 7 |
- 5384138020_A |
- 273 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 4 |
- 5452241022_C |
- 267 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 3 |
- 5384138048_A |
- 107 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 4 |
- 5452241007_A |
- 108 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 6 |
- 5384138009_A |
- 113 |
-
-
- | 10 |
- BXD8 |
- P3 |
- 7 |
- 5384138021_C |
- 115 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 5 |
- 5452241004_F |
- 289 |
-
-
- | 12 |
- BXD9 |
- P3 |
- 4 |
- 5452241022_D |
- 288 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 8 |
- 5237939010_A |
- 117 |
-
-
- | 14 |
- BXD11 |
- P3 |
- 1 |
- 5448576044_D |
- 120 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 6 |
- 5384138009_B |
- 130 |
-
-
- | 16 |
- BXD12 |
- P3 |
- 7 |
- 5384138021_B |
- 132 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 7 |
- 5384138020_F |
- 161 |
-
-
- | 18 |
- BXD13 |
- P3 |
- 5 |
- 5452241004_C |
- 164 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 5 |
- 5452241004_B |
- 158 |
-
-
- | 20 |
- BXD14 |
- P3 |
- 6 |
- 5452241033_D |
- 424 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 3 |
- 5452241008_C |
- 437 |
-
-
- | 22 |
- BXD15 |
- P3 |
- 4 |
- 5452241023_D |
- 438 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 3 |
- 5384138048_D |
- 170 |
-
-
- | 24 |
- BXD16 |
- P3 |
- 4 |
- 5452241007_D |
- 172 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 8 |
- 5448576010_A |
- 390 |
-
-
- | 26 |
- BXD18 |
- P3 |
- 1 |
- 5448576045_E |
- 392 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 8 |
- 5237939010_E |
- 210 |
-
-
- | 28 |
- BXD19 |
- P3 |
- 1 |
- 5448576045_A |
- 211 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 5 |
- 5452241017_B |
- 439 |
-
-
- | 30 |
- BXD20 |
- P3 |
- 6 |
- 5452241033_E |
- 441 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 7 |
- 5384138021_F |
- 341 |
-
-
- | 32 |
- BXD21 |
- P3 |
- 6 |
- 5384138053_F |
- 315 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 8 |
- 5237939012_B |
- 251 |
-
-
- | 34 |
- BXD24a |
- P3 |
- 7 |
- 5384138020_B |
- 250 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 8 |
- 5237939012_D |
- 298 |
-
-
- | 36 |
- BXD27 |
- P3 |
- 1 |
- 5448576045_C |
- 300 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 2 |
- 5384138049_B |
- 550 |
-
-
- | 38 |
- BXD28 |
- P3 |
- 1 |
- 5448576029_F |
- 548 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 2 |
- 5384138047_F |
- 502 |
-
-
- | 40 |
- BXD29 |
- P3 |
- 1 |
- 5448576029_D |
- 501 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 5 |
- 5452241024_D |
- 579 |
-
-
- | 42 |
- BXD31 |
- P3 |
- 6 |
- 5452241035_D |
- 582 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_F |
- 407 |
-
-
- | 44 |
- BXD32 |
- P3 |
- 6 |
- 5452241033_C |
- 408 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 8 |
- 5237939012_F |
- 345 |
-
-
- | 46 |
- BXD34 |
- P3 |
- 4 |
- 5452241022_F |
- 355 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 7 |
- 5384138016_A |
- 429 |
-
-
- | 48 |
- BXD36 |
- P3 |
- 8 |
- 5448576010_D |
- 430 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 2 |
- 5384138041_F |
- 327 |
-
-
- | 50 |
- BXD38 |
- P3 |
- 3 |
- 5384138058_E |
- 328 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 7 |
- 5384138016_E |
- 515 |
-
-
- | 52 |
- BXD39 |
- P3 |
- 5 |
- 5452241024_A |
- 518 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 2 |
- 5384138041_C |
- 373 |
-
-
- | 54 |
- BXD40 |
- P3 |
- 3 |
- 5452241008_A |
- 375 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 3 |
- 5452241008_E |
- 485 |
-
-
- | 56 |
- BXD42 |
- P3 |
- 4 |
- 5452241023_F |
- 486 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 5 |
- 5452241024_F |
- 621 |
-
-
- | 58 |
- BXD51 |
- P3 |
- 6 |
- 5452241035_F |
- 622 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 4 |
- 5452241031_C |
- 554 |
-
-
- | 60 |
- BXD61 |
- P3 |
- 3 |
- 5452241034_A |
- 552 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 2 |
- 5384138049_D |
- 590 |
-
-
- | 62 |
- BXD70 |
- P3 |
- 1 |
- 5448576044_B |
- 589 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 2 |
- 5384138049_E |
- 603 |
-
-
- | 64 |
- BXD73 |
- P3 |
- 8 |
- 5448576011_E |
- 605 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/cases.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/cases.rtf
deleted file mode 100644
index 70216c8..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About the strains used to generate this set of data
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/experiment-design.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/experiment-design.rtf
deleted file mode 100644
index 616db01..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/summary.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/summary.rtf
deleted file mode 100644
index 70d7451..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data generated by Dr. Glenn D. Rosen and colleagues
-
-The Neocortex Developmental data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-Some of these data were used in
-Gaglani SM, Lu L, Williams RW, Rosen GD (2009) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 Full Text HTML Version, Full Text PDF Version
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the Striatal Developmental Transcriptome data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Developmental data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. ABOUT THE NEOCORTEX
diff --git a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/tissue.rtf b/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/tissue.rtf
deleted file mode 100644
index 51f6e74..0000000
--- a/general/datasets/DevNeocortex_ILM6.2P3RInv_1111/tissue.rtf
+++ /dev/null
@@ -1,536 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected neocortical tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn D. Rosen and colleagues.
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 2 |
- 5384138018_F |
- 236 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 3 |
- 5384138058_A |
- 239 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 2 |
- 5384138018_C |
- 168 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 1 |
- 5448576044_F |
- 167 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 7 |
- 5384138020_A |
- 273 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 4 |
- 5452241022_C |
- 267 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 3 |
- 5384138048_A |
- 107 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 4 |
- 5452241007_A |
- 108 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 6 |
- 5384138009_A |
- 113 |
-
-
- | 10 |
- BXD8 |
- P3 |
- 7 |
- 5384138021_C |
- 115 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 5 |
- 5452241004_F |
- 289 |
-
-
- | 12 |
- BXD9 |
- P3 |
- 4 |
- 5452241022_D |
- 288 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 8 |
- 5237939010_A |
- 117 |
-
-
- | 14 |
- BXD11 |
- P3 |
- 1 |
- 5448576044_D |
- 120 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 6 |
- 5384138009_B |
- 130 |
-
-
- | 16 |
- BXD12 |
- P3 |
- 7 |
- 5384138021_B |
- 132 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 7 |
- 5384138020_F |
- 161 |
-
-
- | 18 |
- BXD13 |
- P3 |
- 5 |
- 5452241004_C |
- 164 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 5 |
- 5452241004_B |
- 158 |
-
-
- | 20 |
- BXD14 |
- P3 |
- 6 |
- 5452241033_D |
- 424 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 3 |
- 5452241008_C |
- 437 |
-
-
- | 22 |
- BXD15 |
- P3 |
- 4 |
- 5452241023_D |
- 438 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 3 |
- 5384138048_D |
- 170 |
-
-
- | 24 |
- BXD16 |
- P3 |
- 4 |
- 5452241007_D |
- 172 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 8 |
- 5448576010_A |
- 390 |
-
-
- | 26 |
- BXD18 |
- P3 |
- 1 |
- 5448576045_E |
- 392 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 8 |
- 5237939010_E |
- 210 |
-
-
- | 28 |
- BXD19 |
- P3 |
- 1 |
- 5448576045_A |
- 211 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 5 |
- 5452241017_B |
- 439 |
-
-
- | 30 |
- BXD20 |
- P3 |
- 6 |
- 5452241033_E |
- 441 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 7 |
- 5384138021_F |
- 341 |
-
-
- | 32 |
- BXD21 |
- P3 |
- 6 |
- 5384138053_F |
- 315 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 8 |
- 5237939012_B |
- 251 |
-
-
- | 34 |
- BXD24a |
- P3 |
- 7 |
- 5384138020_B |
- 250 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 8 |
- 5237939012_D |
- 298 |
-
-
- | 36 |
- BXD27 |
- P3 |
- 1 |
- 5448576045_C |
- 300 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 2 |
- 5384138049_B |
- 550 |
-
-
- | 38 |
- BXD28 |
- P3 |
- 1 |
- 5448576029_F |
- 548 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 2 |
- 5384138047_F |
- 502 |
-
-
- | 40 |
- BXD29 |
- P3 |
- 1 |
- 5448576029_D |
- 501 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 5 |
- 5452241024_D |
- 579 |
-
-
- | 42 |
- BXD31 |
- P3 |
- 6 |
- 5452241035_D |
- 582 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_F |
- 407 |
-
-
- | 44 |
- BXD32 |
- P3 |
- 6 |
- 5452241033_C |
- 408 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 8 |
- 5237939012_F |
- 345 |
-
-
- | 46 |
- BXD34 |
- P3 |
- 4 |
- 5452241022_F |
- 355 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 7 |
- 5384138016_A |
- 429 |
-
-
- | 48 |
- BXD36 |
- P3 |
- 8 |
- 5448576010_D |
- 430 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 2 |
- 5384138041_F |
- 327 |
-
-
- | 50 |
- BXD38 |
- P3 |
- 3 |
- 5384138058_E |
- 328 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 7 |
- 5384138016_E |
- 515 |
-
-
- | 52 |
- BXD39 |
- P3 |
- 5 |
- 5452241024_A |
- 518 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 2 |
- 5384138041_C |
- 373 |
-
-
- | 54 |
- BXD40 |
- P3 |
- 3 |
- 5452241008_A |
- 375 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 3 |
- 5452241008_E |
- 485 |
-
-
- | 56 |
- BXD42 |
- P3 |
- 4 |
- 5452241023_F |
- 486 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 5 |
- 5452241024_F |
- 621 |
-
-
- | 58 |
- BXD51 |
- P3 |
- 6 |
- 5452241035_F |
- 622 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 4 |
- 5452241031_C |
- 554 |
-
-
- | 60 |
- BXD61 |
- P3 |
- 3 |
- 5452241034_A |
- 552 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 2 |
- 5384138049_D |
- 590 |
-
-
- | 62 |
- BXD70 |
- P3 |
- 1 |
- 5448576044_B |
- 589 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 2 |
- 5384138049_E |
- 603 |
-
-
- | 64 |
- BXD73 |
- P3 |
- 8 |
- 5448576011_E |
- 605 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/cases.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1110/cases.rtf
deleted file mode 100644
index 74c0f5e..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/experiment-design.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1110/experiment-design.rtf
deleted file mode 100644
index cfea6b0..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/processing.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1110/processing.rtf
deleted file mode 100644
index aee498f..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/summary.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1110/summary.rtf
deleted file mode 100644
index 3515533..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-The BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv ** data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv ** data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse striatum data set may also find the following complementary resources and papers useful:
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. www.rosenlab.net/Movie/P3.mov
-www.rosenlab.net/Movie/P14.mov
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/tissue.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1110/tissue.rtf
deleted file mode 100644
index e9e6151..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1110/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Care was taken to assure that samples were comprised of the dorsal striatum, although it is possible that ventral striatum (accumbens) was occasionally included.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected striatal tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues.
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 8 |
- 5237939012_A |
- 232 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 1 |
- 5448576016_C |
- 234 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 7 |
- 5384138020_C |
- 230 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 6 |
- 5384138053_A |
- 228 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 6 |
- 5384138053_D |
- 270 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 5 |
- 5452241004_E |
- 268 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 2 |
- 5384138018_A |
- 102 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 1 |
- 5448576016_A |
- 101 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 3 |
- 5384138048_B |
- 110 |
-
-
- | 10 |
- BXD9 |
- P3 |
- 2 |
- 5384138041_A |
- 280 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 3 |
- 5384138058_C |
- 278 |
-
-
- | 12 |
- BXD11 |
- P3 |
- 2 |
- 5384138018_B |
- 121 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 3 |
- 5384138048_C |
- 123 |
-
-
- | 14 |
- BXD12 |
- P3 |
- 5 |
- 5452241004_A |
- 127 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 4 |
- 5452241007_B |
- 125 |
-
-
- | 16 |
- BXD13 |
- P3 |
- 8 |
- 5237939010_D |
- 181 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 1 |
- 5448576016_B |
- 183 |
-
-
- | 18 |
- BXD14 |
- P3 |
- 5 |
- 5452241017_A |
- 420 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 4 |
- 5452241023_C |
- 419 |
-
-
- | 20 |
- BXD15 |
- P3 |
- 7 |
- 5384138016_C |
- 475 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 8 |
- 5448576010_F |
- 476 |
-
-
- | 22 |
- BXD16 |
- P3 |
- 6 |
- 5384138009_F |
- 204 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 7 |
- 5384138020_D |
- 205 |
-
-
- | 24 |
- BXD18 |
- P3 |
- 7 |
- 5384138017_B |
- 388 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 3 |
- 5452241008_B |
- 385 |
-
-
- | 26 |
- BXD19 |
- P3 |
- 2 |
- 5384138018_E |
- 212 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 3 |
- 5384138048_F |
- 213 |
-
-
- | 28 |
- BXD20 |
- P3 |
- 2 |
- 5384138047_C |
- 431 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 1 |
- 5448576029_A |
- 431 |
-
-
- | 30 |
- BXD21 |
- P3 |
- 5 |
- 5452241006_A |
- 311 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 4 |
- 5452241022_E |
- 309 |
-
-
- | 32 |
- BXD24a |
- P3 |
- 6 |
- 5384138053_B |
- 247 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 4 |
- 5452241022_B |
- 244 |
-
-
- | 34 |
- BXD27 |
- P3 |
- 7 |
- 5384138021_D |
- 294 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 6 |
- 5384138053_E |
- 293 |
-
-
- | 36 |
- BXD28 |
- P3 |
- 7 |
- 5384138016_F |
- 543 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 8 |
- 5448576011_B |
- 545 |
-
-
- | 38 |
- BXD29 |
- P3 |
- 7 |
- 5384138016_D |
- 495 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 8 |
- 5448576011_A |
- 498 |
-
-
- | 40 |
- BXD31 |
- P3 |
- 4 |
- 5452241031_D |
- 577 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 3 |
- 5452241034_D |
- 575 |
-
-
- | 42 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_E |
- 402 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 4 |
- 5452241023_B |
- 401 |
-
-
- | 44 |
- BXD34 |
- P3 |
- 2 |
- 5384138041_D |
- 348 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 1 |
- 5448576016_E |
- 347 |
-
-
- | 46 |
- BXD36 |
- P3 |
- 2 |
- 5384138047_B |
- 417 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 3 |
- 5452241008_D |
- 418 |
-
-
- | 48 |
- BXD38 |
- P3 |
- 8 |
- 5237939012_E |
- 321 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 1 |
- 5448576016_D |
- 322 |
-
-
- | 50 |
- BXD39 |
- P3 |
- 5 |
- 5452241017_F |
- 511 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 4 |
- 5452241031_A |
- 512 |
-
-
- | 52 |
- BXD40 |
- P3 |
- 8 |
- 5448576010_B |
- 368 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 1 |
- 5448576016_F |
- 371 |
-
-
- | 54 |
- BXD42 |
- P3 |
- 2 |
- 5384138047_E |
- 481 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 1 |
- 5448576029_C |
- 479 |
-
-
- | 56 |
- BXD51 |
- P3 |
- 4 |
- 5452241031_F |
- 616 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 3 |
- 5452241034_F |
- 615 |
-
-
- | 58 |
- BXD61 |
- P3 |
- 5 |
- 5452241024_C |
- 555 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 6 |
- 5452241035_B |
- 557 |
-
-
- | 60 |
- BXD70 |
- P3 |
- 7 |
- 5384138017_E |
- 584 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 8 |
- 5448576011_D |
- 585 |
-
-
- | 62 |
- BXD73 |
- P3 |
- 5 |
- 5452241024_E |
- 600 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 6 |
- 5452241035_E |
- 601 |
-
-
-
- |
-
-
-
-
-
-
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/cases.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1111/cases.rtf
deleted file mode 100644
index 74c0f5e..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/experiment-design.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1111/experiment-design.rtf
deleted file mode 100644
index cfea6b0..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/processing.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1111/processing.rtf
deleted file mode 100644
index aee498f..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/summary.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1111/summary.rtf
deleted file mode 100644
index 3515533..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-The BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv ** data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv ** data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse striatum data set may also find the following complementary resources and papers useful:
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. www.rosenlab.net/Movie/P3.mov
-www.rosenlab.net/Movie/P14.mov
diff --git a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/tissue.rtf b/general/datasets/DevStriatum_ILM6.2P14RInv_1111/tissue.rtf
deleted file mode 100644
index e9e6151..0000000
--- a/general/datasets/DevStriatum_ILM6.2P14RInv_1111/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Care was taken to assure that samples were comprised of the dorsal striatum, although it is possible that ventral striatum (accumbens) was occasionally included.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected striatal tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues.
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 8 |
- 5237939012_A |
- 232 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 1 |
- 5448576016_C |
- 234 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 7 |
- 5384138020_C |
- 230 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 6 |
- 5384138053_A |
- 228 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 6 |
- 5384138053_D |
- 270 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 5 |
- 5452241004_E |
- 268 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 2 |
- 5384138018_A |
- 102 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 1 |
- 5448576016_A |
- 101 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 3 |
- 5384138048_B |
- 110 |
-
-
- | 10 |
- BXD9 |
- P3 |
- 2 |
- 5384138041_A |
- 280 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 3 |
- 5384138058_C |
- 278 |
-
-
- | 12 |
- BXD11 |
- P3 |
- 2 |
- 5384138018_B |
- 121 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 3 |
- 5384138048_C |
- 123 |
-
-
- | 14 |
- BXD12 |
- P3 |
- 5 |
- 5452241004_A |
- 127 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 4 |
- 5452241007_B |
- 125 |
-
-
- | 16 |
- BXD13 |
- P3 |
- 8 |
- 5237939010_D |
- 181 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 1 |
- 5448576016_B |
- 183 |
-
-
- | 18 |
- BXD14 |
- P3 |
- 5 |
- 5452241017_A |
- 420 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 4 |
- 5452241023_C |
- 419 |
-
-
- | 20 |
- BXD15 |
- P3 |
- 7 |
- 5384138016_C |
- 475 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 8 |
- 5448576010_F |
- 476 |
-
-
- | 22 |
- BXD16 |
- P3 |
- 6 |
- 5384138009_F |
- 204 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 7 |
- 5384138020_D |
- 205 |
-
-
- | 24 |
- BXD18 |
- P3 |
- 7 |
- 5384138017_B |
- 388 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 3 |
- 5452241008_B |
- 385 |
-
-
- | 26 |
- BXD19 |
- P3 |
- 2 |
- 5384138018_E |
- 212 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 3 |
- 5384138048_F |
- 213 |
-
-
- | 28 |
- BXD20 |
- P3 |
- 2 |
- 5384138047_C |
- 431 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 1 |
- 5448576029_A |
- 431 |
-
-
- | 30 |
- BXD21 |
- P3 |
- 5 |
- 5452241006_A |
- 311 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 4 |
- 5452241022_E |
- 309 |
-
-
- | 32 |
- BXD24a |
- P3 |
- 6 |
- 5384138053_B |
- 247 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 4 |
- 5452241022_B |
- 244 |
-
-
- | 34 |
- BXD27 |
- P3 |
- 7 |
- 5384138021_D |
- 294 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 6 |
- 5384138053_E |
- 293 |
-
-
- | 36 |
- BXD28 |
- P3 |
- 7 |
- 5384138016_F |
- 543 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 8 |
- 5448576011_B |
- 545 |
-
-
- | 38 |
- BXD29 |
- P3 |
- 7 |
- 5384138016_D |
- 495 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 8 |
- 5448576011_A |
- 498 |
-
-
- | 40 |
- BXD31 |
- P3 |
- 4 |
- 5452241031_D |
- 577 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 3 |
- 5452241034_D |
- 575 |
-
-
- | 42 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_E |
- 402 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 4 |
- 5452241023_B |
- 401 |
-
-
- | 44 |
- BXD34 |
- P3 |
- 2 |
- 5384138041_D |
- 348 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 1 |
- 5448576016_E |
- 347 |
-
-
- | 46 |
- BXD36 |
- P3 |
- 2 |
- 5384138047_B |
- 417 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 3 |
- 5452241008_D |
- 418 |
-
-
- | 48 |
- BXD38 |
- P3 |
- 8 |
- 5237939012_E |
- 321 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 1 |
- 5448576016_D |
- 322 |
-
-
- | 50 |
- BXD39 |
- P3 |
- 5 |
- 5452241017_F |
- 511 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 4 |
- 5452241031_A |
- 512 |
-
-
- | 52 |
- BXD40 |
- P3 |
- 8 |
- 5448576010_B |
- 368 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 1 |
- 5448576016_F |
- 371 |
-
-
- | 54 |
- BXD42 |
- P3 |
- 2 |
- 5384138047_E |
- 481 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 1 |
- 5448576029_C |
- 479 |
-
-
- | 56 |
- BXD51 |
- P3 |
- 4 |
- 5452241031_F |
- 616 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 3 |
- 5452241034_F |
- 615 |
-
-
- | 58 |
- BXD61 |
- P3 |
- 5 |
- 5452241024_C |
- 555 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 6 |
- 5452241035_B |
- 557 |
-
-
- | 60 |
- BXD70 |
- P3 |
- 7 |
- 5384138017_E |
- 584 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 8 |
- 5448576011_D |
- 585 |
-
-
- | 62 |
- BXD73 |
- P3 |
- 5 |
- 5452241024_E |
- 600 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 6 |
- 5452241035_E |
- 601 |
-
-
-
- |
-
-
-
-
-
-
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/cases.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1110/cases.rtf
deleted file mode 100644
index 74c0f5e..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/experiment-design.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1110/experiment-design.rtf
deleted file mode 100644
index cfea6b0..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/processing.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1110/processing.rtf
deleted file mode 100644
index aee498f..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/summary.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1110/summary.rtf
deleted file mode 100644
index 3515533..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-The BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv ** data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv ** data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse striatum data set may also find the following complementary resources and papers useful:
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. www.rosenlab.net/Movie/P3.mov
-www.rosenlab.net/Movie/P14.mov
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/tissue.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1110/tissue.rtf
deleted file mode 100644
index e9e6151..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1110/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Care was taken to assure that samples were comprised of the dorsal striatum, although it is possible that ventral striatum (accumbens) was occasionally included.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected striatal tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues.
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 8 |
- 5237939012_A |
- 232 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 1 |
- 5448576016_C |
- 234 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 7 |
- 5384138020_C |
- 230 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 6 |
- 5384138053_A |
- 228 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 6 |
- 5384138053_D |
- 270 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 5 |
- 5452241004_E |
- 268 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 2 |
- 5384138018_A |
- 102 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 1 |
- 5448576016_A |
- 101 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 3 |
- 5384138048_B |
- 110 |
-
-
- | 10 |
- BXD9 |
- P3 |
- 2 |
- 5384138041_A |
- 280 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 3 |
- 5384138058_C |
- 278 |
-
-
- | 12 |
- BXD11 |
- P3 |
- 2 |
- 5384138018_B |
- 121 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 3 |
- 5384138048_C |
- 123 |
-
-
- | 14 |
- BXD12 |
- P3 |
- 5 |
- 5452241004_A |
- 127 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 4 |
- 5452241007_B |
- 125 |
-
-
- | 16 |
- BXD13 |
- P3 |
- 8 |
- 5237939010_D |
- 181 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 1 |
- 5448576016_B |
- 183 |
-
-
- | 18 |
- BXD14 |
- P3 |
- 5 |
- 5452241017_A |
- 420 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 4 |
- 5452241023_C |
- 419 |
-
-
- | 20 |
- BXD15 |
- P3 |
- 7 |
- 5384138016_C |
- 475 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 8 |
- 5448576010_F |
- 476 |
-
-
- | 22 |
- BXD16 |
- P3 |
- 6 |
- 5384138009_F |
- 204 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 7 |
- 5384138020_D |
- 205 |
-
-
- | 24 |
- BXD18 |
- P3 |
- 7 |
- 5384138017_B |
- 388 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 3 |
- 5452241008_B |
- 385 |
-
-
- | 26 |
- BXD19 |
- P3 |
- 2 |
- 5384138018_E |
- 212 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 3 |
- 5384138048_F |
- 213 |
-
-
- | 28 |
- BXD20 |
- P3 |
- 2 |
- 5384138047_C |
- 431 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 1 |
- 5448576029_A |
- 431 |
-
-
- | 30 |
- BXD21 |
- P3 |
- 5 |
- 5452241006_A |
- 311 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 4 |
- 5452241022_E |
- 309 |
-
-
- | 32 |
- BXD24a |
- P3 |
- 6 |
- 5384138053_B |
- 247 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 4 |
- 5452241022_B |
- 244 |
-
-
- | 34 |
- BXD27 |
- P3 |
- 7 |
- 5384138021_D |
- 294 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 6 |
- 5384138053_E |
- 293 |
-
-
- | 36 |
- BXD28 |
- P3 |
- 7 |
- 5384138016_F |
- 543 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 8 |
- 5448576011_B |
- 545 |
-
-
- | 38 |
- BXD29 |
- P3 |
- 7 |
- 5384138016_D |
- 495 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 8 |
- 5448576011_A |
- 498 |
-
-
- | 40 |
- BXD31 |
- P3 |
- 4 |
- 5452241031_D |
- 577 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 3 |
- 5452241034_D |
- 575 |
-
-
- | 42 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_E |
- 402 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 4 |
- 5452241023_B |
- 401 |
-
-
- | 44 |
- BXD34 |
- P3 |
- 2 |
- 5384138041_D |
- 348 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 1 |
- 5448576016_E |
- 347 |
-
-
- | 46 |
- BXD36 |
- P3 |
- 2 |
- 5384138047_B |
- 417 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 3 |
- 5452241008_D |
- 418 |
-
-
- | 48 |
- BXD38 |
- P3 |
- 8 |
- 5237939012_E |
- 321 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 1 |
- 5448576016_D |
- 322 |
-
-
- | 50 |
- BXD39 |
- P3 |
- 5 |
- 5452241017_F |
- 511 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 4 |
- 5452241031_A |
- 512 |
-
-
- | 52 |
- BXD40 |
- P3 |
- 8 |
- 5448576010_B |
- 368 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 1 |
- 5448576016_F |
- 371 |
-
-
- | 54 |
- BXD42 |
- P3 |
- 2 |
- 5384138047_E |
- 481 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 1 |
- 5448576029_C |
- 479 |
-
-
- | 56 |
- BXD51 |
- P3 |
- 4 |
- 5452241031_F |
- 616 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 3 |
- 5452241034_F |
- 615 |
-
-
- | 58 |
- BXD61 |
- P3 |
- 5 |
- 5452241024_C |
- 555 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 6 |
- 5452241035_B |
- 557 |
-
-
- | 60 |
- BXD70 |
- P3 |
- 7 |
- 5384138017_E |
- 584 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 8 |
- 5448576011_D |
- 585 |
-
-
- | 62 |
- BXD73 |
- P3 |
- 5 |
- 5452241024_E |
- 600 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 6 |
- 5452241035_E |
- 601 |
-
-
-
- |
-
-
-
-
-
-
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/cases.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1111/cases.rtf
deleted file mode 100644
index 74c0f5e..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 28 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 4 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/experiment-design.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1111/experiment-design.rtf
deleted file mode 100644
index cfea6b0..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set consists arrays processed in 8 groups over a 2 month period (from July-August 2010). All groups consisted of 24 samples. All arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Lorne Rose. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/processing.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1111/processing.rtf
deleted file mode 100644
index aee498f..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Samples were processed by Lorne Rose and colleagues in the Illumina Core at UTHSC between July and August 2010. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/summary.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1111/summary.rtf
deleted file mode 100644
index 3515533..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-The BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv ** data set provides estimates of mRNA expression during two developmental ages (postnatal days 3 and 14) in the cerebral cortex from 32 BXD strains. All samples are from normal animals raised and bred in a standard laboratory environment.
-
-All samples were processed using 32 Illumina Sentrix v6.2 BeadArray slides. All samples passed stringent quality control and error checking. This data set is a companion to the BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv ** data set and was processed using identical methods and the same strains. This data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this data set, xxxx probes have LRS values >46 (LOD >10).
-
-Users of these mouse striatum data set may also find the following complementary resources and papers useful:
-
-A movie of the dissection of the brain by Dr. Glenn Rosen. www.rosenlab.net/Movie/P3.mov
-www.rosenlab.net/Movie/P14.mov
diff --git a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/tissue.rtf b/general/datasets/DevStriatum_ILM6.2P3RInv_1111/tissue.rtf
deleted file mode 100644
index e9e6151..0000000
--- a/general/datasets/DevStriatum_ILM6.2P3RInv_1111/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All animals were raised at Beth Israel Deaconess Medical Center in SPF facilities from stock obtained from either Jackson Laboratory or UTHSC. All mice were killed by decapitation. Whole brain dissections were performed at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues. Care was taken to assure that samples were comprised of the dorsal striatum, although it is possible that ventral striatum (accumbens) was occasionally included.
-
-All animals used in this study were either 3 or 14 days of age. A pool of dissected striatal tissue from three naive animals of the same strain and age were collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at Beth Israel Deaconess Medical Center by Glenn Rosen and colleagues.
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Age |
- Batch ID |
- Sample ID |
- Tube ID |
-
-
- | 1 |
- BXD1 |
- P3 |
- 8 |
- 5237939012_A |
- 232 |
-
-
- | 2 |
- BXD1 |
- P3 |
- 1 |
- 5448576016_C |
- 234 |
-
-
- | 3 |
- BXD2 |
- P3 |
- 7 |
- 5384138020_C |
- 230 |
-
-
- | 4 |
- BXD2 |
- P3 |
- 6 |
- 5384138053_A |
- 228 |
-
-
- | 5 |
- BXD5 |
- P3 |
- 6 |
- 5384138053_D |
- 270 |
-
-
- | 6 |
- BXD5 |
- P3 |
- 5 |
- 5452241004_E |
- 268 |
-
-
- | 7 |
- BXD6 |
- P3 |
- 2 |
- 5384138018_A |
- 102 |
-
-
- | 8 |
- BXD6 |
- P3 |
- 1 |
- 5448576016_A |
- 101 |
-
-
- | 9 |
- BXD8 |
- P3 |
- 3 |
- 5384138048_B |
- 110 |
-
-
- | 10 |
- BXD9 |
- P3 |
- 2 |
- 5384138041_A |
- 280 |
-
-
- | 11 |
- BXD9 |
- P3 |
- 3 |
- 5384138058_C |
- 278 |
-
-
- | 12 |
- BXD11 |
- P3 |
- 2 |
- 5384138018_B |
- 121 |
-
-
- | 13 |
- BXD11 |
- P3 |
- 3 |
- 5384138048_C |
- 123 |
-
-
- | 14 |
- BXD12 |
- P3 |
- 5 |
- 5452241004_A |
- 127 |
-
-
- | 15 |
- BXD12 |
- P3 |
- 4 |
- 5452241007_B |
- 125 |
-
-
- | 16 |
- BXD13 |
- P3 |
- 8 |
- 5237939010_D |
- 181 |
-
-
- | 17 |
- BXD13 |
- P3 |
- 1 |
- 5448576016_B |
- 183 |
-
-
- | 18 |
- BXD14 |
- P3 |
- 5 |
- 5452241017_A |
- 420 |
-
-
- | 19 |
- BXD14 |
- P3 |
- 4 |
- 5452241023_C |
- 419 |
-
-
- | 20 |
- BXD15 |
- P3 |
- 7 |
- 5384138016_C |
- 475 |
-
-
- | 21 |
- BXD15 |
- P3 |
- 8 |
- 5448576010_F |
- 476 |
-
-
- | 22 |
- BXD16 |
- P3 |
- 6 |
- 5384138009_F |
- 204 |
-
-
- | 23 |
- BXD16 |
- P3 |
- 7 |
- 5384138020_D |
- 205 |
-
-
- | 24 |
- BXD18 |
- P3 |
- 7 |
- 5384138017_B |
- 388 |
-
-
- | 25 |
- BXD18 |
- P3 |
- 3 |
- 5452241008_B |
- 385 |
-
-
- | 26 |
- BXD19 |
- P3 |
- 2 |
- 5384138018_E |
- 212 |
-
-
- | 27 |
- BXD19 |
- P3 |
- 3 |
- 5384138048_F |
- 213 |
-
-
- | 28 |
- BXD20 |
- P3 |
- 2 |
- 5384138047_C |
- 431 |
-
-
- | 29 |
- BXD20 |
- P3 |
- 1 |
- 5448576029_A |
- 431 |
-
-
- | 30 |
- BXD21 |
- P3 |
- 5 |
- 5452241006_A |
- 311 |
-
-
- | 31 |
- BXD21 |
- P3 |
- 4 |
- 5452241022_E |
- 309 |
-
-
- | 32 |
- BXD24a |
- P3 |
- 6 |
- 5384138053_B |
- 247 |
-
-
- | 33 |
- BXD24a |
- P3 |
- 4 |
- 5452241022_B |
- 244 |
-
-
- | 34 |
- BXD27 |
- P3 |
- 7 |
- 5384138021_D |
- 294 |
-
-
- | 35 |
- BXD27 |
- P3 |
- 6 |
- 5384138053_E |
- 293 |
-
-
- | 36 |
- BXD28 |
- P3 |
- 7 |
- 5384138016_F |
- 543 |
-
-
- | 37 |
- BXD28 |
- P3 |
- 8 |
- 5448576011_B |
- 545 |
-
-
- | 38 |
- BXD29 |
- P3 |
- 7 |
- 5384138016_D |
- 495 |
-
-
- | 39 |
- BXD29 |
- P3 |
- 8 |
- 5448576011_A |
- 498 |
-
-
- | 40 |
- BXD31 |
- P3 |
- 4 |
- 5452241031_D |
- 577 |
-
-
- | 41 |
- BXD31 |
- P3 |
- 3 |
- 5452241034_D |
- 575 |
-
-
- | 42 |
- BXD32 |
- P3 |
- 5 |
- 5452241006_E |
- 402 |
-
-
- | 43 |
- BXD32 |
- P3 |
- 4 |
- 5452241023_B |
- 401 |
-
-
- | 44 |
- BXD34 |
- P3 |
- 2 |
- 5384138041_D |
- 348 |
-
-
- | 45 |
- BXD34 |
- P3 |
- 1 |
- 5448576016_E |
- 347 |
-
-
- | 46 |
- BXD36 |
- P3 |
- 2 |
- 5384138047_B |
- 417 |
-
-
- | 47 |
- BXD36 |
- P3 |
- 3 |
- 5452241008_D |
- 418 |
-
-
- | 48 |
- BXD38 |
- P3 |
- 8 |
- 5237939012_E |
- 321 |
-
-
- | 49 |
- BXD38 |
- P3 |
- 1 |
- 5448576016_D |
- 322 |
-
-
- | 50 |
- BXD39 |
- P3 |
- 5 |
- 5452241017_F |
- 511 |
-
-
- | 51 |
- BXD39 |
- P3 |
- 4 |
- 5452241031_A |
- 512 |
-
-
- | 52 |
- BXD40 |
- P3 |
- 8 |
- 5448576010_B |
- 368 |
-
-
- | 53 |
- BXD40 |
- P3 |
- 1 |
- 5448576016_F |
- 371 |
-
-
- | 54 |
- BXD42 |
- P3 |
- 2 |
- 5384138047_E |
- 481 |
-
-
- | 55 |
- BXD42 |
- P3 |
- 1 |
- 5448576029_C |
- 479 |
-
-
- | 56 |
- BXD51 |
- P3 |
- 4 |
- 5452241031_F |
- 616 |
-
-
- | 57 |
- BXD51 |
- P3 |
- 3 |
- 5452241034_F |
- 615 |
-
-
- | 58 |
- BXD61 |
- P3 |
- 5 |
- 5452241024_C |
- 555 |
-
-
- | 59 |
- BXD61 |
- P3 |
- 6 |
- 5452241035_B |
- 557 |
-
-
- | 60 |
- BXD70 |
- P3 |
- 7 |
- 5384138017_E |
- 584 |
-
-
- | 61 |
- BXD70 |
- P3 |
- 8 |
- 5448576011_D |
- 585 |
-
-
- | 62 |
- BXD73 |
- P3 |
- 5 |
- 5452241024_E |
- 600 |
-
-
- | 63 |
- BXD73 |
- P3 |
- 6 |
- 5452241035_E |
- 601 |
-
-
-
- |
-
-
-
-
-
-
diff --git a/general/datasets/EPFLBXDprot0513/cases.rtf b/general/datasets/EPFLBXDprot0513/cases.rtf
deleted file mode 100644
index ed4ced8..0000000
--- a/general/datasets/EPFLBXDprot0513/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-40 strains of the BXD family (BXD43 – BXD103) and both parental strains (C57BL/6 and DBA/2) were born and raised at the EPFL in Switzerland prior to inclusion in this study. For each strain, 10 male animals were born and then separated evenly into two cohorts at 8 weeks of age: 5 animals per strain on a chow diet (6% kcal/fat, 20% protein, 74% carbohydrate) and 5 animals per strain on high fat diet (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. Animals were fasted overnight prior to sacrifice, which occurred between 9am and 11am after isoflurane anesthesia and perfusion. The gall bladder was removed, and then the livers were immediately frozen in liquid nitrogen.
diff --git a/general/datasets/EPFLBXDprot0513/notes.rtf b/general/datasets/EPFLBXDprot0513/notes.rtf
deleted file mode 100644
index ecdae60..0000000
--- a/general/datasets/EPFLBXDprot0513/notes.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-SWATH
-
-SWATH MS is a novel technique that is based on data-independent acquisition (DIA) which aims to complement traditional mass spectrometry-based proteomics techniques such as shotgun and SRM methods. In principal, it allows a complete and permanent recording of all fragment ions of all peptide precursors in a biological sample and can thus potentially combine the advantages of shotgun (high throughput) with those of SRM (high reproducibility and sensitivity).
-
-The method uniquely combines a DIA methods with a innovative data analysis approach based on targeted data extraction developed in the Aebersold lab. Like in other DIA methods, the mass spectrometer cycles through precursor acquisition windows designed to cover the whole range of 400-1200 m/z - in which most of the proteotypic peptide precursors of an organism fall - within 2-4 seconds. During each cycle, the mass spectrometer will fragment all precursors from a given precursors window (e.g. 475 - 500 m/z for 25 Da windows) and record a complete, high accuracy fragment ion spectrum. The same range will be fragmented again in the next cycle, thus providing a time-resolved recording of fragment ions that elute on the chromatography. Thus the SWATH method provides highly multiplexed fragment ion spectra that are deterministically recorded over the complete chromatographic time.
-
-In the Malmstroem group, we are interested in the data-analysis challenge that is posed by DIA / SWATH data. Traditionally, DIA methods have been analyzed by trying to reconstruct the lineage of precursor and fragment ions based on their chromatographic elution profile, and then analysing the data in a workflow similar to those used in shotgun proteomics. However, these approaches suffered from low sensitivity and propagation of errors due to mis-assignment of fragment ions to precursor ions. We are thus working on automating targeted methods that are conceptually similar to SRM and allow querying the data multiple times with specific hypothesis, thus giving the researcher more control and specificity in the bioinformatic data analysis step. With these novel algorithms, it is potentially possible to explore a much larger part of the data that is present and obtain a nearly complete picture of a proteome.
-
-References
-
-
- - Gillet, L. C., P. Navarro, S. Tate, H. Röst, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold (2012, June). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Molecular & cellular proteomics : MCP 11 (6). PMID 22261725
- - Purvine, S., J.-T. T. Eppel, E. C. Yi, and D. R. Goodlett (2003, June). Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3 (6), 847-850.
- - Plumb, R. S., K. A. Johnson, P. Rainville, B. W. Smith, I. D. Wilson, J. M. Castro-Perez, and J. K. Nicholson (2006). UPLC/MS(e); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid communications in mass spectrometry : RCM 20 (13), 1989-1994.
- - Panchaud, A., A. Scherl, S. A. Shaffer, P. D. von Haller, H. D. Kulasekara, S. I. Miller, and D. R. Goodlett (2009, August). Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Analytical chemistry 81 (15), 6481-6488.
-
diff --git a/general/datasets/EPFLBXDprot0513/platform.rtf b/general/datasets/EPFLBXDprot0513/platform.rtf
deleted file mode 100644
index 4a33b7c..0000000
--- a/general/datasets/EPFLBXDprot0513/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All 81 arrays were Affymetrix Mouse Gene 1.0 ST, run together in a single batch in March/April 2013 at the University of Tennessee Health Science Center.
diff --git a/general/datasets/EPFLBXDprot0513/summary.rtf b/general/datasets/EPFLBXDprot0513/summary.rtf
deleted file mode 100644
index 8797309..0000000
--- a/general/datasets/EPFLBXDprot0513/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Quantitative changes in transcriptome and proteome patterns relate genomic variation to specific phenotypes. Here we applied selected reaction monitoring (SRM), a targeted mass spectrometry method that supports the reliable and reproducible quantification of predetermined sets of proteins across a broad abundance range in complex samples to quantify 157 metabolic proteins in liver extracts from 40 genetically-diverse strains of the BXD mouse genetic reference population, after chow or high fat diet. We observed significant biological variation in protein levels, which were linked to transcript variation in ~30% of the cases. 14 genes mapped to quantitative trait loci (QTLs) at both the transcript and protein level, while a further 18 mapped only as transcripts (eQTLs), and 24 only as proteins (pQTLs). 79% of eQTLs were regulated by cis-mechanisms, as opposed to only 31% of pQTLs, indicating a more direct genetic connection between genes and their transcripts than between genes and their protein products. In some cases, QTLs could be linked to phenotypic changes across the BXDs. One such case indicates a novel animal model for an inborn error of metabolism that has been observed in humans; BXD mice with deficient DHTKD1 protein also exhibit 2-aminoadipic and 2-oxoadipic aciduria like seen in affected patients. Together, these findings show that quantitative, multi-layered genomic, transcriptomic, and proteomic analyses provide more power for connecting genetic variance to phenotypes in complex systems than each layer alone, and provide complementary information to identify novel regulatory networks of metabolic diseases.
-
-Note: please see associated dataset “Liver Proteome” EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (Jul13) RPN” for protein data in the same animals. [NB: Data in review, but still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
-
-Note: please see associated dataset “LISP2” in BXD phenotypes for phenotype data on the same animals. [NB: Still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
diff --git a/general/datasets/EPFLBXDprot0513/tissue.rtf b/general/datasets/EPFLBXDprot0513/tissue.rtf
deleted file mode 100644
index f95e2c4..0000000
--- a/general/datasets/EPFLBXDprot0513/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers were later shattered in liquid nitrogen and ~100 mg fragments were taken at random from the left, right, or caudate lobes. To account for this discrepancy, all ~5 animals per cohort had their RNA prepared, and then were pooled evenly (by µg of RNA) into a single RNA sample for each cohort. These pooled RNA samples of approximately 30 µg RNA were then purified using RNEasy, then sent out for array analysis. All RIN values were > 8.0.
diff --git a/general/datasets/EPFLBXDprotCD0513/cases.rtf b/general/datasets/EPFLBXDprotCD0513/cases.rtf
deleted file mode 100644
index ed4ced8..0000000
--- a/general/datasets/EPFLBXDprotCD0513/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-40 strains of the BXD family (BXD43 – BXD103) and both parental strains (C57BL/6 and DBA/2) were born and raised at the EPFL in Switzerland prior to inclusion in this study. For each strain, 10 male animals were born and then separated evenly into two cohorts at 8 weeks of age: 5 animals per strain on a chow diet (6% kcal/fat, 20% protein, 74% carbohydrate) and 5 animals per strain on high fat diet (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. Animals were fasted overnight prior to sacrifice, which occurred between 9am and 11am after isoflurane anesthesia and perfusion. The gall bladder was removed, and then the livers were immediately frozen in liquid nitrogen.
diff --git a/general/datasets/EPFLBXDprotCD0513/notes.rtf b/general/datasets/EPFLBXDprotCD0513/notes.rtf
deleted file mode 100644
index ecdae60..0000000
--- a/general/datasets/EPFLBXDprotCD0513/notes.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-SWATH
-
-SWATH MS is a novel technique that is based on data-independent acquisition (DIA) which aims to complement traditional mass spectrometry-based proteomics techniques such as shotgun and SRM methods. In principal, it allows a complete and permanent recording of all fragment ions of all peptide precursors in a biological sample and can thus potentially combine the advantages of shotgun (high throughput) with those of SRM (high reproducibility and sensitivity).
-
-The method uniquely combines a DIA methods with a innovative data analysis approach based on targeted data extraction developed in the Aebersold lab. Like in other DIA methods, the mass spectrometer cycles through precursor acquisition windows designed to cover the whole range of 400-1200 m/z - in which most of the proteotypic peptide precursors of an organism fall - within 2-4 seconds. During each cycle, the mass spectrometer will fragment all precursors from a given precursors window (e.g. 475 - 500 m/z for 25 Da windows) and record a complete, high accuracy fragment ion spectrum. The same range will be fragmented again in the next cycle, thus providing a time-resolved recording of fragment ions that elute on the chromatography. Thus the SWATH method provides highly multiplexed fragment ion spectra that are deterministically recorded over the complete chromatographic time.
-
-In the Malmstroem group, we are interested in the data-analysis challenge that is posed by DIA / SWATH data. Traditionally, DIA methods have been analyzed by trying to reconstruct the lineage of precursor and fragment ions based on their chromatographic elution profile, and then analysing the data in a workflow similar to those used in shotgun proteomics. However, these approaches suffered from low sensitivity and propagation of errors due to mis-assignment of fragment ions to precursor ions. We are thus working on automating targeted methods that are conceptually similar to SRM and allow querying the data multiple times with specific hypothesis, thus giving the researcher more control and specificity in the bioinformatic data analysis step. With these novel algorithms, it is potentially possible to explore a much larger part of the data that is present and obtain a nearly complete picture of a proteome.
-
-References
-
-
- - Gillet, L. C., P. Navarro, S. Tate, H. Röst, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold (2012, June). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Molecular & cellular proteomics : MCP 11 (6). PMID 22261725
- - Purvine, S., J.-T. T. Eppel, E. C. Yi, and D. R. Goodlett (2003, June). Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3 (6), 847-850.
- - Plumb, R. S., K. A. Johnson, P. Rainville, B. W. Smith, I. D. Wilson, J. M. Castro-Perez, and J. K. Nicholson (2006). UPLC/MS(e); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid communications in mass spectrometry : RCM 20 (13), 1989-1994.
- - Panchaud, A., A. Scherl, S. A. Shaffer, P. D. von Haller, H. D. Kulasekara, S. I. Miller, and D. R. Goodlett (2009, August). Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Analytical chemistry 81 (15), 6481-6488.
-
diff --git a/general/datasets/EPFLBXDprotCD0513/platform.rtf b/general/datasets/EPFLBXDprotCD0513/platform.rtf
deleted file mode 100644
index 4a33b7c..0000000
--- a/general/datasets/EPFLBXDprotCD0513/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All 81 arrays were Affymetrix Mouse Gene 1.0 ST, run together in a single batch in March/April 2013 at the University of Tennessee Health Science Center.
diff --git a/general/datasets/EPFLBXDprotCD0513/summary.rtf b/general/datasets/EPFLBXDprotCD0513/summary.rtf
deleted file mode 100644
index 8797309..0000000
--- a/general/datasets/EPFLBXDprotCD0513/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Quantitative changes in transcriptome and proteome patterns relate genomic variation to specific phenotypes. Here we applied selected reaction monitoring (SRM), a targeted mass spectrometry method that supports the reliable and reproducible quantification of predetermined sets of proteins across a broad abundance range in complex samples to quantify 157 metabolic proteins in liver extracts from 40 genetically-diverse strains of the BXD mouse genetic reference population, after chow or high fat diet. We observed significant biological variation in protein levels, which were linked to transcript variation in ~30% of the cases. 14 genes mapped to quantitative trait loci (QTLs) at both the transcript and protein level, while a further 18 mapped only as transcripts (eQTLs), and 24 only as proteins (pQTLs). 79% of eQTLs were regulated by cis-mechanisms, as opposed to only 31% of pQTLs, indicating a more direct genetic connection between genes and their transcripts than between genes and their protein products. In some cases, QTLs could be linked to phenotypic changes across the BXDs. One such case indicates a novel animal model for an inborn error of metabolism that has been observed in humans; BXD mice with deficient DHTKD1 protein also exhibit 2-aminoadipic and 2-oxoadipic aciduria like seen in affected patients. Together, these findings show that quantitative, multi-layered genomic, transcriptomic, and proteomic analyses provide more power for connecting genetic variance to phenotypes in complex systems than each layer alone, and provide complementary information to identify novel regulatory networks of metabolic diseases.
-
-Note: please see associated dataset “Liver Proteome” EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (Jul13) RPN” for protein data in the same animals. [NB: Data in review, but still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
-
-Note: please see associated dataset “LISP2” in BXD phenotypes for phenotype data on the same animals. [NB: Still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
diff --git a/general/datasets/EPFLBXDprotCD0513/tissue.rtf b/general/datasets/EPFLBXDprotCD0513/tissue.rtf
deleted file mode 100644
index f95e2c4..0000000
--- a/general/datasets/EPFLBXDprotCD0513/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers were later shattered in liquid nitrogen and ~100 mg fragments were taken at random from the left, right, or caudate lobes. To account for this discrepancy, all ~5 animals per cohort had their RNA prepared, and then were pooled evenly (by µg of RNA) into a single RNA sample for each cohort. These pooled RNA samples of approximately 30 µg RNA were then purified using RNEasy, then sent out for array analysis. All RIN values were > 8.0.
diff --git a/general/datasets/EPFLBXDprotCDRPN0513/cases.rtf b/general/datasets/EPFLBXDprotCDRPN0513/cases.rtf
deleted file mode 100644
index ed4ced8..0000000
--- a/general/datasets/EPFLBXDprotCDRPN0513/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-40 strains of the BXD family (BXD43 – BXD103) and both parental strains (C57BL/6 and DBA/2) were born and raised at the EPFL in Switzerland prior to inclusion in this study. For each strain, 10 male animals were born and then separated evenly into two cohorts at 8 weeks of age: 5 animals per strain on a chow diet (6% kcal/fat, 20% protein, 74% carbohydrate) and 5 animals per strain on high fat diet (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. Animals were fasted overnight prior to sacrifice, which occurred between 9am and 11am after isoflurane anesthesia and perfusion. The gall bladder was removed, and then the livers were immediately frozen in liquid nitrogen.
diff --git a/general/datasets/EPFLBXDprotCDRPN0513/notes.rtf b/general/datasets/EPFLBXDprotCDRPN0513/notes.rtf
deleted file mode 100644
index ecdae60..0000000
--- a/general/datasets/EPFLBXDprotCDRPN0513/notes.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-SWATH
-
-SWATH MS is a novel technique that is based on data-independent acquisition (DIA) which aims to complement traditional mass spectrometry-based proteomics techniques such as shotgun and SRM methods. In principal, it allows a complete and permanent recording of all fragment ions of all peptide precursors in a biological sample and can thus potentially combine the advantages of shotgun (high throughput) with those of SRM (high reproducibility and sensitivity).
-
-The method uniquely combines a DIA methods with a innovative data analysis approach based on targeted data extraction developed in the Aebersold lab. Like in other DIA methods, the mass spectrometer cycles through precursor acquisition windows designed to cover the whole range of 400-1200 m/z - in which most of the proteotypic peptide precursors of an organism fall - within 2-4 seconds. During each cycle, the mass spectrometer will fragment all precursors from a given precursors window (e.g. 475 - 500 m/z for 25 Da windows) and record a complete, high accuracy fragment ion spectrum. The same range will be fragmented again in the next cycle, thus providing a time-resolved recording of fragment ions that elute on the chromatography. Thus the SWATH method provides highly multiplexed fragment ion spectra that are deterministically recorded over the complete chromatographic time.
-
-In the Malmstroem group, we are interested in the data-analysis challenge that is posed by DIA / SWATH data. Traditionally, DIA methods have been analyzed by trying to reconstruct the lineage of precursor and fragment ions based on their chromatographic elution profile, and then analysing the data in a workflow similar to those used in shotgun proteomics. However, these approaches suffered from low sensitivity and propagation of errors due to mis-assignment of fragment ions to precursor ions. We are thus working on automating targeted methods that are conceptually similar to SRM and allow querying the data multiple times with specific hypothesis, thus giving the researcher more control and specificity in the bioinformatic data analysis step. With these novel algorithms, it is potentially possible to explore a much larger part of the data that is present and obtain a nearly complete picture of a proteome.
-
-References
-
-
- - Gillet, L. C., P. Navarro, S. Tate, H. Röst, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold (2012, June). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Molecular & cellular proteomics : MCP 11 (6). PMID 22261725
- - Purvine, S., J.-T. T. Eppel, E. C. Yi, and D. R. Goodlett (2003, June). Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3 (6), 847-850.
- - Plumb, R. S., K. A. Johnson, P. Rainville, B. W. Smith, I. D. Wilson, J. M. Castro-Perez, and J. K. Nicholson (2006). UPLC/MS(e); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid communications in mass spectrometry : RCM 20 (13), 1989-1994.
- - Panchaud, A., A. Scherl, S. A. Shaffer, P. D. von Haller, H. D. Kulasekara, S. I. Miller, and D. R. Goodlett (2009, August). Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Analytical chemistry 81 (15), 6481-6488.
-
diff --git a/general/datasets/EPFLBXDprotCDRPN0513/platform.rtf b/general/datasets/EPFLBXDprotCDRPN0513/platform.rtf
deleted file mode 100644
index 4a33b7c..0000000
--- a/general/datasets/EPFLBXDprotCDRPN0513/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All 81 arrays were Affymetrix Mouse Gene 1.0 ST, run together in a single batch in March/April 2013 at the University of Tennessee Health Science Center.
diff --git a/general/datasets/EPFLBXDprotCDRPN0513/summary.rtf b/general/datasets/EPFLBXDprotCDRPN0513/summary.rtf
deleted file mode 100644
index 8797309..0000000
--- a/general/datasets/EPFLBXDprotCDRPN0513/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Quantitative changes in transcriptome and proteome patterns relate genomic variation to specific phenotypes. Here we applied selected reaction monitoring (SRM), a targeted mass spectrometry method that supports the reliable and reproducible quantification of predetermined sets of proteins across a broad abundance range in complex samples to quantify 157 metabolic proteins in liver extracts from 40 genetically-diverse strains of the BXD mouse genetic reference population, after chow or high fat diet. We observed significant biological variation in protein levels, which were linked to transcript variation in ~30% of the cases. 14 genes mapped to quantitative trait loci (QTLs) at both the transcript and protein level, while a further 18 mapped only as transcripts (eQTLs), and 24 only as proteins (pQTLs). 79% of eQTLs were regulated by cis-mechanisms, as opposed to only 31% of pQTLs, indicating a more direct genetic connection between genes and their transcripts than between genes and their protein products. In some cases, QTLs could be linked to phenotypic changes across the BXDs. One such case indicates a novel animal model for an inborn error of metabolism that has been observed in humans; BXD mice with deficient DHTKD1 protein also exhibit 2-aminoadipic and 2-oxoadipic aciduria like seen in affected patients. Together, these findings show that quantitative, multi-layered genomic, transcriptomic, and proteomic analyses provide more power for connecting genetic variance to phenotypes in complex systems than each layer alone, and provide complementary information to identify novel regulatory networks of metabolic diseases.
-
-Note: please see associated dataset “Liver Proteome” EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (Jul13) RPN” for protein data in the same animals. [NB: Data in review, but still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
-
-Note: please see associated dataset “LISP2” in BXD phenotypes for phenotype data on the same animals. [NB: Still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
diff --git a/general/datasets/EPFLBXDprotCDRPN0513/tissue.rtf b/general/datasets/EPFLBXDprotCDRPN0513/tissue.rtf
deleted file mode 100644
index f95e2c4..0000000
--- a/general/datasets/EPFLBXDprotCDRPN0513/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers were later shattered in liquid nitrogen and ~100 mg fragments were taken at random from the left, right, or caudate lobes. To account for this discrepancy, all ~5 animals per cohort had their RNA prepared, and then were pooled evenly (by µg of RNA) into a single RNA sample for each cohort. These pooled RNA samples of approximately 30 µg RNA were then purified using RNEasy, then sent out for array analysis. All RIN values were > 8.0.
diff --git a/general/datasets/EPFLBXDprotHFD0513/cases.rtf b/general/datasets/EPFLBXDprotHFD0513/cases.rtf
deleted file mode 100644
index ed4ced8..0000000
--- a/general/datasets/EPFLBXDprotHFD0513/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-40 strains of the BXD family (BXD43 – BXD103) and both parental strains (C57BL/6 and DBA/2) were born and raised at the EPFL in Switzerland prior to inclusion in this study. For each strain, 10 male animals were born and then separated evenly into two cohorts at 8 weeks of age: 5 animals per strain on a chow diet (6% kcal/fat, 20% protein, 74% carbohydrate) and 5 animals per strain on high fat diet (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. Animals were fasted overnight prior to sacrifice, which occurred between 9am and 11am after isoflurane anesthesia and perfusion. The gall bladder was removed, and then the livers were immediately frozen in liquid nitrogen.
diff --git a/general/datasets/EPFLBXDprotHFD0513/notes.rtf b/general/datasets/EPFLBXDprotHFD0513/notes.rtf
deleted file mode 100644
index ecdae60..0000000
--- a/general/datasets/EPFLBXDprotHFD0513/notes.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-SWATH
-
-SWATH MS is a novel technique that is based on data-independent acquisition (DIA) which aims to complement traditional mass spectrometry-based proteomics techniques such as shotgun and SRM methods. In principal, it allows a complete and permanent recording of all fragment ions of all peptide precursors in a biological sample and can thus potentially combine the advantages of shotgun (high throughput) with those of SRM (high reproducibility and sensitivity).
-
-The method uniquely combines a DIA methods with a innovative data analysis approach based on targeted data extraction developed in the Aebersold lab. Like in other DIA methods, the mass spectrometer cycles through precursor acquisition windows designed to cover the whole range of 400-1200 m/z - in which most of the proteotypic peptide precursors of an organism fall - within 2-4 seconds. During each cycle, the mass spectrometer will fragment all precursors from a given precursors window (e.g. 475 - 500 m/z for 25 Da windows) and record a complete, high accuracy fragment ion spectrum. The same range will be fragmented again in the next cycle, thus providing a time-resolved recording of fragment ions that elute on the chromatography. Thus the SWATH method provides highly multiplexed fragment ion spectra that are deterministically recorded over the complete chromatographic time.
-
-In the Malmstroem group, we are interested in the data-analysis challenge that is posed by DIA / SWATH data. Traditionally, DIA methods have been analyzed by trying to reconstruct the lineage of precursor and fragment ions based on their chromatographic elution profile, and then analysing the data in a workflow similar to those used in shotgun proteomics. However, these approaches suffered from low sensitivity and propagation of errors due to mis-assignment of fragment ions to precursor ions. We are thus working on automating targeted methods that are conceptually similar to SRM and allow querying the data multiple times with specific hypothesis, thus giving the researcher more control and specificity in the bioinformatic data analysis step. With these novel algorithms, it is potentially possible to explore a much larger part of the data that is present and obtain a nearly complete picture of a proteome.
-
-References
-
-
- - Gillet, L. C., P. Navarro, S. Tate, H. Röst, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold (2012, June). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Molecular & cellular proteomics : MCP 11 (6). PMID 22261725
- - Purvine, S., J.-T. T. Eppel, E. C. Yi, and D. R. Goodlett (2003, June). Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3 (6), 847-850.
- - Plumb, R. S., K. A. Johnson, P. Rainville, B. W. Smith, I. D. Wilson, J. M. Castro-Perez, and J. K. Nicholson (2006). UPLC/MS(e); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid communications in mass spectrometry : RCM 20 (13), 1989-1994.
- - Panchaud, A., A. Scherl, S. A. Shaffer, P. D. von Haller, H. D. Kulasekara, S. I. Miller, and D. R. Goodlett (2009, August). Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Analytical chemistry 81 (15), 6481-6488.
-
diff --git a/general/datasets/EPFLBXDprotHFD0513/platform.rtf b/general/datasets/EPFLBXDprotHFD0513/platform.rtf
deleted file mode 100644
index 4a33b7c..0000000
--- a/general/datasets/EPFLBXDprotHFD0513/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All 81 arrays were Affymetrix Mouse Gene 1.0 ST, run together in a single batch in March/April 2013 at the University of Tennessee Health Science Center.
diff --git a/general/datasets/EPFLBXDprotHFD0513/summary.rtf b/general/datasets/EPFLBXDprotHFD0513/summary.rtf
deleted file mode 100644
index 8797309..0000000
--- a/general/datasets/EPFLBXDprotHFD0513/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Quantitative changes in transcriptome and proteome patterns relate genomic variation to specific phenotypes. Here we applied selected reaction monitoring (SRM), a targeted mass spectrometry method that supports the reliable and reproducible quantification of predetermined sets of proteins across a broad abundance range in complex samples to quantify 157 metabolic proteins in liver extracts from 40 genetically-diverse strains of the BXD mouse genetic reference population, after chow or high fat diet. We observed significant biological variation in protein levels, which were linked to transcript variation in ~30% of the cases. 14 genes mapped to quantitative trait loci (QTLs) at both the transcript and protein level, while a further 18 mapped only as transcripts (eQTLs), and 24 only as proteins (pQTLs). 79% of eQTLs were regulated by cis-mechanisms, as opposed to only 31% of pQTLs, indicating a more direct genetic connection between genes and their transcripts than between genes and their protein products. In some cases, QTLs could be linked to phenotypic changes across the BXDs. One such case indicates a novel animal model for an inborn error of metabolism that has been observed in humans; BXD mice with deficient DHTKD1 protein also exhibit 2-aminoadipic and 2-oxoadipic aciduria like seen in affected patients. Together, these findings show that quantitative, multi-layered genomic, transcriptomic, and proteomic analyses provide more power for connecting genetic variance to phenotypes in complex systems than each layer alone, and provide complementary information to identify novel regulatory networks of metabolic diseases.
-
-Note: please see associated dataset “Liver Proteome” EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (Jul13) RPN” for protein data in the same animals. [NB: Data in review, but still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
-
-Note: please see associated dataset “LISP2” in BXD phenotypes for phenotype data on the same animals. [NB: Still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
diff --git a/general/datasets/EPFLBXDprotHFD0513/tissue.rtf b/general/datasets/EPFLBXDprotHFD0513/tissue.rtf
deleted file mode 100644
index f95e2c4..0000000
--- a/general/datasets/EPFLBXDprotHFD0513/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers were later shattered in liquid nitrogen and ~100 mg fragments were taken at random from the left, right, or caudate lobes. To account for this discrepancy, all ~5 animals per cohort had their RNA prepared, and then were pooled evenly (by µg of RNA) into a single RNA sample for each cohort. These pooled RNA samples of approximately 30 µg RNA were then purified using RNEasy, then sent out for array analysis. All RIN values were > 8.0.
diff --git a/general/datasets/EPFLBXDprotHFDRPN0513/cases.rtf b/general/datasets/EPFLBXDprotHFDRPN0513/cases.rtf
deleted file mode 100644
index ed4ced8..0000000
--- a/general/datasets/EPFLBXDprotHFDRPN0513/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-40 strains of the BXD family (BXD43 – BXD103) and both parental strains (C57BL/6 and DBA/2) were born and raised at the EPFL in Switzerland prior to inclusion in this study. For each strain, 10 male animals were born and then separated evenly into two cohorts at 8 weeks of age: 5 animals per strain on a chow diet (6% kcal/fat, 20% protein, 74% carbohydrate) and 5 animals per strain on high fat diet (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. Animals were fasted overnight prior to sacrifice, which occurred between 9am and 11am after isoflurane anesthesia and perfusion. The gall bladder was removed, and then the livers were immediately frozen in liquid nitrogen.
diff --git a/general/datasets/EPFLBXDprotHFDRPN0513/notes.rtf b/general/datasets/EPFLBXDprotHFDRPN0513/notes.rtf
deleted file mode 100644
index ecdae60..0000000
--- a/general/datasets/EPFLBXDprotHFDRPN0513/notes.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-SWATH
-
-SWATH MS is a novel technique that is based on data-independent acquisition (DIA) which aims to complement traditional mass spectrometry-based proteomics techniques such as shotgun and SRM methods. In principal, it allows a complete and permanent recording of all fragment ions of all peptide precursors in a biological sample and can thus potentially combine the advantages of shotgun (high throughput) with those of SRM (high reproducibility and sensitivity).
-
-The method uniquely combines a DIA methods with a innovative data analysis approach based on targeted data extraction developed in the Aebersold lab. Like in other DIA methods, the mass spectrometer cycles through precursor acquisition windows designed to cover the whole range of 400-1200 m/z - in which most of the proteotypic peptide precursors of an organism fall - within 2-4 seconds. During each cycle, the mass spectrometer will fragment all precursors from a given precursors window (e.g. 475 - 500 m/z for 25 Da windows) and record a complete, high accuracy fragment ion spectrum. The same range will be fragmented again in the next cycle, thus providing a time-resolved recording of fragment ions that elute on the chromatography. Thus the SWATH method provides highly multiplexed fragment ion spectra that are deterministically recorded over the complete chromatographic time.
-
-In the Malmstroem group, we are interested in the data-analysis challenge that is posed by DIA / SWATH data. Traditionally, DIA methods have been analyzed by trying to reconstruct the lineage of precursor and fragment ions based on their chromatographic elution profile, and then analysing the data in a workflow similar to those used in shotgun proteomics. However, these approaches suffered from low sensitivity and propagation of errors due to mis-assignment of fragment ions to precursor ions. We are thus working on automating targeted methods that are conceptually similar to SRM and allow querying the data multiple times with specific hypothesis, thus giving the researcher more control and specificity in the bioinformatic data analysis step. With these novel algorithms, it is potentially possible to explore a much larger part of the data that is present and obtain a nearly complete picture of a proteome.
-
-References
-
-
- - Gillet, L. C., P. Navarro, S. Tate, H. Röst, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold (2012, June). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Molecular & cellular proteomics : MCP 11 (6). PMID 22261725
- - Purvine, S., J.-T. T. Eppel, E. C. Yi, and D. R. Goodlett (2003, June). Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3 (6), 847-850.
- - Plumb, R. S., K. A. Johnson, P. Rainville, B. W. Smith, I. D. Wilson, J. M. Castro-Perez, and J. K. Nicholson (2006). UPLC/MS(e); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid communications in mass spectrometry : RCM 20 (13), 1989-1994.
- - Panchaud, A., A. Scherl, S. A. Shaffer, P. D. von Haller, H. D. Kulasekara, S. I. Miller, and D. R. Goodlett (2009, August). Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Analytical chemistry 81 (15), 6481-6488.
-
diff --git a/general/datasets/EPFLBXDprotHFDRPN0513/platform.rtf b/general/datasets/EPFLBXDprotHFDRPN0513/platform.rtf
deleted file mode 100644
index 4a33b7c..0000000
--- a/general/datasets/EPFLBXDprotHFDRPN0513/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All 81 arrays were Affymetrix Mouse Gene 1.0 ST, run together in a single batch in March/April 2013 at the University of Tennessee Health Science Center.
diff --git a/general/datasets/EPFLBXDprotHFDRPN0513/summary.rtf b/general/datasets/EPFLBXDprotHFDRPN0513/summary.rtf
deleted file mode 100644
index 8797309..0000000
--- a/general/datasets/EPFLBXDprotHFDRPN0513/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Quantitative changes in transcriptome and proteome patterns relate genomic variation to specific phenotypes. Here we applied selected reaction monitoring (SRM), a targeted mass spectrometry method that supports the reliable and reproducible quantification of predetermined sets of proteins across a broad abundance range in complex samples to quantify 157 metabolic proteins in liver extracts from 40 genetically-diverse strains of the BXD mouse genetic reference population, after chow or high fat diet. We observed significant biological variation in protein levels, which were linked to transcript variation in ~30% of the cases. 14 genes mapped to quantitative trait loci (QTLs) at both the transcript and protein level, while a further 18 mapped only as transcripts (eQTLs), and 24 only as proteins (pQTLs). 79% of eQTLs were regulated by cis-mechanisms, as opposed to only 31% of pQTLs, indicating a more direct genetic connection between genes and their transcripts than between genes and their protein products. In some cases, QTLs could be linked to phenotypic changes across the BXDs. One such case indicates a novel animal model for an inborn error of metabolism that has been observed in humans; BXD mice with deficient DHTKD1 protein also exhibit 2-aminoadipic and 2-oxoadipic aciduria like seen in affected patients. Together, these findings show that quantitative, multi-layered genomic, transcriptomic, and proteomic analyses provide more power for connecting genetic variance to phenotypes in complex systems than each layer alone, and provide complementary information to identify novel regulatory networks of metabolic diseases.
-
-Note: please see associated dataset “Liver Proteome” EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (Jul13) RPN” for protein data in the same animals. [NB: Data in review, but still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
-
-Note: please see associated dataset “LISP2” in BXD phenotypes for phenotype data on the same animals. [NB: Still unpublished as of Nov 2013, please contact admin.auwerx@epfl.ch for access]
diff --git a/general/datasets/EPFLBXDprotHFDRPN0513/tissue.rtf b/general/datasets/EPFLBXDprotHFDRPN0513/tissue.rtf
deleted file mode 100644
index f95e2c4..0000000
--- a/general/datasets/EPFLBXDprotHFDRPN0513/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers were later shattered in liquid nitrogen and ~100 mg fragments were taken at random from the left, right, or caudate lobes. To account for this discrepancy, all ~5 animals per cohort had their RNA prepared, and then were pooled evenly (by µg of RNA) into a single RNA sample for each cohort. These pooled RNA samples of approximately 30 µg RNA were then purified using RNEasy, then sent out for array analysis. All RIN values were > 8.0.
diff --git a/general/datasets/EPFLMouseMuscleCDRMA1211/summary.rtf b/general/datasets/EPFLMouseMuscleCDRMA1211/summary.rtf
deleted file mode 100644
index e63dd95..0000000
--- a/general/datasets/EPFLMouseMuscleCDRMA1211/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-Highlights
-
-
- - Inhibition of poly(ADP-ribose) polymerases (PARPs) enhances endurance performance
- - Inhibition of PARPs improves mitochondrial function in skeletal muscle
- - Parp-1 correlates with energy expenditure in heterogeneous mouse populations
- - Genetic and acquired mitochondrial defects can be rescued by PARP inhibition
-
-
-We previously demonstrated that the deletion of the poly(ADP-ribose)polymerase (Parp)-1 gene in mice enhances oxidative metabolism, thereby protecting against diet-induced obesity. However, the therapeutic use of PARP inhibitors to enhance mitochondrial function remains to be explored. Here, we show tight negative correlation between Parp-1 expression and energy expenditure in heterogeneous mouse populations, indicating that variations in PARP-1 activity have an impact on metabolic homeostasis. Notably, these genetic correlations can be translated into pharmacological applications. Long-term treatment with PARP inhibitors enhances fitness in mice by increasing the abundance of mitochondrial respiratory complexes and boosting mitochondrial respiratory capacity. Furthermore, PARP inhibitors reverse mitochondrial defects in primary myotubes of obese humans and attenuate genetic defects of mitochondrial metabolism in human fibroblasts and C. elegans. Overall, our work validates in worm, mouse, and human models that PARP inhibition may be used to treat both genetic and acquired muscle dysfunction linked to defective mitochondrial function.
diff --git a/general/datasets/EPFLMouseMuscleCDRMA1211/tissue.rtf b/general/datasets/EPFLMouseMuscleCDRMA1211/tissue.rtf
deleted file mode 100644
index c40574c..0000000
--- a/general/datasets/EPFLMouseMuscleCDRMA1211/tissue.rtf
+++ /dev/null
@@ -1,25 +0,0 @@
-
-
-
-
- The muscle datasets are all generated from quadriceps muscles. These animals were born, raised, phenotyped, and sacrificed at the EPFL in the group of Johan Auwerx. Animals were all approximately 29 weeks of age and were all male. Chow diet cohorts ("CD") were fed Harlan 2018 (6% kcal/fat, 20% protein, 74% carbohydrate). High fat diet ("HFD") cohorts were fed Harlan 06414 (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. After an overnight fasting and isoflurane anesthesia, animals were sacrificed following a blood draw and perfusion. Quadriceps were cut horizontally from the femur bone and then frozen in liquid nitrogen for an extended period. Cohorts were sacrificed in a staggered fashion, with approximately 1 cohort per week over a period of 2-3 years. mRNA was prepared for the quadriceps in two distinct batches approximately one year apart (Batch 1: late spring 2011; Batch 2: late spring 2012). Microarrays were run on the samples in two distinct batches shortly after being prepared and received.
-
-
-
- Batch 1 is the following cohorts: C57HFD 100HFD 62HFD 83CD C57CD 70CD 75CD 96CD 44HFD 45CD 61HFD 73CD DBACD 45HFD 63CD 87CD 89CD 90HFD 62CD 75HFD DBAHFD 44CD 66CD 87HFD 66HFD 55HFD 55CD 70HFD 51CD 83HFD 80CD 51HFD 73HFD 96HFD 61CD 90CD 80HFD 63HFD
-
-
-
- Batch 2 is the following cohorts: 49HFD 43CD 50CD 89HFD 84CD 100CD 81HFD 98HFD 103CD 68CD 79CD 99CD 71CD 48HFD 64HFD 84HFD 101CD 103HFD 60CD 79HFD 68HFD 48CD 71HFD 65CD 85HFD 99HFD 81CD 49CD 56HFD 97CD 97HFD 92CD 69CD 64CD 69HFD 56CD 65HFD 43HFD 85CD 95CD 98CD
-
-
-
- For all cohorts in these datasets, roughly 2-5 animals (typically around 4) had mRNA extracted separately, and then mRNA were pooled equally for each individual in a cohort. After the mRNA were pooled for the individuals within a cohort—a cohort meaning the same diet, sex, strain, and littermate—the samples were purified using RNEasy.
-
-
-
- Once both cohorts were completed, the two batches were re-normalized together using RMAExpress and the two batches were logged and z-normalized. The mean was set to 8 units and standard deviation was set to 2 units for all samples. This removes negative values from the samples, and reduces the batch effect between the two groups.
- |
-
-
-
diff --git a/general/datasets/EPFLMouseMuscleHFDRMA1211/summary.rtf b/general/datasets/EPFLMouseMuscleHFDRMA1211/summary.rtf
deleted file mode 100644
index e63dd95..0000000
--- a/general/datasets/EPFLMouseMuscleHFDRMA1211/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-Highlights
-
-
- - Inhibition of poly(ADP-ribose) polymerases (PARPs) enhances endurance performance
- - Inhibition of PARPs improves mitochondrial function in skeletal muscle
- - Parp-1 correlates with energy expenditure in heterogeneous mouse populations
- - Genetic and acquired mitochondrial defects can be rescued by PARP inhibition
-
-
-We previously demonstrated that the deletion of the poly(ADP-ribose)polymerase (Parp)-1 gene in mice enhances oxidative metabolism, thereby protecting against diet-induced obesity. However, the therapeutic use of PARP inhibitors to enhance mitochondrial function remains to be explored. Here, we show tight negative correlation between Parp-1 expression and energy expenditure in heterogeneous mouse populations, indicating that variations in PARP-1 activity have an impact on metabolic homeostasis. Notably, these genetic correlations can be translated into pharmacological applications. Long-term treatment with PARP inhibitors enhances fitness in mice by increasing the abundance of mitochondrial respiratory complexes and boosting mitochondrial respiratory capacity. Furthermore, PARP inhibitors reverse mitochondrial defects in primary myotubes of obese humans and attenuate genetic defects of mitochondrial metabolism in human fibroblasts and C. elegans. Overall, our work validates in worm, mouse, and human models that PARP inhibition may be used to treat both genetic and acquired muscle dysfunction linked to defective mitochondrial function.
diff --git a/general/datasets/EPFLMouseMuscleHFDRMA1211/tissue.rtf b/general/datasets/EPFLMouseMuscleHFDRMA1211/tissue.rtf
deleted file mode 100644
index c40574c..0000000
--- a/general/datasets/EPFLMouseMuscleHFDRMA1211/tissue.rtf
+++ /dev/null
@@ -1,25 +0,0 @@
-
-
-
-
- The muscle datasets are all generated from quadriceps muscles. These animals were born, raised, phenotyped, and sacrificed at the EPFL in the group of Johan Auwerx. Animals were all approximately 29 weeks of age and were all male. Chow diet cohorts ("CD") were fed Harlan 2018 (6% kcal/fat, 20% protein, 74% carbohydrate). High fat diet ("HFD") cohorts were fed Harlan 06414 (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. After an overnight fasting and isoflurane anesthesia, animals were sacrificed following a blood draw and perfusion. Quadriceps were cut horizontally from the femur bone and then frozen in liquid nitrogen for an extended period. Cohorts were sacrificed in a staggered fashion, with approximately 1 cohort per week over a period of 2-3 years. mRNA was prepared for the quadriceps in two distinct batches approximately one year apart (Batch 1: late spring 2011; Batch 2: late spring 2012). Microarrays were run on the samples in two distinct batches shortly after being prepared and received.
-
-
-
- Batch 1 is the following cohorts: C57HFD 100HFD 62HFD 83CD C57CD 70CD 75CD 96CD 44HFD 45CD 61HFD 73CD DBACD 45HFD 63CD 87CD 89CD 90HFD 62CD 75HFD DBAHFD 44CD 66CD 87HFD 66HFD 55HFD 55CD 70HFD 51CD 83HFD 80CD 51HFD 73HFD 96HFD 61CD 90CD 80HFD 63HFD
-
-
-
- Batch 2 is the following cohorts: 49HFD 43CD 50CD 89HFD 84CD 100CD 81HFD 98HFD 103CD 68CD 79CD 99CD 71CD 48HFD 64HFD 84HFD 101CD 103HFD 60CD 79HFD 68HFD 48CD 71HFD 65CD 85HFD 99HFD 81CD 49CD 56HFD 97CD 97HFD 92CD 69CD 64CD 69HFD 56CD 65HFD 43HFD 85CD 95CD 98CD
-
-
-
- For all cohorts in these datasets, roughly 2-5 animals (typically around 4) had mRNA extracted separately, and then mRNA were pooled equally for each individual in a cohort. After the mRNA were pooled for the individuals within a cohort—a cohort meaning the same diet, sex, strain, and littermate—the samples were purified using RNEasy.
-
-
-
- Once both cohorts were completed, the two batches were re-normalized together using RMAExpress and the two batches were logged and z-normalized. The mean was set to 8 units and standard deviation was set to 2 units for all samples. This removes negative values from the samples, and reduces the batch effect between the two groups.
- |
-
-
-
diff --git a/general/datasets/EPFLMouseMuscleRMA1211/summary.rtf b/general/datasets/EPFLMouseMuscleRMA1211/summary.rtf
deleted file mode 100644
index e63dd95..0000000
--- a/general/datasets/EPFLMouseMuscleRMA1211/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-Highlights
-
-
- - Inhibition of poly(ADP-ribose) polymerases (PARPs) enhances endurance performance
- - Inhibition of PARPs improves mitochondrial function in skeletal muscle
- - Parp-1 correlates with energy expenditure in heterogeneous mouse populations
- - Genetic and acquired mitochondrial defects can be rescued by PARP inhibition
-
-
-We previously demonstrated that the deletion of the poly(ADP-ribose)polymerase (Parp)-1 gene in mice enhances oxidative metabolism, thereby protecting against diet-induced obesity. However, the therapeutic use of PARP inhibitors to enhance mitochondrial function remains to be explored. Here, we show tight negative correlation between Parp-1 expression and energy expenditure in heterogeneous mouse populations, indicating that variations in PARP-1 activity have an impact on metabolic homeostasis. Notably, these genetic correlations can be translated into pharmacological applications. Long-term treatment with PARP inhibitors enhances fitness in mice by increasing the abundance of mitochondrial respiratory complexes and boosting mitochondrial respiratory capacity. Furthermore, PARP inhibitors reverse mitochondrial defects in primary myotubes of obese humans and attenuate genetic defects of mitochondrial metabolism in human fibroblasts and C. elegans. Overall, our work validates in worm, mouse, and human models that PARP inhibition may be used to treat both genetic and acquired muscle dysfunction linked to defective mitochondrial function.
diff --git a/general/datasets/EPFLMouseMuscleRMA1211/tissue.rtf b/general/datasets/EPFLMouseMuscleRMA1211/tissue.rtf
deleted file mode 100644
index c40574c..0000000
--- a/general/datasets/EPFLMouseMuscleRMA1211/tissue.rtf
+++ /dev/null
@@ -1,25 +0,0 @@
-
-
-
-
- The muscle datasets are all generated from quadriceps muscles. These animals were born, raised, phenotyped, and sacrificed at the EPFL in the group of Johan Auwerx. Animals were all approximately 29 weeks of age and were all male. Chow diet cohorts ("CD") were fed Harlan 2018 (6% kcal/fat, 20% protein, 74% carbohydrate). High fat diet ("HFD") cohorts were fed Harlan 06414 (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. After an overnight fasting and isoflurane anesthesia, animals were sacrificed following a blood draw and perfusion. Quadriceps were cut horizontally from the femur bone and then frozen in liquid nitrogen for an extended period. Cohorts were sacrificed in a staggered fashion, with approximately 1 cohort per week over a period of 2-3 years. mRNA was prepared for the quadriceps in two distinct batches approximately one year apart (Batch 1: late spring 2011; Batch 2: late spring 2012). Microarrays were run on the samples in two distinct batches shortly after being prepared and received.
-
-
-
- Batch 1 is the following cohorts: C57HFD 100HFD 62HFD 83CD C57CD 70CD 75CD 96CD 44HFD 45CD 61HFD 73CD DBACD 45HFD 63CD 87CD 89CD 90HFD 62CD 75HFD DBAHFD 44CD 66CD 87HFD 66HFD 55HFD 55CD 70HFD 51CD 83HFD 80CD 51HFD 73HFD 96HFD 61CD 90CD 80HFD 63HFD
-
-
-
- Batch 2 is the following cohorts: 49HFD 43CD 50CD 89HFD 84CD 100CD 81HFD 98HFD 103CD 68CD 79CD 99CD 71CD 48HFD 64HFD 84HFD 101CD 103HFD 60CD 79HFD 68HFD 48CD 71HFD 65CD 85HFD 99HFD 81CD 49CD 56HFD 97CD 97HFD 92CD 69CD 64CD 69HFD 56CD 65HFD 43HFD 85CD 95CD 98CD
-
-
-
- For all cohorts in these datasets, roughly 2-5 animals (typically around 4) had mRNA extracted separately, and then mRNA were pooled equally for each individual in a cohort. After the mRNA were pooled for the individuals within a cohort—a cohort meaning the same diet, sex, strain, and littermate—the samples were purified using RNEasy.
-
-
-
- Once both cohorts were completed, the two batches were re-normalized together using RMAExpress and the two batches were logged and z-normalized. The mean was set to 8 units and standard deviation was set to 2 units for all samples. This removes negative values from the samples, and reduces the batch effect between the two groups.
- |
-
-
-
diff --git a/general/datasets/EPFLMouseMuscleRMA_Ex1112/summary.rtf b/general/datasets/EPFLMouseMuscleRMA_Ex1112/summary.rtf
deleted file mode 100644
index e63dd95..0000000
--- a/general/datasets/EPFLMouseMuscleRMA_Ex1112/summary.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-Highlights
-
-
- - Inhibition of poly(ADP-ribose) polymerases (PARPs) enhances endurance performance
- - Inhibition of PARPs improves mitochondrial function in skeletal muscle
- - Parp-1 correlates with energy expenditure in heterogeneous mouse populations
- - Genetic and acquired mitochondrial defects can be rescued by PARP inhibition
-
-
-We previously demonstrated that the deletion of the poly(ADP-ribose)polymerase (Parp)-1 gene in mice enhances oxidative metabolism, thereby protecting against diet-induced obesity. However, the therapeutic use of PARP inhibitors to enhance mitochondrial function remains to be explored. Here, we show tight negative correlation between Parp-1 expression and energy expenditure in heterogeneous mouse populations, indicating that variations in PARP-1 activity have an impact on metabolic homeostasis. Notably, these genetic correlations can be translated into pharmacological applications. Long-term treatment with PARP inhibitors enhances fitness in mice by increasing the abundance of mitochondrial respiratory complexes and boosting mitochondrial respiratory capacity. Furthermore, PARP inhibitors reverse mitochondrial defects in primary myotubes of obese humans and attenuate genetic defects of mitochondrial metabolism in human fibroblasts and C. elegans. Overall, our work validates in worm, mouse, and human models that PARP inhibition may be used to treat both genetic and acquired muscle dysfunction linked to defective mitochondrial function.
diff --git a/general/datasets/EPFLMouseMuscleRMA_Ex1112/tissue.rtf b/general/datasets/EPFLMouseMuscleRMA_Ex1112/tissue.rtf
deleted file mode 100644
index c40574c..0000000
--- a/general/datasets/EPFLMouseMuscleRMA_Ex1112/tissue.rtf
+++ /dev/null
@@ -1,25 +0,0 @@
-
-
-
-
- The muscle datasets are all generated from quadriceps muscles. These animals were born, raised, phenotyped, and sacrificed at the EPFL in the group of Johan Auwerx. Animals were all approximately 29 weeks of age and were all male. Chow diet cohorts ("CD") were fed Harlan 2018 (6% kcal/fat, 20% protein, 74% carbohydrate). High fat diet ("HFD") cohorts were fed Harlan 06414 (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, when the animals could rest. After an overnight fasting and isoflurane anesthesia, animals were sacrificed following a blood draw and perfusion. Quadriceps were cut horizontally from the femur bone and then frozen in liquid nitrogen for an extended period. Cohorts were sacrificed in a staggered fashion, with approximately 1 cohort per week over a period of 2-3 years. mRNA was prepared for the quadriceps in two distinct batches approximately one year apart (Batch 1: late spring 2011; Batch 2: late spring 2012). Microarrays were run on the samples in two distinct batches shortly after being prepared and received.
-
-
-
- Batch 1 is the following cohorts: C57HFD 100HFD 62HFD 83CD C57CD 70CD 75CD 96CD 44HFD 45CD 61HFD 73CD DBACD 45HFD 63CD 87CD 89CD 90HFD 62CD 75HFD DBAHFD 44CD 66CD 87HFD 66HFD 55HFD 55CD 70HFD 51CD 83HFD 80CD 51HFD 73HFD 96HFD 61CD 90CD 80HFD 63HFD
-
-
-
- Batch 2 is the following cohorts: 49HFD 43CD 50CD 89HFD 84CD 100CD 81HFD 98HFD 103CD 68CD 79CD 99CD 71CD 48HFD 64HFD 84HFD 101CD 103HFD 60CD 79HFD 68HFD 48CD 71HFD 65CD 85HFD 99HFD 81CD 49CD 56HFD 97CD 97HFD 92CD 69CD 64CD 69HFD 56CD 65HFD 43HFD 85CD 95CD 98CD
-
-
-
- For all cohorts in these datasets, roughly 2-5 animals (typically around 4) had mRNA extracted separately, and then mRNA were pooled equally for each individual in a cohort. After the mRNA were pooled for the individuals within a cohort—a cohort meaning the same diet, sex, strain, and littermate—the samples were purified using RNEasy.
-
-
-
- Once both cohorts were completed, the two batches were re-normalized together using RMAExpress and the two batches were logged and z-normalized. The mean was set to 8 units and standard deviation was set to 2 units for all samples. This removes negative values from the samples, and reduces the batch effect between the two groups.
- |
-
-
-
diff --git a/general/datasets/EYE_M2_0406_R/acknowledgment.rtf b/general/datasets/EYE_M2_0406_R/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/EYE_M2_0406_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/EYE_M2_0406_R/cases.rtf b/general/datasets/EYE_M2_0406_R/cases.rtf
deleted file mode 100644
index 5cb5539..0000000
--- a/general/datasets/EYE_M2_0406_R/cases.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-We used a set of 55 BXD recombinant inbred strains, 14 conventional inbred strains including C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1s. BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D2). Physical maps in WebQTL incorporate approximately 2 million B6 vs D2 SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) have been included in the MDP. Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J. These reciprocal F1 can be used to detect some imprinted genes.
-
diff --git a/general/datasets/EYE_M2_0406_R/notes.rtf b/general/datasets/EYE_M2_0406_R/notes.rtf
deleted file mode 100644
index 39475ab..0000000
--- a/general/datasets/EYE_M2_0406_R/notes.rtf
+++ /dev/null
@@ -1,18 +0,0 @@
-This study includes the following datasets:
-
-
- -
-
Eye M430v2 (Apr06) RMA
-
- -
-
Eye M430v2 (Apr06) PDNN
-
- -
-
Eye M430v2 (Apr06) MAS5
-
- -
-
Eye M430v2 (Sep06) RMA
-
-
-
-This text file originally generated by RWW, May 26, 2006. Updated by RWW, May 27, 2006.
diff --git a/general/datasets/EYE_M2_0406_R/platform.rtf b/general/datasets/EYE_M2_0406_R/platform.rtf
deleted file mode 100644
index ac743ee..0000000
--- a/general/datasets/EYE_M2_0406_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/EYE_M2_0406_R/processing.rtf b/general/datasets/EYE_M2_0406_R/processing.rtf
deleted file mode 100644
index d23bc47..0000000
--- a/general/datasets/EYE_M2_0406_R/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the two batches together in RMA.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing all arrays were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (C3H/HeJ and BXD24) and samples from wild subspecies such as CAST/Ei, PWD/Ph, and PWK/Ph. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. We tended to keep arrays that "conformed" to the expectation. The assumption in these cases is that anomolous data are much more likely due to experimental problem and errors than to informative biological variation. Approximately 8 arrays total were discarded in batches 1 and 2 combined.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We then categorized arrays into XXX major "technical groups" depending on expression patterns as noted in scatterplots. This process of defining technical groups was done in DataDesk by manually "typing" arrays. These technical groups are apparently due to subtle within-batch effect that we do not yet understand and that cannot be corrected by quantile normalization. These XXX major technical groups are not obviously related to strain, sex, age, or any other known biological effect or variable. They are also not obviously related to any of the Affymetrix QC data types (3'/5' ratios, gain, etc.). Once the technical groups were defined, we forced the means of each probe set in the XX technical groups to the same value. This simple process partially removes a technical error of unknown origin in large expression array data sets.
-
-We reviewed the final data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of 140 arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g. 1000) represented the QTL harvest for the full data set. We then dropped a single array from the data set (n = 139 arrays), recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 950 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs (1000-950). Values ranged from -90 (good0 to +38 (bad). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a final method to polish a data set. By applying this procedure we discovered that a set of XX (7?) arrays could be excluded while simultaneously improving the total number of QTLs with values above 50.
-
-During this final process we discovered that nearly XX arrays in the second batch had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of very high quality.
-
diff --git a/general/datasets/EYE_M2_0406_R/summary.rtf b/general/datasets/EYE_M2_0406_R/summary.rtf
deleted file mode 100644
index 68a4484..0000000
--- a/general/datasets/EYE_M2_0406_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATA SET. The HEIMED April 2006 data set provides estimates of mRNA expression in whole eyes of 71 lines of young adult mice generated using 132 Affymetrix M430 2.0 arrays. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools; one male, one female, for each straion. This data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/EYE_M2_0406_R/tissue.rtf b/general/datasets/EYE_M2_0406_R/tissue.rtf
deleted file mode 100644
index d8d345f..0000000
--- a/general/datasets/EYE_M2_0406_R/tissue.rtf
+++ /dev/null
@@ -1,7112 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 4 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2) in the first batch of arrays (the November 05 data set) of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table). This same protocol was used for all samples in the second batch added in April 2006.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The first and second batches of array data, collectively represents a reasonably well balanced sample of males and females belonging to 62 strains, but without within-strain-by-sex replication. Six strains are represented only by male sample pools (BXD15, 28, 29, 55, 98, and DBA/2J. Four strains are represented only by a female pool sample (BXD1, 27, 73 and 86). Please use the probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males) as quantitative surrogates for the sex balance in this data set.
-
-Batch Structure: This data set consists of a two batches: the original batch that makes up the November 2005 data set and a new batch of 63 arrays (R0857E through R2649E, and R2682E through R2742E, non-consecutive identifiers) run in January 2006 by Dr. Yan Jiao. The arrays in the two batches are from two different lots. All arrays in the second batch were from Lot 4016879 (expiration date 12.28.06). We started working with a total of 140 arrays that passed initial crude quality control based on RNA quality and initial Affymetrix report file information such as 3'/5' ratio, scale factor, and percent present calls. A total of 130 arrays were finally approved for inclusion in this April 2006 data set. The complex normalization procedure is described below.
-
-The table below summarizes information on strain, age, sex, original CEL filename, Affymetrix quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-IN PROGRESS: PLEASE NOTE THAT THIS TABLE IS NOW BEING UPDATED TO INCLUDE BATCH 2 OF EARLY 2006.
-
-
-
-
-
- | ID |
-
- tube ID
- |
-
- group_type
- |
-
- Strain
- |
-
- age
- |
-
- Sex
- |
-
- original
-
- CEL
-
- filename
- |
-
- PDNN
-
- 2Z
-
- outlier
- |
-
- RMA
-
- 2Z
-
- outlier
- |
-
- scale
-
- factor
- |
-
- background
-
- average
- |
-
- present
- |
-
- absent
- |
-
- marginal
- |
-
- AFFX-b-
-
- ActinMur(3'/5')
- |
-
- AFFX-
-
- GapdhMur(3'/5')
- |
-
- Source
- |
-
-
- |
- 1
- |
-
- R2533E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 60
- |
-
- M
- |
-
- R2533E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.11
- |
-
- 94
- |
-
- 57.90%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 2
- |
-
- R2595E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 59
- |
-
- F
- |
-
- R2595E.CEL
- |
-
- 0.033
- |
-
- 0.036
- |
-
- 1.79
- |
-
- 115
- |
-
- 61.00%
- |
-
- 37.50%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 3
- |
-
- R0754E2
- |
-
- GDP
- |
-
- A/J
- |
-
- 60
- |
-
- M
- |
-
- R0754E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.72
- |
-
- 86
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.36
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 4
- |
-
- R2546E1
- |
-
- GDP
- |
-
- A/J
- |
-
- 66
- |
-
- F
- |
-
- R2545E.CEL
- |
-
- 0.024
- |
-
- 0.029
- |
-
- 1.99
- |
-
- 96
- |
-
- 58.60%
- |
-
- 39.70%
- |
-
- 1.70%
- |
-
- 1.47
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 5
- |
-
- R2601E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- F
- |
-
- R2601E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 2.55
- |
-
- 92
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 6
- |
-
- R2602E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- M
- |
-
- R2602E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 2.60
- |
-
- 84
- |
-
- 59.70%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 7
- |
-
- R1672E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- M
- |
-
- R1672E.CEL
- |
-
- 0.043
- |
-
- 0.039
- |
-
- 2.22
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 8
- |
-
- R1676E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- F
- |
-
- R1676E.CEL
- |
-
- 0.083
- |
-
- 0.085
- |
-
- 2.69
- |
-
- 98
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.74
- |
-
- JAX
- |
-
-
- |
- 9
- |
-
- R2581E1
- |
-
- BXD
- |
-
- BXD11
- |
-
- 65
- |
-
- F
- |
-
- R2581E.CEL
- |
-
- 0.009
- |
-
- 0.021
- |
-
- 1.94
- |
-
- 89
- |
-
- 62.10%
- |
-
- 36.40%
- |
-
- 1.60%
- |
-
- 1.55
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 10
- |
-
- R2543E1
- |
-
- BXD
- |
-
- BXD12
- |
-
- 63
- |
-
- M
- |
-
- R2543E.CEL
- |
-
- 0.018
- |
-
- 0.017
- |
-
- 1.61
- |
-
- 118
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 11
- |
-
- R2586E1
- |
-
- BXD
- |
-
- BXD13
- |
-
- 60
- |
-
- F
- |
-
- R2586E.CEL
- |
-
- 0.259
- |
-
- 0.258
- |
-
- 2.01
- |
-
- 74
- |
-
- 56.40%
- |
-
- 42.00%
- |
-
- 1.60%
- |
-
- 2.85
- |
-
- 3.81
- |
-
- Glenn
- |
-
-
- |
- 12
- |
-
- R2557E1
- |
-
- BXD
- |
-
- BXD14
- |
-
- 60
- |
-
- F
- |
-
- R2557E.CEL
- |
-
- 0.012
- |
-
- 0.027
- |
-
- 1.83
- |
-
- 99
- |
-
- 62.50%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 13
- |
-
- R2567E1
- |
-
- BXD
- |
-
- BXD16
- |
-
- 60
- |
-
- M
- |
-
- R2567E.CEL
- |
-
- 0.048
- |
-
- 0.058
- |
-
- 2.24
- |
-
- 82
- |
-
- 56.70%
- |
-
- 41.60%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.75
- |
-
- Glenn
- |
-
-
- |
- 14
- |
-
- R2559E1
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- M
- |
-
- R2559E.CEL
- |
-
- 0.01
- |
-
- 0.012
- |
-
- 1.65
- |
-
- 104
- |
-
- 60.80%
- |
-
- 37.70%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 15
- |
-
- R2560E1
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- F
- |
-
- R2560E.CEL
- |
-
- 0.009
- |
-
- 0.012
- |
-
- 1.79
- |
-
- 98
- |
-
- 60.90%
- |
-
- 37.50%
- |
-
- 1.60%
- |
-
- 1.35
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 16
- |
-
- R2597E1
- |
-
- BXD
- |
-
- BXD2
- |
-
- 61
- |
-
- M
- |
-
- R2597E.CEL
- |
-
- 0.005
- |
-
- 0.012
- |
-
- 2.37
- |
-
- 94
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 17
- |
-
- R2584E1
- |
-
- BXD
- |
-
- BXD20
- |
-
- 59
- |
-
- F
- |
-
- R2584E.CEL
- |
-
- 0.011
- |
-
- 0.017
- |
-
- 2.07
- |
-
- 84
- |
-
- 59.30%
- |
-
- 39.10%
- |
-
- 1.60%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 18
- |
-
- R2541E2
- |
-
- BXD
- |
-
- BXD21
- |
-
- 61
- |
-
- M
- |
-
- R2541E2.CEL
- |
-
- 0.049
- |
-
- 0.084
- |
-
- 2.63
- |
-
- 125
- |
-
- 56.00%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.29
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 19
- |
-
- R2553E1
- |
-
- BXD
- |
-
- BXD22
- |
-
- 58
- |
-
- F
- |
-
- R2553E.CEL
- |
-
- 0.004
- |
-
- 0.01
- |
-
- 1.95
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.50%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 20
- |
-
- R2558E1
- |
-
- BXD
- |
-
- BXD23
- |
-
- 60
- |
-
- F
- |
-
- R2558E-2.CEL
- |
-
- 0.018
- |
-
- 0.027
- |
-
- 1.91
- |
-
- 115
- |
-
- 59.90%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.20
- |
-
- 0.82
- |
-
- Glenn
- |
-
-
- |
- 21
- |
-
- R2589E2
- |
-
- BXD
- |
-
- BXD24
- |
-
- 59
- |
-
- M
- |
-
- R2589E2.CEL
- |
-
- 0.132
- |
-
- 0.176
- |
-
- 2.61
- |
-
- 112
- |
-
- 57.50%
- |
-
- 40.90%
- |
-
- 1.60%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 22
- |
-
- R2573E1
- |
-
- BXD
- |
-
- BXD25
- |
-
- 67
- |
-
- F
- |
-
- R2573E-2.CEL
- |
-
- 0.055
- |
-
- 0.063
- |
-
- 3.15
- |
-
- 72
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.77
- |
-
- 0.97
- |
-
- UAB
- |
-
-
- |
- 23
- |
-
- R2562E1
- |
-
- BXD
- |
-
- BXD29
- |
-
- 60
- |
-
- M
- |
-
- R2562E.CEL
- |
-
- 0.007
- |
-
- 0.01
- |
-
- 1.65
- |
-
- 116
- |
-
- 59.90%
- |
-
- 38.40%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- Glenn
- |
-
-
- |
- 24
- |
-
- R2598E1
- |
-
- BXD
- |
-
- BXD31
- |
-
- 61
- |
-
- M
- |
-
- R2598E.CEL
- |
-
- 0.006
- |
-
- 0.013
- |
-
- 1.99
- |
-
- 106
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 25
- |
-
- R2563E1
- |
-
- BXD
- |
-
- BXD32
- |
-
- 63
- |
-
- F
- |
-
- R2563E.CEL
- |
-
- 0.023
- |
-
- 0.025
- |
-
- 1.55
- |
-
- 102
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.40%
- |
-
- 1.50
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 26
- |
-
- R2542E1
- |
-
- BXD
- |
-
- BXD33
- |
-
- 67
- |
-
- F
- |
-
- R2542E.CEL
- |
-
- 0.058
- |
-
- 0.062
- |
-
- 2.13
- |
-
- 97
- |
-
- 56.50%
- |
-
- 41.80%
- |
-
- 1.60%
- |
-
- 1.91
- |
-
- 0.93
- |
-
- UTM RW
- |
-
-
- |
- 27
- |
-
- R2585E1
- |
-
- BXD
- |
-
- BXD34
- |
-
- 60
- |
-
- M
- |
-
- R2585E.CEL
- |
-
- 0.024
- |
-
- 0.032
- |
-
- 2.64
- |
-
- 75
- |
-
- 58.30%
- |
-
- 40.00%
- |
-
- 1.70%
- |
-
- 1.25
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 28
- |
-
- R2532E1
- |
-
- BXD
- |
-
- BXD38
- |
-
- 62
- |
-
- M
- |
-
- R2532E.CEL
- |
-
- 0.002
- |
-
- 0.006
- |
-
- 2.04
- |
-
- 94
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 29
- |
-
- R2574E1
- |
-
- BXD
- |
-
- BXD39
- |
-
- 70
- |
-
- F
- |
-
- R2574E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 1.98
- |
-
- 91
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 30
- |
-
- R2590E1
- |
-
- BXD
- |
-
- BXD40
- |
-
- 60
- |
-
- M
- |
-
- R2590E.CEL
- |
-
- 0.007
- |
-
- 0.012
- |
-
- 2.71
- |
-
- 77
- |
-
- 59.10%
- |
-
- 39.30%
- |
-
- 1.50%
- |
-
- 1.40
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 31
- |
-
- R2596E1
- |
-
- BXD
- |
-
- BXD42
- |
-
- 59
- |
-
- M
- |
-
- R2596E.CEL
- |
-
- 0.016
- |
-
- 0.03
- |
-
- 2.63
- |
-
- 108
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 32
- |
-
- R2605E1
- |
-
- BXD
- |
-
- BXD43
- |
-
- 79
- |
-
- M
- |
-
- R2607E.CEL
- |
-
- 0.006
- |
-
- 0.01
- |
-
- 1.82
- |
-
- 131
- |
-
- 60.50%
- |
-
- 38.20%
- |
-
- 1.30%
- |
-
- 1.32
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 33
- |
-
- R2594E1
- |
-
- BXD
- |
-
- BXD44
- |
-
- 63
- |
-
- F
- |
-
- R2594E.CEL
- |
-
- 0.014
- |
-
- 0.024
- |
-
- 1.77
- |
-
- 117
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 34
- |
-
- R2592E1
- |
-
- BXD
- |
-
- BXD45
- |
-
- 62
- |
-
- M
- |
-
- R2592E.CEL
- |
-
- 0.005
- |
-
- 0.011
- |
-
- 1.85
- |
-
- 106
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.43
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 35
- |
-
- R2606E1
- |
-
- BXD
- |
-
- BXD48
- |
-
- 78
- |
-
- M
- |
-
- R2606E.CEL
- |
-
- 0.007
- |
-
- 0.015
- |
-
- 2.56
- |
-
- 106
- |
-
- 58.90%
- |
-
- 39.70%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.83
- |
-
- UTM RW
- |
-
-
- |
- 36
- |
-
- R2591E1
- |
-
- BXD
- |
-
- BXD5
- |
-
- 60
- |
-
- F
- |
-
- R2591E.CEL
- |
-
- 0.052
- |
-
- 0.014
- |
-
- 1.70
- |
-
- 136
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 37
- |
-
- R2603E1
- |
-
- BXD
- |
-
- BXD51
- |
-
- 66
- |
-
- F
- |
-
- R2603E.CEL
- |
-
- 0.007
- |
-
- 0.02
- |
-
- 2.49
- |
-
- 115
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 38
- |
-
- R2570E1
- |
-
- BXD
- |
-
- BXD6
- |
-
- 65
- |
-
- F
- |
-
- R2570E.CEL
- |
-
- 0.013
- |
-
- 0.017
- |
-
- 1.99
- |
-
- 87
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 39
- |
-
- R2534E2
- |
-
- BXD
- |
-
- BXD61
- |
-
- 70
- |
-
- F
- |
-
- R2534E2.CEL
- |
-
- 0.03
- |
-
- 0.058
- |
-
- 2.47
- |
-
- 118
- |
-
- 57.90%
- |
-
- 40.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 40
- |
-
- R2611E1
- |
-
- BXD
- |
-
- BXD64
- |
-
- 68
- |
-
- M
- |
-
- R2611E.CEL
- |
-
- 0.067
- |
-
- 0.068
- |
-
- 2.29
- |
-
- 92
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 1.06
- |
-
- UTM RW
- |
-
-
- |
- 41
- |
-
- R2583E1
- |
-
- BXD
- |
-
- BXD65
- |
-
- 60
- |
-
- M
- |
-
- R2583E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.49
- |
-
- 70
- |
-
- 56.90%
- |
-
- 41.50%
- |
-
- 1.60%
- |
-
- 1.67
- |
-
- 1.01
- |
-
- UTM RW
- |
-
-
- |
- 42
- |
-
- R2536E2
- |
-
- BXD
- |
-
- BXD66
- |
-
- 64
- |
-
- F
- |
-
- R2536E2.CEL
- |
-
- 0.067
- |
-
- 0.139
- |
-
- 2.74
- |
-
- 109
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.70%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 43
- |
-
- R2551E1
- |
-
- BXD
- |
-
- BXD68
- |
-
- 67
- |
-
- F
- |
-
- R2551E.CEL
- |
-
- 0.294
- |
-
- 0.291
- |
-
- 2.49
- |
-
- 92
- |
-
- 54.30%
- |
-
- 44.10%
- |
-
- 1.60%
- |
-
- 2.91
- |
-
- 1.55
- |
-
- UTM RW
- |
-
-
- |
- 44
- |
-
- R2593E1
- |
-
- BXD
- |
-
- BXD69
- |
-
- 59
- |
-
- F
- |
-
- R2593E.CEL
- |
-
- 0.027
- |
-
- 0.038
- |
-
- 1.67
- |
-
- 128
- |
-
- 59.20%
- |
-
- 39.50%
- |
-
- 1.30%
- |
-
- 1.47
- |
-
- 0.92
- |
-
- UTM RW
- |
-
-
- |
- 45
- |
-
- R2537E2
- |
-
- BXD
- |
-
- BXD70
- |
-
- 59
- |
-
- M
- |
-
- R2537E2.CEL
- |
-
- 0.049
- |
-
- 0.092
- |
-
- 2.93
- |
-
- 99
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.29
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 46
- |
-
- R2565E1
- |
-
- BXD
- |
-
- BXD75
- |
-
- 61
- |
-
- F
- |
-
- R2565E.CEL
- |
-
- 0.118
- |
-
- 0.124
- |
-
- 1.79
- |
-
- 102
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 2.31
- |
-
- 3.47
- |
-
- UTM RW
- |
-
-
- |
- 47
- |
-
- R2538E1
- |
-
- BXD
- |
-
- BXD8
- |
-
- 77
- |
-
- F
- |
-
- R2538E.CEL
- |
-
- 0.033
- |
-
- 0.056
- |
-
- 1.91
- |
-
- 102
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 48
- |
-
- R2579E1
- |
-
- BXD
- |
-
- BXD80
- |
-
- 65
- |
-
- F
- |
-
- R2579E.CEL
- |
-
- 0.013
- |
-
- 0.026
- |
-
- 2.42
- |
-
- 72
- |
-
- 59.20%
- |
-
- 39.40%
- |
-
- 1.50%
- |
-
- 1.73
- |
-
- 0.82
- |
-
- UTM RW
- |
-
-
- |
- 49
- |
-
- R2540E1
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- M
- |
-
- R2540E.CEL
- |
-
- 0.014
- |
-
- 0.034
- |
-
- 2.33
- |
-
- 93
- |
-
- 61.10%
- |
-
- 37.40%
- |
-
- 1.40%
- |
-
- 1.22
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 50
- |
-
- R2545E1
- |
-
- BXD
- |
-
- BXD89
- |
-
- 67
- |
-
- M
- |
-
- R2546E.CEL
- |
-
- 0.266
- |
-
- 0.257
- |
-
- 1.67
- |
-
- 105
- |
-
- 56.20%
- |
-
- 42.30%
- |
-
- 1.50%
- |
-
- 3.60
- |
-
- 9.84
- |
-
- UTM RW
- |
-
-
- |
- 51
- |
-
- R2569E1
- |
-
- BXD
- |
-
- BXD9
- |
-
- 67
- |
-
- M
- |
-
- R2569E.CEL
- |
-
- 0.256
- |
-
- 0.239
- |
-
- 1.75
- |
-
- 87
- |
-
- 55.10%
- |
-
- 43.40%
- |
-
- 1.50%
- |
-
- 2.82
- |
-
- 3.14
- |
-
- UTM RW
- |
-
-
- |
- 52
- |
-
- R2578E2
- |
-
- BXD
- |
-
- BXD90
- |
-
- 61
- |
-
- F
- |
-
- R2578E2.CEL
- |
-
- 0.041
- |
-
- 0.062
- |
-
- 2.79
- |
-
- 92
- |
-
- 58.60%
- |
-
- 39.80%
- |
-
- 1.60%
- |
-
- 1.52
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 53
- |
-
- R2554E1
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- M
- |
-
- R2554E.CEL
- |
-
- 0.005
- |
-
- 0.008
- |
-
- 2.18
- |
-
- 93
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 54
- |
-
- R2577E1
- |
-
- BXD
- |
-
- BXD97
- |
-
- 55
- |
-
- M
- |
-
- R2577E.CEL
- |
-
- 0.065
- |
-
- 0.069
- |
-
- 2.07
- |
-
- 77
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.87
- |
-
- 1.29
- |
-
- UTM RW
- |
-
-
- |
- 55
- |
-
- R1700E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- F
- |
-
- R1700E.CEL
- |
-
- 0.152
- |
-
- 0.168
- |
-
- 2.98
- |
-
- 69
- |
-
- 60.80%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.48
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 56
- |
-
- R1704E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- M
- |
-
- R1704E.CEL
- |
-
- 0.154
- |
-
- 0.165
- |
-
- 2.58
- |
-
- 88
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.84
- |
-
- UTM RW
- |
-
-
- |
- 57
- |
-
- R0872E2
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 66
- |
-
- M
- |
-
- R0872E.CEL
- |
-
- 0.014
- |
-
- 0.023
- |
-
- 3.13
- |
-
- 89
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 58
- |
-
- R2607E1
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 67
- |
-
- F
- |
-
- R2605E.CEL
- |
-
- 0.008
- |
-
- 0.018
- |
-
- 2.43
- |
-
- 115
- |
-
- 58.60%
- |
-
- 40.00%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 59
- |
-
- R2564E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- F
- |
-
- R2564E.CEL
- |
-
- 0.124
- |
-
- 0.105
- |
-
- 1.94
- |
-
- 89
- |
-
- 58.50%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.60
- |
-
- 0.77
- |
-
- JAX
- |
-
-
- |
- 60
- |
-
- R2580E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- M
- |
-
- R2580E.CEL
- |
-
- 0.123
- |
-
- 0.109
- |
-
- 2.09
- |
-
- 95
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.70%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 61
- |
-
- R2600E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 72
- |
-
- F
- |
-
- R2600E.CEL
- |
-
- 0.008
- |
-
- 0.02
- |
-
- 2.47
- |
-
- 95
- |
-
- 58.10%
- |
-
- 40.20%
- |
-
- 1.70%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 62
- |
-
- R2604E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 69
- |
-
- M
- |
-
- R2604E.CEL
- |
-
- 0.005
- |
-
- 0.014
- |
-
- 2.66
- |
-
- 90
- |
-
- 59.40%
- |
-
- 39.20%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 63
- |
-
- R2572E1
- |
-
- GDP BXD
- |
-
- DBA/2J
- |
-
- 65
- |
-
- M
- |
-
- R2572E.CEL
- |
-
- 0.091
- |
-
- 0.106
- |
-
- 2.41
- |
-
- 79
- |
-
- 55.50%
- |
-
- 42.90%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 64
- |
-
- R2636E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- F
- |
-
- R2636E.CEL
- |
-
- 0.044
- |
-
- 0.043
- |
-
- 2.61
- |
-
- 93
- |
-
- 58.90%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 65
- |
-
- R2637E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- M
- |
-
- R2637E.CEL
- |
-
- 0.056
- |
-
- 0.036
- |
-
- 2.19
- |
-
- 103
- |
-
- 59.40%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 66
- |
-
- R0999E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 57
- |
-
- F
- |
-
- R0999E.CEL
- |
-
- 0.021
- |
-
- 0.023
- |
-
- 2.45
- |
-
- 82
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 67
- |
-
- R1004E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 65
- |
-
- M
- |
-
- R1004E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.44
- |
-
- 92
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 68
- |
-
- R1688E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 66
- |
-
- F
- |
-
- R1688E.CEL
- |
-
- 0.028
- |
-
- 0.033
- |
-
- 2.66
- |
-
- 98
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 69
- |
-
- R2566E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 76
- |
-
- M
- |
-
- R2566E-2.CEL
- |
-
- 0.036
- |
-
- 0.04
- |
-
- 3.03
- |
-
- 69
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 70
- |
-
- R2535E1
- |
-
- GDP
- |
-
- NZO/H1LtJ
- |
-
- 62
- |
-
- F
- |
-
- R2535E.CEL
- |
-
- 0.037
- |
-
- 0.062
- |
-
- 1.89
- |
-
- 86
- |
-
- 60.40%
- |
-
- 38.20%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 71
- |
-
- R2550E1
- |
-
- GDP
- |
-
- NZO/HILtJ
- |
-
- 96
- |
-
- M
- |
-
- R2550E.CEL
- |
-
- 0.025
- |
-
- 0.029
- |
-
- 1.79
- |
-
- 87
- |
-
- 60.70%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 72
- |
-
- R2634E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- F
- |
-
- R2635E.CEL
- |
-
- 0.126
- |
-
- 0.114
- |
-
- 3.29
- |
-
- 90
- |
-
- 55.90%
- |
-
- 42.50%
- |
-
- 1.60%
- |
-
- 1.57
- |
-
- 0.81
- |
-
- JAX
- |
-
-
- |
- 73
- |
-
- R2635E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- M
- |
-
- R2634E.CEL
- |
-
- 0.15
- |
-
- 0.137
- |
-
- 3.72
- |
-
- 80
- |
-
- 54.20%
- |
-
- 44.10%
- |
-
- 1.70%
- |
-
- 1.53
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 74
- |
-
- R2544E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 63
- |
-
- F
- |
-
- R2544E.CEL
- |
-
- 0.174
- |
-
- 0.175
- |
-
- 2.20
- |
-
- 108
- |
-
- 54.90%
- |
-
- 43.50%
- |
-
- 1.70%
- |
-
- 1.36
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 75
- |
-
- R2549E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 83
- |
-
- M
- |
-
- R2549E.CEL
- |
-
- 0.103
- |
-
- 0.087
- |
-
- 2.28
- |
-
- 84
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 0.83
- |
-
- JAX
- |
-
-
- |
- 76
- |
-
- R2368E1
- |
-
- GDP
- |
-
- WSB/EI
- |
-
- 67
- |
-
- F
- |
-
- R2368E.CEL
- |
-
- 0.041
- |
-
- 0.047
- |
-
- 2.57
- |
-
- 86
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.29
- |
-
- 0.74
- |
-
- UTM RW
- |
-
-
- |
- 77
- |
-
- R2704E
- |
-
- BXD
- |
-
- BXD1
- |
-
- 59
- |
-
- F
- |
-
- R2704E.CEL
- |
-
- 0.029
- |
-
- 0.03
- |
-
- 2.066
- |
-
- 139.61
- |
-
- 56.60%
- |
-
- 41.90%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 78
- |
-
- R2612E
- |
-
- BXD
- |
-
- BXD11
- |
-
- 70
- |
-
- M
- |
-
- R2612E.CEL
- |
-
- 0.101
- |
-
- 0.112
- |
-
- 1.83
- |
-
- 142.03
- |
-
- 58.20%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.78
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 79
- |
-
- R2742E
- |
-
- BXD
- |
-
- BXD12
- |
-
- 71
- |
-
- F
- |
-
- R2742E.CEL
- |
-
- 0.073
- |
-
- 0.077
- |
-
- 2.127
- |
-
- 134.14
- |
-
- 57.00%
- |
-
- 41.60%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 80
- |
-
- R1086E
- |
-
- BXD
- |
-
- BXD23
- |
-
- 55
- |
-
- M
- |
-
- R1086E.CEL
- |
-
- 0.043
- |
-
- 0.034
- |
-
- 2.233
- |
-
- 125.05
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 81
- |
-
- R2716E
- |
-
- BXD
- |
-
- BXD15
- |
-
- 60
- |
-
- M
- |
-
- R2716E.CEL
- |
-
- 0.035
- |
-
- 0.037
- |
-
- 2.015
- |
-
- 150.83
- |
-
- 56.40%
- |
-
- 42.10%
- |
-
- 1.60%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 82
- |
-
- R2711E
- |
-
- BXD
- |
-
- BXD16
- |
-
- 61
- |
-
- F
- |
-
- R2711E.CEL
- |
-
- 0.032
- |
-
- 0.021
- |
-
- 1.953
- |
-
- 118.53
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 83
- |
-
- R2720E
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- F
- |
-
- R2720E.CEL
- |
-
- 0.014
- |
-
- 0.019
- |
-
- 2.32
- |
-
- 99.93
- |
-
- 59.50%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 84
- |
-
- R2713E
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- M
- |
-
- R2713E.CEL
- |
-
- 0.055
- |
-
- 0.021
- |
-
- 1.67
- |
-
- 120.82
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 85
- |
-
- R1231E
- |
-
- BXD
- |
-
- BXD2
- |
-
- 64
- |
-
- F
- |
-
- R1231E.CEL
- |
-
- 0.044
- |
-
- 0.037
- |
-
- 2.197
- |
-
- 138.73
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 86
- |
-
- R2731E
- |
-
- BXD
- |
-
- BXD20
- |
-
- 60
- |
-
- M
- |
-
- R2731E.CEL
- |
-
- 0.017
- |
-
- 0.019
- |
-
- 1.825
- |
-
- 147
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 87
- |
-
- R2702E
- |
-
- BXD
- |
-
- BXD21
- |
-
- 59
- |
-
- F
- |
-
- R2702E.CEL
- |
-
- 0.009
- |
-
- 0.008
- |
-
- 1.811
- |
-
- 128.65
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.26
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 88
- |
-
- R2700E
- |
-
- BXD
- |
-
- BXD22
- |
-
- 59
- |
-
- M
- |
-
- R2700E.CEL
- |
-
- 0.01
- |
-
- 0.015
- |
-
- 1.858
- |
-
- 102.96
- |
-
- 61.50%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.48
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 89
- |
-
- R1128E
- |
-
- BXD
- |
-
- BXD14
- |
-
- 65
- |
-
- M
- |
-
- R1128E.CEL
- |
-
- 0.037
- |
-
- 0.038
- |
-
- 2.366
- |
-
- 118.39
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 90
- |
-
- R2719E
- |
-
- BXD
- |
-
- BXD24
- |
-
- 123
- |
-
- F
- |
-
- R2719E.CEL
- |
-
- 0.112
- |
-
- 0.111
- |
-
- 1.47
- |
-
- 140.38
- |
-
- 61.50%
- |
-
- 37.20%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 91
- |
-
- R2683E
- |
-
- BXD
- |
-
- BXD25
- |
-
- 58
- |
-
- M
- |
-
- R2683E.CEL
- |
-
- 0.068
- |
-
- 0.068
- |
-
- 1.777
- |
-
- 115.64
- |
-
- 58.30%
- |
-
- 40.30%
- |
-
- 1.40%
- |
-
- 2.01
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 92
- |
-
- R2703E
- |
-
- BXD
- |
-
- BXD27
- |
-
- 60
- |
-
- F
- |
-
- R2703E.CEL
- |
-
- 0.008
- |
-
- 0.012
- |
-
- 1.263
- |
-
- 134.78
- |
-
- 62.60%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 93
- |
-
- R2721E
- |
-
- BXD
- |
-
- BXD28
- |
-
- 60
- |
-
- M
- |
-
- R2721E.CEL
- |
-
- 0.04
- |
-
- 0.048
- |
-
- 2.065
- |
-
- 157.39
- |
-
- 56.10%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 94
- |
-
- R1258E
- |
-
- BXD
- |
-
- BXD31
- |
-
- 57
- |
-
- F
- |
-
- R1258E.CEL
- |
-
- 0.037
- |
-
- 0.036
- |
-
- 2.063
- |
-
- 117.09
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.54
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 95
- |
-
- R1216E
- |
-
- BXD
- |
-
- BXD32
- |
-
- 76
- |
-
- M
- |
-
- R1216E.CEL
- |
-
- 0.05
- |
-
- 0.049
- |
-
- 2.23
- |
-
- 111.99
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 96
- |
-
- R857E
- |
-
- BXD
- |
-
- BXD33
- |
-
- 77
- |
-
- M
- |
-
- R857E.CEL
- |
-
- 0.078
- |
-
- 0.108
- |
-
- 1.737
- |
-
- 113.98
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.30%
- |
-
- 1.6
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 97
- |
-
- R859E
- |
-
- BXD
- |
-
- BXD90
- |
-
- 72
- |
-
- M
- |
-
- R859E.CEL
- |
-
- 0.028
- |
-
- 0.02
- |
-
- 1.847
- |
-
- 152.22
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 98
- |
-
- R1207E
- |
-
- BXD
- |
-
- BXD66
- |
-
- 83
- |
-
- M
- |
-
- R1207E.CEL
- |
-
- 0.017
- |
-
- 0.012
- |
-
- 1.681
- |
-
- 136.86
- |
-
- 60.40%
- |
-
- 38.10%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 99
- |
-
- R2710E
- |
-
- BXD
- |
-
- BXD38
- |
-
- 55
- |
-
- F
- |
-
- R2710E.CEL
- |
-
- 0.033
- |
-
- 0.031
- |
-
- 2.112
- |
-
- 122.1
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 100
- |
-
- R2695E
- |
-
- BXD
- |
-
- BXD39
- |
-
- 59
- |
-
- M
- |
-
- R2695E.CEL
- |
-
- 0.018
- |
-
- 0.016
- |
-
- 1.638
- |
-
- 122.7
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 101
- |
-
- R2699E
- |
-
- BXD
- |
-
- BXD40
- |
-
- 59
- |
-
- F
- |
-
- R2699E.CEL
- |
-
- 0.014
- |
-
- 0.015
- |
-
- 1.827
- |
-
- 105.23
- |
-
- 61.70%
- |
-
- 36.90%
- |
-
- 1.40%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 102
- |
-
- R2696E
- |
-
- BXD
- |
-
- BXD42
- |
-
- 58
- |
-
- F
- |
-
- R2696E.CEL
- |
-
- 0.01
- |
-
- 0.017
- |
-
- 1.622
- |
-
- 118.95
- |
-
- 62.00%
- |
-
- 36.60%
- |
-
- 1.50%
- |
-
- 1.53
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 103
- |
-
- R943E-2
- |
-
- BXD
- |
-
- BXD64
- |
-
- 56
- |
-
- F
- |
-
- R943E-2.CEL
- |
-
- 0.024
- |
-
- 0.021
- |
-
- 1.591
- |
-
- 141.34
- |
-
- 60.10%
- |
-
- 38.40%
- |
-
- 1.50%
- |
-
- 1.32
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 104
- |
-
- R967E
- |
-
- BXD
- |
-
- BXD48
- |
-
- 64
- |
-
- F
- |
-
- R967E.CEL
- |
-
- 0.101
- |
-
- 0.052
- |
-
- 1.948
- |
-
- 130.95
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.63
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 105
- |
-
- R2714E
- |
-
- BXD
- |
-
- BXD5
- |
-
- 58
- |
-
- M
- |
-
- R2714E.CEL
- |
-
- 0.047
- |
-
- 0.014
- |
-
- 1.404
- |
-
- 144.35
- |
-
- 60.60%
- |
-
- 37.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 106
- |
-
- R1042E
- |
-
- BXD
- |
-
- BXD51
- |
-
- 62
- |
-
- M
- |
-
- R1042E.CEL
- |
-
- 0.028
- |
-
- 0.027
- |
-
- 2.352
- |
-
- 104.12
- |
-
- 58.70%
- |
-
- 39.90%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 107
- |
-
- R2690E
- |
-
- BXD
- |
-
- BXD55
- |
-
- 65
- |
-
- M
- |
-
- R2690E.CEL
- |
-
- 0.081
- |
-
- 0.067
- |
-
- 1.887
- |
-
- 164.01
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 108
- |
-
- R2694E
- |
-
- BXD
- |
-
- BXD6
- |
-
- 58
- |
-
- M
- |
-
- R2694E.CEL
- |
-
- 0.012
- |
-
- 0.018
- |
-
- 1.983
- |
-
- 97.23
- |
-
- 61.60%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 109
- |
-
- R975E
- |
-
- BXD
- |
-
- BXD70
- |
-
- 64
- |
-
- F
- |
-
- R975E.CEL
- |
-
- 0.028
- |
-
- 0.024
- |
-
- 1.841
- |
-
- 137.97
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 110
- |
-
- R2684E
- |
-
- BXD
- |
-
- BXD61
- |
-
- 62
- |
-
- M
- |
-
- R2684E.CEL
- |
-
- 0.031
- |
-
- 0.032
- |
-
- 2.01
- |
-
- 131.03
- |
-
- 57.00%
- |
-
- 41.50%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 111
- |
-
- R994E
- |
-
- BXD
- |
-
- BXD43
- |
-
- 60
- |
-
- F
- |
-
- R994E.CEL
- |
-
- 0.013
- |
-
- 0.014
- |
-
- 1.966
- |
-
- 113.12
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.40%
- |
-
- 1.66
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 112
- |
-
- R2610E
- |
-
- BXD
- |
-
- BXD44
- |
-
- 68
- |
-
- M
- |
-
- R2610E.CEL
- |
-
- 0.013
- |
-
- 0.009
- |
-
- 1.814
- |
-
- 142.91
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.35
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 113
- |
-
- R2689E
- |
-
- BXD
- |
-
- BXD65
- |
-
- 63
- |
-
- F
- |
-
- R2689E.CEL
- |
-
- 0.008
- |
-
- 0.008
- |
-
- 1.721
- |
-
- 142.44
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 114
- |
-
- R2727E
- |
-
- BXD
- |
-
- BXD69
- |
-
- 65
- |
-
- M
- |
-
- R2727E.CEL
- |
-
- 0.01
- |
-
- 0.008
- |
-
- 1.578
- |
-
- 143.86
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 115
- |
-
- R2726E
- |
-
- BXD
- |
-
- BXD68
- |
-
- 64
- |
-
- M
- |
-
- R2726E.CEL
- |
-
- 0.125
- |
-
- 0.025
- |
-
- 1.811
- |
-
- 153.09
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 116
- |
-
- R2732E
- |
-
- BXD
- |
-
- BXD45
- |
-
- 63
- |
-
- F
- |
-
- R2732E.CEL
- |
-
- 0.039
- |
-
- 0.036
- |
-
- 2.154
- |
-
- 122.45
- |
-
- 56.50%
- |
-
- 42.10%
- |
-
- 1.40%
- |
-
- 1.8
- |
-
- 0.83
- |
-
- GU
- |
-
-
- |
- 117
- |
-
- R2709E
- |
-
- BXD
- |
-
- BXD8
- |
-
- 61
- |
-
- M
- |
-
- R2709E.CEL
- |
-
- 0.012
- |
-
- 0.011
- |
-
- 1.99
- |
-
- 99.79
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 118
- |
-
- R2686E
- |
-
- BXD
- |
-
- BXD80
- |
-
- 61
- |
-
- M
- |
-
- R2686E.CEL
- |
-
- 0.046
- |
-
- 0.05
- |
-
- 2.342
- |
-
- 119.63
- |
-
- 56.00%
- |
-
- 42.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 119
- |
-
- R2692E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 63
- |
-
- F
- |
-
- R2692E.CEL
- |
-
- 0.006
- |
-
- 0.007
- |
-
- 1.423
- |
-
- 160.87
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.46
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 120
- |
-
- R2715E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 91
- |
-
- M
- |
-
- R2715E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 1.488
- |
-
- 142.6
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 121
- |
-
- R1405E
- |
-
- BXD
- |
-
- BXD86
- |
-
- 58
- |
-
- F
- |
-
- R1405E.CEL
- |
-
- 0.053
- |
-
- 0.052
- |
-
- 2.351
- |
-
- 119.34
- |
-
- 56.40%
- |
-
- 42.20%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 122
- |
-
- R2724E
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- F
- |
-
- R2724E.CEL
- |
-
- 0.013
- |
-
- 0.019
- |
-
- 1.906
- |
-
- 113.71
- |
-
- 60.70%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 123
- |
-
- R1451E
- |
-
- BXD
- |
-
- BXD34
- |
-
- 61
- |
-
- F
- |
-
- R1451E.CEL
- |
-
- 0.01
- |
-
- 0.009
- |
-
- 1.843
- |
-
- 140.05
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 124
- |
-
- R1433E
- |
-
- BXD
- |
-
- BXD89
- |
-
- 63
- |
-
- F
- |
-
- R1433E.CEL
- |
-
- 0.029
- |
-
- 0.026
- |
-
- 2.241
- |
-
- 115.86
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 125
- |
-
- R2733E
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- F
- |
-
- R2733E.CEL
- |
-
- 0.024
- |
-
- 0.054
- |
-
- 1.7
- |
-
- 113.99
- |
-
- 62.10%
- |
-
- 36.60%
- |
-
- 1.30%
- |
-
- 1.4
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 126
- |
-
- R2649E
- |
-
- BXD
- |
-
- BXD97
- |
-
- 74
- |
-
- F
- |
-
- R2649E.CEL
- |
-
- 0.029
- |
-
- 0.032
- |
-
- 2.343
- |
-
- 119.04
- |
-
- 57.50%
- |
-
- 41.20%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 127
- |
-
- R2688E
- |
-
- BXD
- |
-
- BXD98
- |
-
- 67
- |
-
- M
- |
-
- R2688E.CEL
- |
-
- 0.032
- |
-
- 0.03
- |
-
- 1.772
- |
-
- 145.24
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.48
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 128
- |
-
- R877E
- |
-
- BXD
- |
-
- BXD13
- |
-
- 76
- |
-
- M
- |
-
- R877E.CEL
- |
-
- 0.026
- |
-
- 0.067
- |
-
- 1.558
- |
-
- 125.63
- |
-
- 61.20%
- |
-
- 37.50%
- |
-
- 1.20%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 129
- |
-
- R1397E-re
- |
-
- BXD
- |
-
- BXD75
- |
-
- 58
- |
-
- M
- |
-
- R1397E-re.CEL
- |
-
- 0.032
- |
-
- 0.01
- |
-
- 1.449
- |
-
- 189.71
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 130
- |
-
- R2779E
- |
-
- BXD
- |
-
- BXD73
- |
-
- 64
- |
-
- F
- |
-
- R2779E.CEL
- |
-
- 0.012
- |
-
- 0.038
- |
-
- 1.746
- |
-
- 121.11
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 131
- |
-
- R2708E
- |
-
- BXD
- |
-
- BXD9
- |
-
- 60
- |
-
- F
- |
-
- R2708E.CEL
- |
-
- 0.024
- |
-
- 0.045
- |
-
- 1.966
- |
-
- 126.46
- |
-
- 57.70%
- |
-
- 40.70%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.84
- |
-
- GU
- |
-
-
- |
- 132
- |
-
- R2547E1
- |
-
- GDP
- |
-
- WSB/Ei
- |
-
- 67
- |
-
- M
- |
-
- R2547E.CEL
- |
-
- 0.041
- |
-
- 0.039
- |
-
- 2.14
- |
-
- 90
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.60%
- |
-
- 1.32
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
-
diff --git a/general/datasets/EYE_M2_1105_M/acknowledgment.rtf b/general/datasets/EYE_M2_1105_M/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/EYE_M2_1105_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/EYE_M2_1105_M/cases.rtf b/general/datasets/EYE_M2_1105_M/cases.rtf
deleted file mode 100644
index 687970b..0000000
--- a/general/datasets/EYE_M2_1105_M/cases.rtf
+++ /dev/null
@@ -1,51 +0,0 @@
-We have used a set of 14 conventional inbred strains, reciprocal F1s between C57BL/6J (B6 or B) and DBA/2J D2 (or D), and 47 BXD recombinant inbred strains. The BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
diff --git a/general/datasets/EYE_M2_1105_M/notes.rtf b/general/datasets/EYE_M2_1105_M/notes.rtf
deleted file mode 100644
index 48a01ef..0000000
--- a/general/datasets/EYE_M2_1105_M/notes.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-CAUTION: DO NOT USE THE PDNN TRANSFORM of the HEIMED EYE Database. USE RMA INSTEAD. This April 2005 data freeze provides estimates of mRNA expression in adult eye from 50 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 47 BXD recombinant inbred strains. Data were generated at UTHSC. Samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
-
-
-This text file originally generated by RWW, Nov 4, 2005. Updated by RWW, Nov 5, 2005. Modified Nov 7 with help of Y. Jiao.
-
diff --git a/general/datasets/EYE_M2_1105_M/platform.rtf b/general/datasets/EYE_M2_1105_M/platform.rtf
deleted file mode 100644
index fa332f1..0000000
--- a/general/datasets/EYE_M2_1105_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are essentially duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contain the same probe sequence as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/EYE_M2_1105_M/processing.rtf b/general/datasets/EYE_M2_1105_M/processing.rtf
deleted file mode 100644
index ff25e0d..0000000
--- a/general/datasets/EYE_M2_1105_M/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
diff --git a/general/datasets/EYE_M2_1105_M/summary.rtf b/general/datasets/EYE_M2_1105_M/summary.rtf
deleted file mode 100644
index 6c0fcbd..0000000
--- a/general/datasets/EYE_M2_1105_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATASET. The HEIMED November 2005 data set provides estimates of mRNA expression in whole eyes of 63 lines of mice without significant biological replication. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). Pooled RNA samples were hybridized to Affymetrix M430 2.0 arrays. This particular data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/EYE_M2_1105_M/tissue.rtf b/general/datasets/EYE_M2_1105_M/tissue.rtf
deleted file mode 100644
index ec39390..0000000
--- a/general/datasets/EYE_M2_1105_M/tissue.rtf
+++ /dev/null
@@ -1,1554 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations of brown and beige colored mice tend to have faint residual pigmentation that does affect hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 5 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2), of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table).
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The current first batch of array data, represents a balanced sample of males and females, but without within-strain replication. We expect to add roughly 100 additional samples inthe next few months.
-
-Batch Structure: This data set consists of a single batch. The great majority of arrays are from a single lot.
-
-The table below summarizes information on strain, age, sex, original CEL filename, several quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
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-
-
-
-
-
-
-
- | Id |
- tube ID |
- group type |
- Strain |
- age |
- sex |
- original CEL filename |
- PDNN 2Z outlier |
- RMA 2Z outlier |
- scale factor |
- background average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur(3'/5') |
- AFFX-GapdhMur(3'/5') |
- source |
-
-
- | 1 |
- R2607E1 |
- GDP BXD |
- C57BL/6J |
- 67 |
- F |
- R2605E.CEL |
- 0.005 |
- 0.009 |
- 2.428 |
- 115.12 |
- 0.586 |
- 0.4 |
- 0.014 |
- 1.31 |
- 0.76 |
- UTM RW |
-
-
- | 2 |
- R0872E2 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- R0872E.CEL |
- 0.013 |
- 0.012 |
- 3.128 |
- 88.58 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.3 |
- 0.79 |
- UTM RW |
-
-
- | 3 |
- R2572E1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- R2572E.CEL |
- 0.041 |
- 0.051 |
- 2.406 |
- 79.07 |
- 0.555 |
- 0.429 |
- 0.016 |
- 1.37 |
- 0.79 |
- UTM RW |
-
-
- | 4 |
- R2601E1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- R2601E.CEL |
- 0.003 |
- 0.004 |
- 2.545 |
- 91.96 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.44 |
- 0.78 |
- UTM RW |
-
-
- | 5 |
- R2602E1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- R2602E.CEL |
- 0.001 |
- 0.004 |
- 2.599 |
- 84.44 |
- 0.597 |
- 0.388 |
- 0.015 |
- 1.37 |
- 0.78 |
- UTM RW |
-
-
- | 6 |
- R2600E1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- R2600E.CEL |
- 0.003 |
- 0.008 |
- 2.47 |
- 94.75 |
- 0.581 |
- 0.402 |
- 0.017 |
- 1.41 |
- 0.78 |
- UTM RW |
-
-
- | 7 |
- R2604E1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- R2604E.CEL |
- 0.003 |
- 0.007 |
- 2.657 |
- 89.63 |
- 0.594 |
- 0.392 |
- 0.015 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 8 |
- R2597E1 |
- BXD |
- BXD2 |
- 61 |
- M |
- R2597E.CEL |
- 0.003 |
- 0.007 |
- 2.374 |
- 93.56 |
- 0.603 |
- 0.383 |
- 0.015 |
- 1.34 |
- 0.77 |
- Glenn |
-
-
- | 9 |
- R2591E1 |
- BXD |
- BXD5 |
- 60 |
- F |
- R2591E.CEL |
- 0.051 |
- 0.009 |
- 1.7 |
- 136.48 |
- 0.585 |
- 0.4 |
- 0.015 |
- 1.33 |
- 0.78 |
- Glenn |
-
-
- | 10 |
- R2570E1 |
- BXD |
- BXD6 |
- 65 |
- F |
- R2570E.CEL |
- 0.002 |
- 0.006 |
- 1.987 |
- 86.73 |
- 0.585 |
- 0.4 |
- 0.015 |
- 1.46 |
- 0.76 |
- UTM RW |
-
-
- | 11 |
- R2538E1 |
- BXD |
- BXD8 |
- 77 |
- F |
- R2538E.CEL |
- 0.037 |
- 0.028 |
- 1.905 |
- 101.98 |
- 0.612 |
- 0.373 |
- 0.015 |
- 1.52 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R2569E1 |
- BXD |
- BXD9 |
- 67 |
- M |
- R2569E.CEL |
- 0.014 |
- 0.027 |
- 1.753 |
- 87.36 |
- 0.551 |
- 0.434 |
- 0.015 |
- 2.82 |
- 3.14 |
- UTM RW |
-
-
- | 13 |
- R2581E1 |
- BXD |
- BXD11 |
- 65 |
- F |
- R2581E.CEL |
- 0.006 |
- 0.012 |
- 1.941 |
- 88.55 |
- 0.621 |
- 0.364 |
- 0.016 |
- 1.55 |
- 0.81 |
- UTM RW |
-
-
- | 14 |
- R2543E1 |
- BXD |
- BXD12 |
- 63 |
- M |
- R2543E.CEL |
- 0.036 |
- 0.007 |
- 1.605 |
- 117.69 |
- 0.586 |
- 0.399 |
- 0.016 |
- 1.43 |
- 0.77 |
- UTM RW |
-
-
- | 15 |
- R2586E1 |
- BXD |
- BXD13 |
- 60 |
- F |
- R2586E.CEL |
- 0.020 |
- 0.035 |
- 2.006 |
- 73.61 |
- 0.564 |
- 0.42 |
- 0.016 |
- 2.85 |
- 3.81 |
- Glenn |
-
-
- | 16 |
- R2557E1 |
- BXD |
- BXD14 |
- 60 |
- F |
- R2557E.CEL |
- 0.014 |
- 0.017 |
- 1.83 |
- 98.76 |
- 0.625 |
- 0.361 |
- 0.014 |
- 1.31 |
- 0.78 |
- Glenn |
-
-
- | 17 |
- R2567E1 |
- BXD |
- BXD16 |
- 60 |
- M |
- R2567E.CEL |
- 0.016 |
- 0.025 |
- 2.239 |
- 82.35 |
- 0.567 |
- 0.416 |
- 0.017 |
- 1.37 |
- 0.75 |
- Glenn |
-
-
- | 18 |
- R2559E1 |
- BXD |
- BXD18 |
- 59 |
- M |
- R2559E.CEL |
- 0.035 |
- 0.006 |
- 1.654 |
- 103.68 |
- 0.608 |
- 0.377 |
- 0.015 |
- 1.27 |
- 0.78 |
- Glenn |
-
-
- | 19 |
- R2560E1 |
- BXD |
- BXD19 |
- 60 |
- F |
- R2560E.CEL |
- 0.026 |
- 0.007 |
- 1.792 |
- 98.33 |
- 0.609 |
- 0.375 |
- 0.016 |
- 1.35 |
- 0.8 |
- Glenn |
-
-
- | 20 |
- R2584E1 |
- BXD |
- BXD20 |
- 59 |
- F |
- R2584E.CEL |
- 0.003 |
- 0.007 |
- 2.07 |
- 83.82 |
- 0.593 |
- 0.391 |
- 0.016 |
- 1.4 |
- 0.76 |
- Glenn |
-
-
- | 21 |
- R2541E2 |
- BXD |
- BXD21 |
- 61 |
- M |
- R2541E2.CEL |
- 0.049 |
- 0.036 |
- 2.625 |
- 125.08 |
- 0.56 |
- 0.424 |
- 0.015 |
- 1.29 |
- 0.78 |
- UTM RW |
-
-
- | 22 |
- R2553E1 |
- BXD |
- BXD22 |
- 58 |
- F |
- R2553E.CEL |
- 0.003 |
- 0.005 |
- 1.952 |
- 111.3 |
- 0.599 |
- 0.385 |
- 0.015 |
- 1.28 |
- 0.76 |
- Glenn |
-
-
- | 23 |
- R2558E1 |
- BXD |
- BXD23 |
- 60 |
- F |
- R2558E2.CEL |
- 0.013 |
- 0.015 |
- 1.908 |
- 114.53 |
- 0.599 |
- 0.388 |
- 0.014 |
- 1.2 |
- 0.82 |
- Glenn |
-
-
- | 24 |
- R2589E2 |
- BXD |
- BXD24-rd* |
- 59 |
- M |
- R2589E2.CEL |
- 0.098 |
- 0.098 |
- 2.606 |
- 112.19 |
- 0.575 |
- 0.409 |
- 0.016 |
- 1.24 |
- 0.8 |
- Glenn |
-
-
- | 25 |
- R2573E1 |
- BXD |
- BXD25 |
- 67 |
- F |
- R2573E2.CEL |
- 0.009 |
- 0.018 |
- 3.153 |
- 71.88 |
- 0.579 |
- 0.407 |
- 0.014 |
- 1.77 |
- 0.97 |
- UAB |
-
-
- | 26 |
- R2562E1 |
- BXD |
- BXD28 |
- 60 |
- F |
- R2562E.CEL |
- 0.003 |
- 0.005 |
- 1.649 |
- 116.35 |
- 0.599 |
- 0.384 |
- 0.017 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 27 |
- R2561E1 |
- BXD |
- BXD29 |
- 60 |
- F |
- R2561E.CEL |
- 0.019 |
- 0.029 |
- 1.952 |
- 93.32 |
- 0.583 |
- 0.402 |
- 0.015 |
- 2.19 |
- 1 |
- Glenn |
-
-
- | 28 |
- R2598E1 |
- BXD |
- BXD31 |
- 61 |
- M |
- R2598E.CEL |
- 0.003 |
- 0.006 |
- 1.989 |
- 106.48 |
- 0.609 |
- 0.376 |
- 0.015 |
- 1.27 |
- 0.78 |
- UTM RW |
-
-
- | 29 |
- R2563E1 |
- BXD |
- BXD32 |
- 63 |
- F |
- R2563E.CEL |
- 0.008 |
- 0.011 |
- 1.547 |
- 101.52 |
- 0.619 |
- 0.367 |
- 0.014 |
- 1.5 |
- 0.8 |
- UTM RW |
-
-
- | 30 |
- R2542E1 |
- BXD |
- BXD33 |
- 67 |
- F |
- R2542E.CEL |
- 0.010 |
- 0.016 |
- 2.128 |
- 97.08 |
- 0.565 |
- 0.418 |
- 0.016 |
- 1.91 |
- 0.93 |
- UTM RW |
-
-
- | 31 |
- R2585E1 |
- BXD |
- BXD34 |
- 60 |
- M |
- R2585E.CEL |
- 0.007 |
- 0.014 |
- 2.64 |
- 75.13 |
- 0.583 |
- 0.4 |
- 0.017 |
- 1.25 |
- 0.77 |
- Glenn |
-
-
- | 32 |
- R2532E1 |
- BXD |
- BXD38 |
- 62 |
- M |
- R2532E.CEL |
- 0.002 |
- 0.003 |
- 2.038 |
- 93.65 |
- 0.598 |
- 0.387 |
- 0.015 |
- 1.37 |
- 0.8 |
- UTM RW |
-
-
- | 33 |
- R2574E1 |
- BXD |
- BXD39 |
- 70 |
- F |
- R2574E.CEL |
- 0.001 |
- 0.004 |
- 1.981 |
- 90.64 |
- 0.612 |
- 0.373 |
- 0.015 |
- 1.39 |
- 0.78 |
- UTM RW |
-
-
- | 34 |
- R2590E1 |
- BXD |
- BXD40 |
- 60 |
- M |
- R2590E.CEL |
- 0.004 |
- 0.007 |
- 2.708 |
- 77.3 |
- 0.591 |
- 0.393 |
- 0.015 |
- 1.4 |
- 0.77 |
- Glenn |
-
-
- | 35 |
- R2596E1 |
- BXD |
- BXD42 |
- 59 |
- M |
- R2596E.CEL |
- 0.013 |
- 0.017 |
- 2.632 |
- 108.46 |
- 0.59 |
- 0.396 |
- 0.015 |
- 1.24 |
- 0.8 |
- Glenn |
-
-
- | 36 |
- R2605E1 |
- BXD |
- BXD43 |
- 79 |
- M |
- R2607E.CEL |
- 0.003 |
- 0.006 |
- 1.817 |
- 131.22 |
- 0.605 |
- 0.382 |
- 0.013 |
- 1.32 |
- 0.8 |
- UTM RW |
-
-
- | 37 |
- R2594E1 |
- BXD |
- BXD44 |
- 63 |
- F |
- R2594E.CEL |
- 0.004 |
- 0.009 |
- 1.766 |
- 117.33 |
- 0.598 |
- 0.388 |
- 0.014 |
- 1.35 |
- 0.85 |
- UTM RW |
-
-
- | 38 |
- R2592E1 |
- BXD |
- BXD45 |
- 62 |
- M |
- R2592E.CEL |
- 0.002 |
- 0.004 |
- 1.85 |
- 106.16 |
- 0.601 |
- 0.386 |
- 0.013 |
- 1.43 |
- 0.85 |
- UTM RW |
-
-
- | 39 |
- R2606E1 |
- BXD |
- BXD48 |
- 78 |
- M |
- R2606E.CEL |
- 0.003 |
- 0.010 |
- 2.556 |
- 106.16 |
- 0.589 |
- 0.397 |
- 0.014 |
- 1.35 |
- 0.83 |
- UTM RW |
-
-
- | 40 |
- R2603E1 |
- BXD |
- BXD51 |
- 66 |
- F |
- R2603E.CEL |
- 0.003 |
- 0.009 |
- 2.488 |
- 115.16 |
- 0.577 |
- 0.408 |
- 0.015 |
- 1.24 |
- 0.79 |
- UTM RW |
-
-
- | 41 |
- R2534E2 |
- BXD |
- BXD61* |
- 70 |
- F |
- R2534E2.CEL |
- 0.030 |
- 0.028 |
- 2.473 |
- 117.76 |
- 0.579 |
- 0.406 |
- 0.015 |
- 1.42 |
- 0.79 |
- UTM RW |
-
-
- | 42 |
- R2611E1 |
- BXD |
- BXD64 |
- 68 |
- M |
- R2611E.CEL |
- 0.013 |
- 0.022 |
- 2.292 |
- 91.99 |
- 0.58 |
- 0.405 |
- 0.015 |
- 1.57 |
- 1.06 |
- UTM RW |
-
-
- | 43 |
- R2583E1 |
- BXD |
- BXD65 |
- 60 |
- M |
- R2583E.CEL |
- 0.005 |
- 0.010 |
- 2.492 |
- 70.43 |
- 0.569 |
- 0.415 |
- 0.016 |
- 1.67 |
- 1.01 |
- UTM RW |
-
-
- | 44 |
- R2536E2 |
- BXD |
- BXD66* |
- 64 |
- F |
- R2536E2.CEL |
- 0.039 |
- 0.065 |
- 2.74 |
- 108.62 |
- 0.561 |
- 0.423 |
- 0.017 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 45 |
- R2551E1 |
- BXD |
- BXD68 |
- 67 |
- F |
- R2551E.CEL |
- 0.037 |
- 0.039 |
- 2.493 |
- 92.38 |
- 0.543 |
- 0.441 |
- 0.016 |
- 2.91 |
- 1.55 |
- UTM RW |
-
-
- | 46 |
- R2593E1 |
- BXD |
- BXD69 |
- 59 |
- F |
- R2593E.CEL |
- 0.008 |
- 0.013 |
- 1.672 |
- 127.6 |
- 0.592 |
- 0.395 |
- 0.013 |
- 1.47 |
- 0.92 |
- UTM RW |
-
-
- | 47 |
- R2537E2 |
- BXD |
- BXD70* |
- 59 |
- M |
- R2537E2.CEL |
- 0.046 |
- 0.044 |
- 2.93 |
- 98.66 |
- 0.58 |
- 0.405 |
- 0.016 |
- 1.29 |
- 0.75 |
- UTM RW |
-
-
- | 48 |
- R2565E1 |
- BXD |
- BXD75 |
- 61 |
- F |
- R2565E.CEL |
- 0.009 |
- 0.017 |
- 1.79 |
- 101.68 |
- 0.58 |
- 0.405 |
- 0.015 |
- 2.31 |
- 3.47 |
- UTM RW |
-
-
- | 49 |
- R2579E1 |
- BXD |
- BXD80 |
- 65 |
- F |
- R2579E.CEL |
- 0.005 |
- 0.010 |
- 2.419 |
- 72.13 |
- 0.592 |
- 0.394 |
- 0.015 |
- 1.73 |
- 0.82 |
- UTM RW |
-
-
- | 50 |
- R2540E1 |
- BXD |
- BXD87 |
- 63 |
- M |
- R2540E.CEL |
- 0.013 |
- 0.016 |
- 2.333 |
- 93.15 |
- 0.611 |
- 0.374 |
- 0.014 |
- 1.22 |
- 0.81 |
- UTM RW |
-
-
- | 51 |
- R2545E1 |
- BXD |
- BXD89 |
- 67 |
- M |
- R2546E.CEL |
- 0.046 |
- 0.046 |
- 1.667 |
- 104.76 |
- 0.562 |
- 0.423 |
- 0.015 |
- 3.6 |
- 9.84 |
- UTM RW |
-
-
- | 52 |
- R2578E2 |
- BXD |
- BXD90* |
- 61 |
- F |
- R2578E2.CEL |
- 0.033 |
- 0.034 |
- 2.785 |
- 92.27 |
- 0.586 |
- 0.398 |
- 0.016 |
- 1.52 |
- 0.77 |
- UTM RW |
-
-
- | 53 |
- R2554E1 |
- BXD |
- BXD96 |
- 67 |
- M |
- R2554E.CEL |
- 0.004 |
- 0.004 |
- 2.177 |
- 93.02 |
- 0.602 |
- 0.383 |
- 0.015 |
- 1.46 |
- 0.77 |
- UTM RW |
-
-
- | 54 |
- R2577E1 |
- BXD |
- BXD97 |
- 55 |
- M |
- R2577E.CEL |
- 0.019 |
- 0.016 |
- 2.07 |
- 76.58 |
- 0.595 |
- 0.391 |
- 0.014 |
- 1.87 |
- 1.29 |
- UTM RW |
-
-
- | 55 |
- R2595E1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- R2595E.CEL |
- 0.017 |
- 0.021 |
- 1.792 |
- 115.39 |
- 0.61 |
- 0.375 |
- 0.015 |
- 1.46 |
- 0.77 |
- UTM RW |
-
-
- | 56 |
- R2533E1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- R2533E.CEL |
- 0.021 |
- 0.013 |
- 2.107 |
- 93.55 |
- 0.579 |
- 0.405 |
- 0.016 |
- 1.37 |
- 0.78 |
- UTM RW |
-
-
- | 57 |
- R2546E1 |
- GDP |
- A/J |
- 66 |
- F |
- R2545E.CEL |
- 0.018 |
- 0.014 |
- 1.989 |
- 95.59 |
- 0.586 |
- 0.397 |
- 0.017 |
- 1.47 |
- 0.78 |
- UTM RW |
-
-
- | 58 |
- R0754E2 |
- GDP |
- A/J |
- 60 |
- M |
- R0754E.CEL |
- 0.014 |
- 0.016 |
- 2.718 |
- 85.63 |
- 0.598 |
- 0.387 |
- 0.015 |
- 1.36 |
- 0.76 |
- JAX |
-
-
- | 59 |
- R1676E1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- R1676E.CEL |
- 0.042 |
- 0.041 |
- 2.685 |
- 98.37 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.46 |
- 0.74 |
- JAX |
-
-
- | 60 |
- R1672E1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- R1672E.CEL |
- 0.022 |
- 0.022 |
- 2.216 |
- 110.52 |
- 0.599 |
- 0.386 |
- 0.015 |
- 1.26 |
- 0.8 |
- JAX |
-
-
- | 61 |
- R1700E1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- R1700E.CEL |
- 0.090 |
- 0.092 |
- 2.978 |
- 68.77 |
- 0.608 |
- 0.379 |
- 0.014 |
- 1.48 |
- 0.78 |
- UTM RW |
-
-
- | 62 |
- R1704E1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- R1704E.CEL |
- 0.086 |
- 0.089 |
- 2.581 |
- 88.29 |
- 0.601 |
- 0.386 |
- 0.013 |
- 1.38 |
- 0.84 |
- UTM RW |
-
-
- | 63 |
- R2564E1 |
- GDP |
- CAST/Ei |
- 64 |
- F |
- R2564E.CEL |
- 0.078 |
- 0.064 |
- 1.937 |
- 88.89 |
- 0.585 |
- 0.399 |
- 0.016 |
- 1.6 |
- 0.77 |
- JAX |
-
-
- | 64 |
- R2580E1 |
- GDP |
- CAST/Ei |
- 64 |
- M |
- R2580E.CEL |
- 0.076 |
- 0.067 |
- 2.089 |
- 94.64 |
- 0.582 |
- 0.401 |
- 0.017 |
- 1.4 |
- 0.76 |
- JAX |
-
-
- | 65 |
- R2636E1 |
- GDP |
- KK/HIJ |
- 64 |
- F |
- R2636E.CEL |
- 0.023 |
- 0.026 |
- 2.61 |
- 93.1 |
- 0.589 |
- 0.395 |
- 0.015 |
- 1.39 |
- 0.76 |
- UTM RW |
-
-
- | 66 |
- R2637E1 |
- GDP |
- KK/HIJ |
- 64 |
- M |
- R2637E.CEL |
- 0.039 |
- 0.020 |
- 2.189 |
- 102.78 |
- 0.594 |
- 0.39 |
- 0.015 |
- 1.3 |
- 0.79 |
- UTM RW |
-
-
- | 67 |
- R0999E1 |
- GDP |
- LG/J |
- 57 |
- F |
- R0999E.CEL |
- 0.012 |
- 0.012 |
- 2.448 |
- 82.09 |
- 0.594 |
- 0.391 |
- 0.015 |
- 1.38 |
- 0.79 |
- UTM RW |
-
-
- | 68 |
- R1004E1 |
- GDP |
- LG/J |
- 65 |
- M |
- R1004E.CEL |
- 0.013 |
- 0.015 |
- 2.438 |
- 91.71 |
- 0.587 |
- 0.398 |
- 0.015 |
- 1.38 |
- 0.79 |
- UTM RW |
-
-
- | 69 |
- R1688E1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- R1688E.CEL |
- 0.017 |
- 0.019 |
- 2.664 |
- 97.65 |
- 0.586 |
- 0.399 |
- 0.015 |
- 1.26 |
- 0.8 |
- JAX |
-
-
- | 70 |
- R2566E1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- R2566E2.CEL |
- 0.019 |
- 0.025 |
- 3.031 |
- 69.44 |
- 0.598 |
- 0.388 |
- 0.015 |
- 1.38 |
- 0.75 |
- UTM RW |
-
-
- | 71 |
- R2550E1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- R2550E.CEL |
- 0.023 |
- 0.015 |
- 1.794 |
- 87.16 |
- 0.607 |
- 0.378 |
- 0.015 |
- 1.52 |
- 0.82 |
- JAX |
-
-
- | 72 |
- R2535E1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- R2535E.CEL |
- 0.046 |
- 0.025 |
- 1.893 |
- 85.67 |
- 0.604 |
- 0.382 |
- 0.014 |
- 1.41 |
- 0.85 |
- JAX |
-
-
- | 73 |
- R2634E1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- R2635E.CEL |
- 0.077 |
- 0.069 |
- 3.292 |
- 89.8 |
- 0.559 |
- 0.425 |
- 0.016 |
- 1.57 |
- 0.81 |
- JAX |
-
-
- | 74 |
- R2635E1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- R2634E.CEL |
- 0.088 |
- 0.081 |
- 3.722 |
- 80.05 |
- 0.542 |
- 0.441 |
- 0.017 |
- 1.53 |
- 0.85 |
- JAX |
-
-
- | 75 |
- R2544E1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- R2544E.CEL |
- 0.106 |
- 0.100 |
- 2.196 |
- 107.51 |
- 0.549 |
- 0.435 |
- 0.017 |
- 1.36 |
- 0.82 |
- JAX |
-
-
- | 76 |
- R2549E1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- R2549E.CEL |
- 0.065 |
- 0.048 |
- 2.275 |
- 83.8 |
- 0.573 |
- 0.412 |
- 0.015 |
- 1.57 |
- 0.83 |
- JAX |
-
-
- | 77 |
- R2368E1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- R2368E.CEL |
- 0.025 |
- 0.028 |
- 2.567 |
- 85.7 |
- 0.595 |
- 0.391 |
- 0.014 |
- 1.29 |
- 0.74 |
- UTM RW |
-
-
- | 78 |
- R2547E1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- R2547E.CEL |
- 0.032 |
- 0.021 |
- 2.135 |
- 90.04 |
- 0.582 |
- 0.401 |
- 0.016 |
- 1.32 |
- 0.77 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/EYE_M2_1105_P/acknowledgment.rtf b/general/datasets/EYE_M2_1105_P/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/EYE_M2_1105_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/EYE_M2_1105_P/cases.rtf b/general/datasets/EYE_M2_1105_P/cases.rtf
deleted file mode 100644
index 687970b..0000000
--- a/general/datasets/EYE_M2_1105_P/cases.rtf
+++ /dev/null
@@ -1,51 +0,0 @@
-We have used a set of 14 conventional inbred strains, reciprocal F1s between C57BL/6J (B6 or B) and DBA/2J D2 (or D), and 47 BXD recombinant inbred strains. The BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
diff --git a/general/datasets/EYE_M2_1105_P/notes.rtf b/general/datasets/EYE_M2_1105_P/notes.rtf
deleted file mode 100644
index 48a01ef..0000000
--- a/general/datasets/EYE_M2_1105_P/notes.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-CAUTION: DO NOT USE THE PDNN TRANSFORM of the HEIMED EYE Database. USE RMA INSTEAD. This April 2005 data freeze provides estimates of mRNA expression in adult eye from 50 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 47 BXD recombinant inbred strains. Data were generated at UTHSC. Samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
-
-
-This text file originally generated by RWW, Nov 4, 2005. Updated by RWW, Nov 5, 2005. Modified Nov 7 with help of Y. Jiao.
-
diff --git a/general/datasets/EYE_M2_1105_P/platform.rtf b/general/datasets/EYE_M2_1105_P/platform.rtf
deleted file mode 100644
index fa332f1..0000000
--- a/general/datasets/EYE_M2_1105_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are essentially duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contain the same probe sequence as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/EYE_M2_1105_P/processing.rtf b/general/datasets/EYE_M2_1105_P/processing.rtf
deleted file mode 100644
index ff25e0d..0000000
--- a/general/datasets/EYE_M2_1105_P/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
diff --git a/general/datasets/EYE_M2_1105_P/summary.rtf b/general/datasets/EYE_M2_1105_P/summary.rtf
deleted file mode 100644
index 6c0fcbd..0000000
--- a/general/datasets/EYE_M2_1105_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATASET. The HEIMED November 2005 data set provides estimates of mRNA expression in whole eyes of 63 lines of mice without significant biological replication. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). Pooled RNA samples were hybridized to Affymetrix M430 2.0 arrays. This particular data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/EYE_M2_1105_P/tissue.rtf b/general/datasets/EYE_M2_1105_P/tissue.rtf
deleted file mode 100644
index ec39390..0000000
--- a/general/datasets/EYE_M2_1105_P/tissue.rtf
+++ /dev/null
@@ -1,1554 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations of brown and beige colored mice tend to have faint residual pigmentation that does affect hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 5 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2), of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table).
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The current first batch of array data, represents a balanced sample of males and females, but without within-strain replication. We expect to add roughly 100 additional samples inthe next few months.
-
-Batch Structure: This data set consists of a single batch. The great majority of arrays are from a single lot.
-
-The table below summarizes information on strain, age, sex, original CEL filename, several quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Id |
- tube ID |
- group type |
- Strain |
- age |
- sex |
- original CEL filename |
- PDNN 2Z outlier |
- RMA 2Z outlier |
- scale factor |
- background average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur(3'/5') |
- AFFX-GapdhMur(3'/5') |
- source |
-
-
- | 1 |
- R2607E1 |
- GDP BXD |
- C57BL/6J |
- 67 |
- F |
- R2605E.CEL |
- 0.005 |
- 0.009 |
- 2.428 |
- 115.12 |
- 0.586 |
- 0.4 |
- 0.014 |
- 1.31 |
- 0.76 |
- UTM RW |
-
-
- | 2 |
- R0872E2 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- R0872E.CEL |
- 0.013 |
- 0.012 |
- 3.128 |
- 88.58 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.3 |
- 0.79 |
- UTM RW |
-
-
- | 3 |
- R2572E1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- R2572E.CEL |
- 0.041 |
- 0.051 |
- 2.406 |
- 79.07 |
- 0.555 |
- 0.429 |
- 0.016 |
- 1.37 |
- 0.79 |
- UTM RW |
-
-
- | 4 |
- R2601E1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- R2601E.CEL |
- 0.003 |
- 0.004 |
- 2.545 |
- 91.96 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.44 |
- 0.78 |
- UTM RW |
-
-
- | 5 |
- R2602E1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- R2602E.CEL |
- 0.001 |
- 0.004 |
- 2.599 |
- 84.44 |
- 0.597 |
- 0.388 |
- 0.015 |
- 1.37 |
- 0.78 |
- UTM RW |
-
-
- | 6 |
- R2600E1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- R2600E.CEL |
- 0.003 |
- 0.008 |
- 2.47 |
- 94.75 |
- 0.581 |
- 0.402 |
- 0.017 |
- 1.41 |
- 0.78 |
- UTM RW |
-
-
- | 7 |
- R2604E1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- R2604E.CEL |
- 0.003 |
- 0.007 |
- 2.657 |
- 89.63 |
- 0.594 |
- 0.392 |
- 0.015 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 8 |
- R2597E1 |
- BXD |
- BXD2 |
- 61 |
- M |
- R2597E.CEL |
- 0.003 |
- 0.007 |
- 2.374 |
- 93.56 |
- 0.603 |
- 0.383 |
- 0.015 |
- 1.34 |
- 0.77 |
- Glenn |
-
-
- | 9 |
- R2591E1 |
- BXD |
- BXD5 |
- 60 |
- F |
- R2591E.CEL |
- 0.051 |
- 0.009 |
- 1.7 |
- 136.48 |
- 0.585 |
- 0.4 |
- 0.015 |
- 1.33 |
- 0.78 |
- Glenn |
-
-
- | 10 |
- R2570E1 |
- BXD |
- BXD6 |
- 65 |
- F |
- R2570E.CEL |
- 0.002 |
- 0.006 |
- 1.987 |
- 86.73 |
- 0.585 |
- 0.4 |
- 0.015 |
- 1.46 |
- 0.76 |
- UTM RW |
-
-
- | 11 |
- R2538E1 |
- BXD |
- BXD8 |
- 77 |
- F |
- R2538E.CEL |
- 0.037 |
- 0.028 |
- 1.905 |
- 101.98 |
- 0.612 |
- 0.373 |
- 0.015 |
- 1.52 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R2569E1 |
- BXD |
- BXD9 |
- 67 |
- M |
- R2569E.CEL |
- 0.014 |
- 0.027 |
- 1.753 |
- 87.36 |
- 0.551 |
- 0.434 |
- 0.015 |
- 2.82 |
- 3.14 |
- UTM RW |
-
-
- | 13 |
- R2581E1 |
- BXD |
- BXD11 |
- 65 |
- F |
- R2581E.CEL |
- 0.006 |
- 0.012 |
- 1.941 |
- 88.55 |
- 0.621 |
- 0.364 |
- 0.016 |
- 1.55 |
- 0.81 |
- UTM RW |
-
-
- | 14 |
- R2543E1 |
- BXD |
- BXD12 |
- 63 |
- M |
- R2543E.CEL |
- 0.036 |
- 0.007 |
- 1.605 |
- 117.69 |
- 0.586 |
- 0.399 |
- 0.016 |
- 1.43 |
- 0.77 |
- UTM RW |
-
-
- | 15 |
- R2586E1 |
- BXD |
- BXD13 |
- 60 |
- F |
- R2586E.CEL |
- 0.020 |
- 0.035 |
- 2.006 |
- 73.61 |
- 0.564 |
- 0.42 |
- 0.016 |
- 2.85 |
- 3.81 |
- Glenn |
-
-
- | 16 |
- R2557E1 |
- BXD |
- BXD14 |
- 60 |
- F |
- R2557E.CEL |
- 0.014 |
- 0.017 |
- 1.83 |
- 98.76 |
- 0.625 |
- 0.361 |
- 0.014 |
- 1.31 |
- 0.78 |
- Glenn |
-
-
- | 17 |
- R2567E1 |
- BXD |
- BXD16 |
- 60 |
- M |
- R2567E.CEL |
- 0.016 |
- 0.025 |
- 2.239 |
- 82.35 |
- 0.567 |
- 0.416 |
- 0.017 |
- 1.37 |
- 0.75 |
- Glenn |
-
-
- | 18 |
- R2559E1 |
- BXD |
- BXD18 |
- 59 |
- M |
- R2559E.CEL |
- 0.035 |
- 0.006 |
- 1.654 |
- 103.68 |
- 0.608 |
- 0.377 |
- 0.015 |
- 1.27 |
- 0.78 |
- Glenn |
-
-
- | 19 |
- R2560E1 |
- BXD |
- BXD19 |
- 60 |
- F |
- R2560E.CEL |
- 0.026 |
- 0.007 |
- 1.792 |
- 98.33 |
- 0.609 |
- 0.375 |
- 0.016 |
- 1.35 |
- 0.8 |
- Glenn |
-
-
- | 20 |
- R2584E1 |
- BXD |
- BXD20 |
- 59 |
- F |
- R2584E.CEL |
- 0.003 |
- 0.007 |
- 2.07 |
- 83.82 |
- 0.593 |
- 0.391 |
- 0.016 |
- 1.4 |
- 0.76 |
- Glenn |
-
-
- | 21 |
- R2541E2 |
- BXD |
- BXD21 |
- 61 |
- M |
- R2541E2.CEL |
- 0.049 |
- 0.036 |
- 2.625 |
- 125.08 |
- 0.56 |
- 0.424 |
- 0.015 |
- 1.29 |
- 0.78 |
- UTM RW |
-
-
- | 22 |
- R2553E1 |
- BXD |
- BXD22 |
- 58 |
- F |
- R2553E.CEL |
- 0.003 |
- 0.005 |
- 1.952 |
- 111.3 |
- 0.599 |
- 0.385 |
- 0.015 |
- 1.28 |
- 0.76 |
- Glenn |
-
-
- | 23 |
- R2558E1 |
- BXD |
- BXD23 |
- 60 |
- F |
- R2558E2.CEL |
- 0.013 |
- 0.015 |
- 1.908 |
- 114.53 |
- 0.599 |
- 0.388 |
- 0.014 |
- 1.2 |
- 0.82 |
- Glenn |
-
-
- | 24 |
- R2589E2 |
- BXD |
- BXD24-rd* |
- 59 |
- M |
- R2589E2.CEL |
- 0.098 |
- 0.098 |
- 2.606 |
- 112.19 |
- 0.575 |
- 0.409 |
- 0.016 |
- 1.24 |
- 0.8 |
- Glenn |
-
-
- | 25 |
- R2573E1 |
- BXD |
- BXD25 |
- 67 |
- F |
- R2573E2.CEL |
- 0.009 |
- 0.018 |
- 3.153 |
- 71.88 |
- 0.579 |
- 0.407 |
- 0.014 |
- 1.77 |
- 0.97 |
- UAB |
-
-
- | 26 |
- R2562E1 |
- BXD |
- BXD28 |
- 60 |
- F |
- R2562E.CEL |
- 0.003 |
- 0.005 |
- 1.649 |
- 116.35 |
- 0.599 |
- 0.384 |
- 0.017 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 27 |
- R2561E1 |
- BXD |
- BXD29 |
- 60 |
- F |
- R2561E.CEL |
- 0.019 |
- 0.029 |
- 1.952 |
- 93.32 |
- 0.583 |
- 0.402 |
- 0.015 |
- 2.19 |
- 1 |
- Glenn |
-
-
- | 28 |
- R2598E1 |
- BXD |
- BXD31 |
- 61 |
- M |
- R2598E.CEL |
- 0.003 |
- 0.006 |
- 1.989 |
- 106.48 |
- 0.609 |
- 0.376 |
- 0.015 |
- 1.27 |
- 0.78 |
- UTM RW |
-
-
- | 29 |
- R2563E1 |
- BXD |
- BXD32 |
- 63 |
- F |
- R2563E.CEL |
- 0.008 |
- 0.011 |
- 1.547 |
- 101.52 |
- 0.619 |
- 0.367 |
- 0.014 |
- 1.5 |
- 0.8 |
- UTM RW |
-
-
- | 30 |
- R2542E1 |
- BXD |
- BXD33 |
- 67 |
- F |
- R2542E.CEL |
- 0.010 |
- 0.016 |
- 2.128 |
- 97.08 |
- 0.565 |
- 0.418 |
- 0.016 |
- 1.91 |
- 0.93 |
- UTM RW |
-
-
- | 31 |
- R2585E1 |
- BXD |
- BXD34 |
- 60 |
- M |
- R2585E.CEL |
- 0.007 |
- 0.014 |
- 2.64 |
- 75.13 |
- 0.583 |
- 0.4 |
- 0.017 |
- 1.25 |
- 0.77 |
- Glenn |
-
-
- | 32 |
- R2532E1 |
- BXD |
- BXD38 |
- 62 |
- M |
- R2532E.CEL |
- 0.002 |
- 0.003 |
- 2.038 |
- 93.65 |
- 0.598 |
- 0.387 |
- 0.015 |
- 1.37 |
- 0.8 |
- UTM RW |
-
-
- | 33 |
- R2574E1 |
- BXD |
- BXD39 |
- 70 |
- F |
- R2574E.CEL |
- 0.001 |
- 0.004 |
- 1.981 |
- 90.64 |
- 0.612 |
- 0.373 |
- 0.015 |
- 1.39 |
- 0.78 |
- UTM RW |
-
-
- | 34 |
- R2590E1 |
- BXD |
- BXD40 |
- 60 |
- M |
- R2590E.CEL |
- 0.004 |
- 0.007 |
- 2.708 |
- 77.3 |
- 0.591 |
- 0.393 |
- 0.015 |
- 1.4 |
- 0.77 |
- Glenn |
-
-
- | 35 |
- R2596E1 |
- BXD |
- BXD42 |
- 59 |
- M |
- R2596E.CEL |
- 0.013 |
- 0.017 |
- 2.632 |
- 108.46 |
- 0.59 |
- 0.396 |
- 0.015 |
- 1.24 |
- 0.8 |
- Glenn |
-
-
- | 36 |
- R2605E1 |
- BXD |
- BXD43 |
- 79 |
- M |
- R2607E.CEL |
- 0.003 |
- 0.006 |
- 1.817 |
- 131.22 |
- 0.605 |
- 0.382 |
- 0.013 |
- 1.32 |
- 0.8 |
- UTM RW |
-
-
- | 37 |
- R2594E1 |
- BXD |
- BXD44 |
- 63 |
- F |
- R2594E.CEL |
- 0.004 |
- 0.009 |
- 1.766 |
- 117.33 |
- 0.598 |
- 0.388 |
- 0.014 |
- 1.35 |
- 0.85 |
- UTM RW |
-
-
- | 38 |
- R2592E1 |
- BXD |
- BXD45 |
- 62 |
- M |
- R2592E.CEL |
- 0.002 |
- 0.004 |
- 1.85 |
- 106.16 |
- 0.601 |
- 0.386 |
- 0.013 |
- 1.43 |
- 0.85 |
- UTM RW |
-
-
- | 39 |
- R2606E1 |
- BXD |
- BXD48 |
- 78 |
- M |
- R2606E.CEL |
- 0.003 |
- 0.010 |
- 2.556 |
- 106.16 |
- 0.589 |
- 0.397 |
- 0.014 |
- 1.35 |
- 0.83 |
- UTM RW |
-
-
- | 40 |
- R2603E1 |
- BXD |
- BXD51 |
- 66 |
- F |
- R2603E.CEL |
- 0.003 |
- 0.009 |
- 2.488 |
- 115.16 |
- 0.577 |
- 0.408 |
- 0.015 |
- 1.24 |
- 0.79 |
- UTM RW |
-
-
- | 41 |
- R2534E2 |
- BXD |
- BXD61* |
- 70 |
- F |
- R2534E2.CEL |
- 0.030 |
- 0.028 |
- 2.473 |
- 117.76 |
- 0.579 |
- 0.406 |
- 0.015 |
- 1.42 |
- 0.79 |
- UTM RW |
-
-
- | 42 |
- R2611E1 |
- BXD |
- BXD64 |
- 68 |
- M |
- R2611E.CEL |
- 0.013 |
- 0.022 |
- 2.292 |
- 91.99 |
- 0.58 |
- 0.405 |
- 0.015 |
- 1.57 |
- 1.06 |
- UTM RW |
-
-
- | 43 |
- R2583E1 |
- BXD |
- BXD65 |
- 60 |
- M |
- R2583E.CEL |
- 0.005 |
- 0.010 |
- 2.492 |
- 70.43 |
- 0.569 |
- 0.415 |
- 0.016 |
- 1.67 |
- 1.01 |
- UTM RW |
-
-
- | 44 |
- R2536E2 |
- BXD |
- BXD66* |
- 64 |
- F |
- R2536E2.CEL |
- 0.039 |
- 0.065 |
- 2.74 |
- 108.62 |
- 0.561 |
- 0.423 |
- 0.017 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 45 |
- R2551E1 |
- BXD |
- BXD68 |
- 67 |
- F |
- R2551E.CEL |
- 0.037 |
- 0.039 |
- 2.493 |
- 92.38 |
- 0.543 |
- 0.441 |
- 0.016 |
- 2.91 |
- 1.55 |
- UTM RW |
-
-
- | 46 |
- R2593E1 |
- BXD |
- BXD69 |
- 59 |
- F |
- R2593E.CEL |
- 0.008 |
- 0.013 |
- 1.672 |
- 127.6 |
- 0.592 |
- 0.395 |
- 0.013 |
- 1.47 |
- 0.92 |
- UTM RW |
-
-
- | 47 |
- R2537E2 |
- BXD |
- BXD70* |
- 59 |
- M |
- R2537E2.CEL |
- 0.046 |
- 0.044 |
- 2.93 |
- 98.66 |
- 0.58 |
- 0.405 |
- 0.016 |
- 1.29 |
- 0.75 |
- UTM RW |
-
-
- | 48 |
- R2565E1 |
- BXD |
- BXD75 |
- 61 |
- F |
- R2565E.CEL |
- 0.009 |
- 0.017 |
- 1.79 |
- 101.68 |
- 0.58 |
- 0.405 |
- 0.015 |
- 2.31 |
- 3.47 |
- UTM RW |
-
-
- | 49 |
- R2579E1 |
- BXD |
- BXD80 |
- 65 |
- F |
- R2579E.CEL |
- 0.005 |
- 0.010 |
- 2.419 |
- 72.13 |
- 0.592 |
- 0.394 |
- 0.015 |
- 1.73 |
- 0.82 |
- UTM RW |
-
-
- | 50 |
- R2540E1 |
- BXD |
- BXD87 |
- 63 |
- M |
- R2540E.CEL |
- 0.013 |
- 0.016 |
- 2.333 |
- 93.15 |
- 0.611 |
- 0.374 |
- 0.014 |
- 1.22 |
- 0.81 |
- UTM RW |
-
-
- | 51 |
- R2545E1 |
- BXD |
- BXD89 |
- 67 |
- M |
- R2546E.CEL |
- 0.046 |
- 0.046 |
- 1.667 |
- 104.76 |
- 0.562 |
- 0.423 |
- 0.015 |
- 3.6 |
- 9.84 |
- UTM RW |
-
-
- | 52 |
- R2578E2 |
- BXD |
- BXD90* |
- 61 |
- F |
- R2578E2.CEL |
- 0.033 |
- 0.034 |
- 2.785 |
- 92.27 |
- 0.586 |
- 0.398 |
- 0.016 |
- 1.52 |
- 0.77 |
- UTM RW |
-
-
- | 53 |
- R2554E1 |
- BXD |
- BXD96 |
- 67 |
- M |
- R2554E.CEL |
- 0.004 |
- 0.004 |
- 2.177 |
- 93.02 |
- 0.602 |
- 0.383 |
- 0.015 |
- 1.46 |
- 0.77 |
- UTM RW |
-
-
- | 54 |
- R2577E1 |
- BXD |
- BXD97 |
- 55 |
- M |
- R2577E.CEL |
- 0.019 |
- 0.016 |
- 2.07 |
- 76.58 |
- 0.595 |
- 0.391 |
- 0.014 |
- 1.87 |
- 1.29 |
- UTM RW |
-
-
- | 55 |
- R2595E1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- R2595E.CEL |
- 0.017 |
- 0.021 |
- 1.792 |
- 115.39 |
- 0.61 |
- 0.375 |
- 0.015 |
- 1.46 |
- 0.77 |
- UTM RW |
-
-
- | 56 |
- R2533E1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- R2533E.CEL |
- 0.021 |
- 0.013 |
- 2.107 |
- 93.55 |
- 0.579 |
- 0.405 |
- 0.016 |
- 1.37 |
- 0.78 |
- UTM RW |
-
-
- | 57 |
- R2546E1 |
- GDP |
- A/J |
- 66 |
- F |
- R2545E.CEL |
- 0.018 |
- 0.014 |
- 1.989 |
- 95.59 |
- 0.586 |
- 0.397 |
- 0.017 |
- 1.47 |
- 0.78 |
- UTM RW |
-
-
- | 58 |
- R0754E2 |
- GDP |
- A/J |
- 60 |
- M |
- R0754E.CEL |
- 0.014 |
- 0.016 |
- 2.718 |
- 85.63 |
- 0.598 |
- 0.387 |
- 0.015 |
- 1.36 |
- 0.76 |
- JAX |
-
-
- | 59 |
- R1676E1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- R1676E.CEL |
- 0.042 |
- 0.041 |
- 2.685 |
- 98.37 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.46 |
- 0.74 |
- JAX |
-
-
- | 60 |
- R1672E1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- R1672E.CEL |
- 0.022 |
- 0.022 |
- 2.216 |
- 110.52 |
- 0.599 |
- 0.386 |
- 0.015 |
- 1.26 |
- 0.8 |
- JAX |
-
-
- | 61 |
- R1700E1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- R1700E.CEL |
- 0.090 |
- 0.092 |
- 2.978 |
- 68.77 |
- 0.608 |
- 0.379 |
- 0.014 |
- 1.48 |
- 0.78 |
- UTM RW |
-
-
- | 62 |
- R1704E1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- R1704E.CEL |
- 0.086 |
- 0.089 |
- 2.581 |
- 88.29 |
- 0.601 |
- 0.386 |
- 0.013 |
- 1.38 |
- 0.84 |
- UTM RW |
-
-
- | 63 |
- R2564E1 |
- GDP |
- CAST/Ei |
- 64 |
- F |
- R2564E.CEL |
- 0.078 |
- 0.064 |
- 1.937 |
- 88.89 |
- 0.585 |
- 0.399 |
- 0.016 |
- 1.6 |
- 0.77 |
- JAX |
-
-
- | 64 |
- R2580E1 |
- GDP |
- CAST/Ei |
- 64 |
- M |
- R2580E.CEL |
- 0.076 |
- 0.067 |
- 2.089 |
- 94.64 |
- 0.582 |
- 0.401 |
- 0.017 |
- 1.4 |
- 0.76 |
- JAX |
-
-
- | 65 |
- R2636E1 |
- GDP |
- KK/HIJ |
- 64 |
- F |
- R2636E.CEL |
- 0.023 |
- 0.026 |
- 2.61 |
- 93.1 |
- 0.589 |
- 0.395 |
- 0.015 |
- 1.39 |
- 0.76 |
- UTM RW |
-
-
- | 66 |
- R2637E1 |
- GDP |
- KK/HIJ |
- 64 |
- M |
- R2637E.CEL |
- 0.039 |
- 0.020 |
- 2.189 |
- 102.78 |
- 0.594 |
- 0.39 |
- 0.015 |
- 1.3 |
- 0.79 |
- UTM RW |
-
-
- | 67 |
- R0999E1 |
- GDP |
- LG/J |
- 57 |
- F |
- R0999E.CEL |
- 0.012 |
- 0.012 |
- 2.448 |
- 82.09 |
- 0.594 |
- 0.391 |
- 0.015 |
- 1.38 |
- 0.79 |
- UTM RW |
-
-
- | 68 |
- R1004E1 |
- GDP |
- LG/J |
- 65 |
- M |
- R1004E.CEL |
- 0.013 |
- 0.015 |
- 2.438 |
- 91.71 |
- 0.587 |
- 0.398 |
- 0.015 |
- 1.38 |
- 0.79 |
- UTM RW |
-
-
- | 69 |
- R1688E1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- R1688E.CEL |
- 0.017 |
- 0.019 |
- 2.664 |
- 97.65 |
- 0.586 |
- 0.399 |
- 0.015 |
- 1.26 |
- 0.8 |
- JAX |
-
-
- | 70 |
- R2566E1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- R2566E2.CEL |
- 0.019 |
- 0.025 |
- 3.031 |
- 69.44 |
- 0.598 |
- 0.388 |
- 0.015 |
- 1.38 |
- 0.75 |
- UTM RW |
-
-
- | 71 |
- R2550E1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- R2550E.CEL |
- 0.023 |
- 0.015 |
- 1.794 |
- 87.16 |
- 0.607 |
- 0.378 |
- 0.015 |
- 1.52 |
- 0.82 |
- JAX |
-
-
- | 72 |
- R2535E1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- R2535E.CEL |
- 0.046 |
- 0.025 |
- 1.893 |
- 85.67 |
- 0.604 |
- 0.382 |
- 0.014 |
- 1.41 |
- 0.85 |
- JAX |
-
-
- | 73 |
- R2634E1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- R2635E.CEL |
- 0.077 |
- 0.069 |
- 3.292 |
- 89.8 |
- 0.559 |
- 0.425 |
- 0.016 |
- 1.57 |
- 0.81 |
- JAX |
-
-
- | 74 |
- R2635E1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- R2634E.CEL |
- 0.088 |
- 0.081 |
- 3.722 |
- 80.05 |
- 0.542 |
- 0.441 |
- 0.017 |
- 1.53 |
- 0.85 |
- JAX |
-
-
- | 75 |
- R2544E1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- R2544E.CEL |
- 0.106 |
- 0.100 |
- 2.196 |
- 107.51 |
- 0.549 |
- 0.435 |
- 0.017 |
- 1.36 |
- 0.82 |
- JAX |
-
-
- | 76 |
- R2549E1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- R2549E.CEL |
- 0.065 |
- 0.048 |
- 2.275 |
- 83.8 |
- 0.573 |
- 0.412 |
- 0.015 |
- 1.57 |
- 0.83 |
- JAX |
-
-
- | 77 |
- R2368E1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- R2368E.CEL |
- 0.025 |
- 0.028 |
- 2.567 |
- 85.7 |
- 0.595 |
- 0.391 |
- 0.014 |
- 1.29 |
- 0.74 |
- UTM RW |
-
-
- | 78 |
- R2547E1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- R2547E.CEL |
- 0.032 |
- 0.021 |
- 2.135 |
- 90.04 |
- 0.582 |
- 0.401 |
- 0.016 |
- 1.32 |
- 0.77 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/EYE_M2_1105_R/acknowledgment.rtf b/general/datasets/EYE_M2_1105_R/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/EYE_M2_1105_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/EYE_M2_1105_R/cases.rtf b/general/datasets/EYE_M2_1105_R/cases.rtf
deleted file mode 100644
index 687970b..0000000
--- a/general/datasets/EYE_M2_1105_R/cases.rtf
+++ /dev/null
@@ -1,51 +0,0 @@
-We have used a set of 14 conventional inbred strains, reciprocal F1s between C57BL/6J (B6 or B) and DBA/2J D2 (or D), and 47 BXD recombinant inbred strains. The BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
diff --git a/general/datasets/EYE_M2_1105_R/notes.rtf b/general/datasets/EYE_M2_1105_R/notes.rtf
deleted file mode 100644
index 48a01ef..0000000
--- a/general/datasets/EYE_M2_1105_R/notes.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-CAUTION: DO NOT USE THE PDNN TRANSFORM of the HEIMED EYE Database. USE RMA INSTEAD. This April 2005 data freeze provides estimates of mRNA expression in adult eye from 50 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 47 BXD recombinant inbred strains. Data were generated at UTHSC. Samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
-
-
-This text file originally generated by RWW, Nov 4, 2005. Updated by RWW, Nov 5, 2005. Modified Nov 7 with help of Y. Jiao.
-
diff --git a/general/datasets/EYE_M2_1105_R/platform.rtf b/general/datasets/EYE_M2_1105_R/platform.rtf
deleted file mode 100644
index fa332f1..0000000
--- a/general/datasets/EYE_M2_1105_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are essentially duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contain the same probe sequence as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/EYE_M2_1105_R/processing.rtf b/general/datasets/EYE_M2_1105_R/processing.rtf
deleted file mode 100644
index ff25e0d..0000000
--- a/general/datasets/EYE_M2_1105_R/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
diff --git a/general/datasets/EYE_M2_1105_R/summary.rtf b/general/datasets/EYE_M2_1105_R/summary.rtf
deleted file mode 100644
index 6c0fcbd..0000000
--- a/general/datasets/EYE_M2_1105_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATASET. The HEIMED November 2005 data set provides estimates of mRNA expression in whole eyes of 63 lines of mice without significant biological replication. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). Pooled RNA samples were hybridized to Affymetrix M430 2.0 arrays. This particular data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/EYE_M2_1105_R/tissue.rtf b/general/datasets/EYE_M2_1105_R/tissue.rtf
deleted file mode 100644
index ec39390..0000000
--- a/general/datasets/EYE_M2_1105_R/tissue.rtf
+++ /dev/null
@@ -1,1554 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations of brown and beige colored mice tend to have faint residual pigmentation that does affect hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 5 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2), of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table).
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The current first batch of array data, represents a balanced sample of males and females, but without within-strain replication. We expect to add roughly 100 additional samples inthe next few months.
-
-Batch Structure: This data set consists of a single batch. The great majority of arrays are from a single lot.
-
-The table below summarizes information on strain, age, sex, original CEL filename, several quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Id |
- tube ID |
- group type |
- Strain |
- age |
- sex |
- original CEL filename |
- PDNN 2Z outlier |
- RMA 2Z outlier |
- scale factor |
- background average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur(3'/5') |
- AFFX-GapdhMur(3'/5') |
- source |
-
-
- | 1 |
- R2607E1 |
- GDP BXD |
- C57BL/6J |
- 67 |
- F |
- R2605E.CEL |
- 0.005 |
- 0.009 |
- 2.428 |
- 115.12 |
- 0.586 |
- 0.4 |
- 0.014 |
- 1.31 |
- 0.76 |
- UTM RW |
-
-
- | 2 |
- R0872E2 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- R0872E.CEL |
- 0.013 |
- 0.012 |
- 3.128 |
- 88.58 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.3 |
- 0.79 |
- UTM RW |
-
-
- | 3 |
- R2572E1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- R2572E.CEL |
- 0.041 |
- 0.051 |
- 2.406 |
- 79.07 |
- 0.555 |
- 0.429 |
- 0.016 |
- 1.37 |
- 0.79 |
- UTM RW |
-
-
- | 4 |
- R2601E1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- R2601E.CEL |
- 0.003 |
- 0.004 |
- 2.545 |
- 91.96 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.44 |
- 0.78 |
- UTM RW |
-
-
- | 5 |
- R2602E1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- R2602E.CEL |
- 0.001 |
- 0.004 |
- 2.599 |
- 84.44 |
- 0.597 |
- 0.388 |
- 0.015 |
- 1.37 |
- 0.78 |
- UTM RW |
-
-
- | 6 |
- R2600E1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- R2600E.CEL |
- 0.003 |
- 0.008 |
- 2.47 |
- 94.75 |
- 0.581 |
- 0.402 |
- 0.017 |
- 1.41 |
- 0.78 |
- UTM RW |
-
-
- | 7 |
- R2604E1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- R2604E.CEL |
- 0.003 |
- 0.007 |
- 2.657 |
- 89.63 |
- 0.594 |
- 0.392 |
- 0.015 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 8 |
- R2597E1 |
- BXD |
- BXD2 |
- 61 |
- M |
- R2597E.CEL |
- 0.003 |
- 0.007 |
- 2.374 |
- 93.56 |
- 0.603 |
- 0.383 |
- 0.015 |
- 1.34 |
- 0.77 |
- Glenn |
-
-
- | 9 |
- R2591E1 |
- BXD |
- BXD5 |
- 60 |
- F |
- R2591E.CEL |
- 0.051 |
- 0.009 |
- 1.7 |
- 136.48 |
- 0.585 |
- 0.4 |
- 0.015 |
- 1.33 |
- 0.78 |
- Glenn |
-
-
- | 10 |
- R2570E1 |
- BXD |
- BXD6 |
- 65 |
- F |
- R2570E.CEL |
- 0.002 |
- 0.006 |
- 1.987 |
- 86.73 |
- 0.585 |
- 0.4 |
- 0.015 |
- 1.46 |
- 0.76 |
- UTM RW |
-
-
- | 11 |
- R2538E1 |
- BXD |
- BXD8 |
- 77 |
- F |
- R2538E.CEL |
- 0.037 |
- 0.028 |
- 1.905 |
- 101.98 |
- 0.612 |
- 0.373 |
- 0.015 |
- 1.52 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R2569E1 |
- BXD |
- BXD9 |
- 67 |
- M |
- R2569E.CEL |
- 0.014 |
- 0.027 |
- 1.753 |
- 87.36 |
- 0.551 |
- 0.434 |
- 0.015 |
- 2.82 |
- 3.14 |
- UTM RW |
-
-
- | 13 |
- R2581E1 |
- BXD |
- BXD11 |
- 65 |
- F |
- R2581E.CEL |
- 0.006 |
- 0.012 |
- 1.941 |
- 88.55 |
- 0.621 |
- 0.364 |
- 0.016 |
- 1.55 |
- 0.81 |
- UTM RW |
-
-
- | 14 |
- R2543E1 |
- BXD |
- BXD12 |
- 63 |
- M |
- R2543E.CEL |
- 0.036 |
- 0.007 |
- 1.605 |
- 117.69 |
- 0.586 |
- 0.399 |
- 0.016 |
- 1.43 |
- 0.77 |
- UTM RW |
-
-
- | 15 |
- R2586E1 |
- BXD |
- BXD13 |
- 60 |
- F |
- R2586E.CEL |
- 0.020 |
- 0.035 |
- 2.006 |
- 73.61 |
- 0.564 |
- 0.42 |
- 0.016 |
- 2.85 |
- 3.81 |
- Glenn |
-
-
- | 16 |
- R2557E1 |
- BXD |
- BXD14 |
- 60 |
- F |
- R2557E.CEL |
- 0.014 |
- 0.017 |
- 1.83 |
- 98.76 |
- 0.625 |
- 0.361 |
- 0.014 |
- 1.31 |
- 0.78 |
- Glenn |
-
-
- | 17 |
- R2567E1 |
- BXD |
- BXD16 |
- 60 |
- M |
- R2567E.CEL |
- 0.016 |
- 0.025 |
- 2.239 |
- 82.35 |
- 0.567 |
- 0.416 |
- 0.017 |
- 1.37 |
- 0.75 |
- Glenn |
-
-
- | 18 |
- R2559E1 |
- BXD |
- BXD18 |
- 59 |
- M |
- R2559E.CEL |
- 0.035 |
- 0.006 |
- 1.654 |
- 103.68 |
- 0.608 |
- 0.377 |
- 0.015 |
- 1.27 |
- 0.78 |
- Glenn |
-
-
- | 19 |
- R2560E1 |
- BXD |
- BXD19 |
- 60 |
- F |
- R2560E.CEL |
- 0.026 |
- 0.007 |
- 1.792 |
- 98.33 |
- 0.609 |
- 0.375 |
- 0.016 |
- 1.35 |
- 0.8 |
- Glenn |
-
-
- | 20 |
- R2584E1 |
- BXD |
- BXD20 |
- 59 |
- F |
- R2584E.CEL |
- 0.003 |
- 0.007 |
- 2.07 |
- 83.82 |
- 0.593 |
- 0.391 |
- 0.016 |
- 1.4 |
- 0.76 |
- Glenn |
-
-
- | 21 |
- R2541E2 |
- BXD |
- BXD21 |
- 61 |
- M |
- R2541E2.CEL |
- 0.049 |
- 0.036 |
- 2.625 |
- 125.08 |
- 0.56 |
- 0.424 |
- 0.015 |
- 1.29 |
- 0.78 |
- UTM RW |
-
-
- | 22 |
- R2553E1 |
- BXD |
- BXD22 |
- 58 |
- F |
- R2553E.CEL |
- 0.003 |
- 0.005 |
- 1.952 |
- 111.3 |
- 0.599 |
- 0.385 |
- 0.015 |
- 1.28 |
- 0.76 |
- Glenn |
-
-
- | 23 |
- R2558E1 |
- BXD |
- BXD23 |
- 60 |
- F |
- R2558E2.CEL |
- 0.013 |
- 0.015 |
- 1.908 |
- 114.53 |
- 0.599 |
- 0.388 |
- 0.014 |
- 1.2 |
- 0.82 |
- Glenn |
-
-
- | 24 |
- R2589E2 |
- BXD |
- BXD24-rd* |
- 59 |
- M |
- R2589E2.CEL |
- 0.098 |
- 0.098 |
- 2.606 |
- 112.19 |
- 0.575 |
- 0.409 |
- 0.016 |
- 1.24 |
- 0.8 |
- Glenn |
-
-
- | 25 |
- R2573E1 |
- BXD |
- BXD25 |
- 67 |
- F |
- R2573E2.CEL |
- 0.009 |
- 0.018 |
- 3.153 |
- 71.88 |
- 0.579 |
- 0.407 |
- 0.014 |
- 1.77 |
- 0.97 |
- UAB |
-
-
- | 26 |
- R2562E1 |
- BXD |
- BXD28 |
- 60 |
- F |
- R2562E.CEL |
- 0.003 |
- 0.005 |
- 1.649 |
- 116.35 |
- 0.599 |
- 0.384 |
- 0.017 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 27 |
- R2561E1 |
- BXD |
- BXD29 |
- 60 |
- F |
- R2561E.CEL |
- 0.019 |
- 0.029 |
- 1.952 |
- 93.32 |
- 0.583 |
- 0.402 |
- 0.015 |
- 2.19 |
- 1 |
- Glenn |
-
-
- | 28 |
- R2598E1 |
- BXD |
- BXD31 |
- 61 |
- M |
- R2598E.CEL |
- 0.003 |
- 0.006 |
- 1.989 |
- 106.48 |
- 0.609 |
- 0.376 |
- 0.015 |
- 1.27 |
- 0.78 |
- UTM RW |
-
-
- | 29 |
- R2563E1 |
- BXD |
- BXD32 |
- 63 |
- F |
- R2563E.CEL |
- 0.008 |
- 0.011 |
- 1.547 |
- 101.52 |
- 0.619 |
- 0.367 |
- 0.014 |
- 1.5 |
- 0.8 |
- UTM RW |
-
-
- | 30 |
- R2542E1 |
- BXD |
- BXD33 |
- 67 |
- F |
- R2542E.CEL |
- 0.010 |
- 0.016 |
- 2.128 |
- 97.08 |
- 0.565 |
- 0.418 |
- 0.016 |
- 1.91 |
- 0.93 |
- UTM RW |
-
-
- | 31 |
- R2585E1 |
- BXD |
- BXD34 |
- 60 |
- M |
- R2585E.CEL |
- 0.007 |
- 0.014 |
- 2.64 |
- 75.13 |
- 0.583 |
- 0.4 |
- 0.017 |
- 1.25 |
- 0.77 |
- Glenn |
-
-
- | 32 |
- R2532E1 |
- BXD |
- BXD38 |
- 62 |
- M |
- R2532E.CEL |
- 0.002 |
- 0.003 |
- 2.038 |
- 93.65 |
- 0.598 |
- 0.387 |
- 0.015 |
- 1.37 |
- 0.8 |
- UTM RW |
-
-
- | 33 |
- R2574E1 |
- BXD |
- BXD39 |
- 70 |
- F |
- R2574E.CEL |
- 0.001 |
- 0.004 |
- 1.981 |
- 90.64 |
- 0.612 |
- 0.373 |
- 0.015 |
- 1.39 |
- 0.78 |
- UTM RW |
-
-
- | 34 |
- R2590E1 |
- BXD |
- BXD40 |
- 60 |
- M |
- R2590E.CEL |
- 0.004 |
- 0.007 |
- 2.708 |
- 77.3 |
- 0.591 |
- 0.393 |
- 0.015 |
- 1.4 |
- 0.77 |
- Glenn |
-
-
- | 35 |
- R2596E1 |
- BXD |
- BXD42 |
- 59 |
- M |
- R2596E.CEL |
- 0.013 |
- 0.017 |
- 2.632 |
- 108.46 |
- 0.59 |
- 0.396 |
- 0.015 |
- 1.24 |
- 0.8 |
- Glenn |
-
-
- | 36 |
- R2605E1 |
- BXD |
- BXD43 |
- 79 |
- M |
- R2607E.CEL |
- 0.003 |
- 0.006 |
- 1.817 |
- 131.22 |
- 0.605 |
- 0.382 |
- 0.013 |
- 1.32 |
- 0.8 |
- UTM RW |
-
-
- | 37 |
- R2594E1 |
- BXD |
- BXD44 |
- 63 |
- F |
- R2594E.CEL |
- 0.004 |
- 0.009 |
- 1.766 |
- 117.33 |
- 0.598 |
- 0.388 |
- 0.014 |
- 1.35 |
- 0.85 |
- UTM RW |
-
-
- | 38 |
- R2592E1 |
- BXD |
- BXD45 |
- 62 |
- M |
- R2592E.CEL |
- 0.002 |
- 0.004 |
- 1.85 |
- 106.16 |
- 0.601 |
- 0.386 |
- 0.013 |
- 1.43 |
- 0.85 |
- UTM RW |
-
-
- | 39 |
- R2606E1 |
- BXD |
- BXD48 |
- 78 |
- M |
- R2606E.CEL |
- 0.003 |
- 0.010 |
- 2.556 |
- 106.16 |
- 0.589 |
- 0.397 |
- 0.014 |
- 1.35 |
- 0.83 |
- UTM RW |
-
-
- | 40 |
- R2603E1 |
- BXD |
- BXD51 |
- 66 |
- F |
- R2603E.CEL |
- 0.003 |
- 0.009 |
- 2.488 |
- 115.16 |
- 0.577 |
- 0.408 |
- 0.015 |
- 1.24 |
- 0.79 |
- UTM RW |
-
-
- | 41 |
- R2534E2 |
- BXD |
- BXD61* |
- 70 |
- F |
- R2534E2.CEL |
- 0.030 |
- 0.028 |
- 2.473 |
- 117.76 |
- 0.579 |
- 0.406 |
- 0.015 |
- 1.42 |
- 0.79 |
- UTM RW |
-
-
- | 42 |
- R2611E1 |
- BXD |
- BXD64 |
- 68 |
- M |
- R2611E.CEL |
- 0.013 |
- 0.022 |
- 2.292 |
- 91.99 |
- 0.58 |
- 0.405 |
- 0.015 |
- 1.57 |
- 1.06 |
- UTM RW |
-
-
- | 43 |
- R2583E1 |
- BXD |
- BXD65 |
- 60 |
- M |
- R2583E.CEL |
- 0.005 |
- 0.010 |
- 2.492 |
- 70.43 |
- 0.569 |
- 0.415 |
- 0.016 |
- 1.67 |
- 1.01 |
- UTM RW |
-
-
- | 44 |
- R2536E2 |
- BXD |
- BXD66* |
- 64 |
- F |
- R2536E2.CEL |
- 0.039 |
- 0.065 |
- 2.74 |
- 108.62 |
- 0.561 |
- 0.423 |
- 0.017 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 45 |
- R2551E1 |
- BXD |
- BXD68 |
- 67 |
- F |
- R2551E.CEL |
- 0.037 |
- 0.039 |
- 2.493 |
- 92.38 |
- 0.543 |
- 0.441 |
- 0.016 |
- 2.91 |
- 1.55 |
- UTM RW |
-
-
- | 46 |
- R2593E1 |
- BXD |
- BXD69 |
- 59 |
- F |
- R2593E.CEL |
- 0.008 |
- 0.013 |
- 1.672 |
- 127.6 |
- 0.592 |
- 0.395 |
- 0.013 |
- 1.47 |
- 0.92 |
- UTM RW |
-
-
- | 47 |
- R2537E2 |
- BXD |
- BXD70* |
- 59 |
- M |
- R2537E2.CEL |
- 0.046 |
- 0.044 |
- 2.93 |
- 98.66 |
- 0.58 |
- 0.405 |
- 0.016 |
- 1.29 |
- 0.75 |
- UTM RW |
-
-
- | 48 |
- R2565E1 |
- BXD |
- BXD75 |
- 61 |
- F |
- R2565E.CEL |
- 0.009 |
- 0.017 |
- 1.79 |
- 101.68 |
- 0.58 |
- 0.405 |
- 0.015 |
- 2.31 |
- 3.47 |
- UTM RW |
-
-
- | 49 |
- R2579E1 |
- BXD |
- BXD80 |
- 65 |
- F |
- R2579E.CEL |
- 0.005 |
- 0.010 |
- 2.419 |
- 72.13 |
- 0.592 |
- 0.394 |
- 0.015 |
- 1.73 |
- 0.82 |
- UTM RW |
-
-
- | 50 |
- R2540E1 |
- BXD |
- BXD87 |
- 63 |
- M |
- R2540E.CEL |
- 0.013 |
- 0.016 |
- 2.333 |
- 93.15 |
- 0.611 |
- 0.374 |
- 0.014 |
- 1.22 |
- 0.81 |
- UTM RW |
-
-
- | 51 |
- R2545E1 |
- BXD |
- BXD89 |
- 67 |
- M |
- R2546E.CEL |
- 0.046 |
- 0.046 |
- 1.667 |
- 104.76 |
- 0.562 |
- 0.423 |
- 0.015 |
- 3.6 |
- 9.84 |
- UTM RW |
-
-
- | 52 |
- R2578E2 |
- BXD |
- BXD90* |
- 61 |
- F |
- R2578E2.CEL |
- 0.033 |
- 0.034 |
- 2.785 |
- 92.27 |
- 0.586 |
- 0.398 |
- 0.016 |
- 1.52 |
- 0.77 |
- UTM RW |
-
-
- | 53 |
- R2554E1 |
- BXD |
- BXD96 |
- 67 |
- M |
- R2554E.CEL |
- 0.004 |
- 0.004 |
- 2.177 |
- 93.02 |
- 0.602 |
- 0.383 |
- 0.015 |
- 1.46 |
- 0.77 |
- UTM RW |
-
-
- | 54 |
- R2577E1 |
- BXD |
- BXD97 |
- 55 |
- M |
- R2577E.CEL |
- 0.019 |
- 0.016 |
- 2.07 |
- 76.58 |
- 0.595 |
- 0.391 |
- 0.014 |
- 1.87 |
- 1.29 |
- UTM RW |
-
-
- | 55 |
- R2595E1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- R2595E.CEL |
- 0.017 |
- 0.021 |
- 1.792 |
- 115.39 |
- 0.61 |
- 0.375 |
- 0.015 |
- 1.46 |
- 0.77 |
- UTM RW |
-
-
- | 56 |
- R2533E1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- R2533E.CEL |
- 0.021 |
- 0.013 |
- 2.107 |
- 93.55 |
- 0.579 |
- 0.405 |
- 0.016 |
- 1.37 |
- 0.78 |
- UTM RW |
-
-
- | 57 |
- R2546E1 |
- GDP |
- A/J |
- 66 |
- F |
- R2545E.CEL |
- 0.018 |
- 0.014 |
- 1.989 |
- 95.59 |
- 0.586 |
- 0.397 |
- 0.017 |
- 1.47 |
- 0.78 |
- UTM RW |
-
-
- | 58 |
- R0754E2 |
- GDP |
- A/J |
- 60 |
- M |
- R0754E.CEL |
- 0.014 |
- 0.016 |
- 2.718 |
- 85.63 |
- 0.598 |
- 0.387 |
- 0.015 |
- 1.36 |
- 0.76 |
- JAX |
-
-
- | 59 |
- R1676E1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- R1676E.CEL |
- 0.042 |
- 0.041 |
- 2.685 |
- 98.37 |
- 0.589 |
- 0.396 |
- 0.015 |
- 1.46 |
- 0.74 |
- JAX |
-
-
- | 60 |
- R1672E1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- R1672E.CEL |
- 0.022 |
- 0.022 |
- 2.216 |
- 110.52 |
- 0.599 |
- 0.386 |
- 0.015 |
- 1.26 |
- 0.8 |
- JAX |
-
-
- | 61 |
- R1700E1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- R1700E.CEL |
- 0.090 |
- 0.092 |
- 2.978 |
- 68.77 |
- 0.608 |
- 0.379 |
- 0.014 |
- 1.48 |
- 0.78 |
- UTM RW |
-
-
- | 62 |
- R1704E1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- R1704E.CEL |
- 0.086 |
- 0.089 |
- 2.581 |
- 88.29 |
- 0.601 |
- 0.386 |
- 0.013 |
- 1.38 |
- 0.84 |
- UTM RW |
-
-
- | 63 |
- R2564E1 |
- GDP |
- CAST/Ei |
- 64 |
- F |
- R2564E.CEL |
- 0.078 |
- 0.064 |
- 1.937 |
- 88.89 |
- 0.585 |
- 0.399 |
- 0.016 |
- 1.6 |
- 0.77 |
- JAX |
-
-
- | 64 |
- R2580E1 |
- GDP |
- CAST/Ei |
- 64 |
- M |
- R2580E.CEL |
- 0.076 |
- 0.067 |
- 2.089 |
- 94.64 |
- 0.582 |
- 0.401 |
- 0.017 |
- 1.4 |
- 0.76 |
- JAX |
-
-
- | 65 |
- R2636E1 |
- GDP |
- KK/HIJ |
- 64 |
- F |
- R2636E.CEL |
- 0.023 |
- 0.026 |
- 2.61 |
- 93.1 |
- 0.589 |
- 0.395 |
- 0.015 |
- 1.39 |
- 0.76 |
- UTM RW |
-
-
- | 66 |
- R2637E1 |
- GDP |
- KK/HIJ |
- 64 |
- M |
- R2637E.CEL |
- 0.039 |
- 0.020 |
- 2.189 |
- 102.78 |
- 0.594 |
- 0.39 |
- 0.015 |
- 1.3 |
- 0.79 |
- UTM RW |
-
-
- | 67 |
- R0999E1 |
- GDP |
- LG/J |
- 57 |
- F |
- R0999E.CEL |
- 0.012 |
- 0.012 |
- 2.448 |
- 82.09 |
- 0.594 |
- 0.391 |
- 0.015 |
- 1.38 |
- 0.79 |
- UTM RW |
-
-
- | 68 |
- R1004E1 |
- GDP |
- LG/J |
- 65 |
- M |
- R1004E.CEL |
- 0.013 |
- 0.015 |
- 2.438 |
- 91.71 |
- 0.587 |
- 0.398 |
- 0.015 |
- 1.38 |
- 0.79 |
- UTM RW |
-
-
- | 69 |
- R1688E1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- R1688E.CEL |
- 0.017 |
- 0.019 |
- 2.664 |
- 97.65 |
- 0.586 |
- 0.399 |
- 0.015 |
- 1.26 |
- 0.8 |
- JAX |
-
-
- | 70 |
- R2566E1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- R2566E2.CEL |
- 0.019 |
- 0.025 |
- 3.031 |
- 69.44 |
- 0.598 |
- 0.388 |
- 0.015 |
- 1.38 |
- 0.75 |
- UTM RW |
-
-
- | 71 |
- R2550E1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- R2550E.CEL |
- 0.023 |
- 0.015 |
- 1.794 |
- 87.16 |
- 0.607 |
- 0.378 |
- 0.015 |
- 1.52 |
- 0.82 |
- JAX |
-
-
- | 72 |
- R2535E1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- R2535E.CEL |
- 0.046 |
- 0.025 |
- 1.893 |
- 85.67 |
- 0.604 |
- 0.382 |
- 0.014 |
- 1.41 |
- 0.85 |
- JAX |
-
-
- | 73 |
- R2634E1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- R2635E.CEL |
- 0.077 |
- 0.069 |
- 3.292 |
- 89.8 |
- 0.559 |
- 0.425 |
- 0.016 |
- 1.57 |
- 0.81 |
- JAX |
-
-
- | 74 |
- R2635E1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- R2634E.CEL |
- 0.088 |
- 0.081 |
- 3.722 |
- 80.05 |
- 0.542 |
- 0.441 |
- 0.017 |
- 1.53 |
- 0.85 |
- JAX |
-
-
- | 75 |
- R2544E1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- R2544E.CEL |
- 0.106 |
- 0.100 |
- 2.196 |
- 107.51 |
- 0.549 |
- 0.435 |
- 0.017 |
- 1.36 |
- 0.82 |
- JAX |
-
-
- | 76 |
- R2549E1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- R2549E.CEL |
- 0.065 |
- 0.048 |
- 2.275 |
- 83.8 |
- 0.573 |
- 0.412 |
- 0.015 |
- 1.57 |
- 0.83 |
- JAX |
-
-
- | 77 |
- R2368E1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- R2368E.CEL |
- 0.025 |
- 0.028 |
- 2.567 |
- 85.7 |
- 0.595 |
- 0.391 |
- 0.014 |
- 1.29 |
- 0.74 |
- UTM RW |
-
-
- | 78 |
- R2547E1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- R2547E.CEL |
- 0.032 |
- 0.021 |
- 2.135 |
- 90.04 |
- 0.582 |
- 0.401 |
- 0.016 |
- 1.32 |
- 0.77 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf
deleted file mode 100644
index 5cbb536..0000000
--- a/general/datasets/Eye_AXBXA_1008_RankInv/acknowledgment.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-
-All array data were generated with funds from Dr. Benjamin Reese to RW Williams and Lu Lu as part of NIH NEI grant EY011087 (Dispersion Patterns for Retinal Neuroblasts). Arrays were scanned in the UTHSC NEI Vision Core with support from P30 EY013080. Some informatics support, including annotation of the array, was provided by NIDA and NIAAA grants to RWW and LL (NIH U01AA13499, U24AA13513 Lu Lu, PI).
-
-
- About this text file:
-
-
-Data uploaded by Arthur Centeno, Oct 1, 2008. This text file originally generated by RWW on Oct 10, 2008. Updated by RWW, May 11, 2009, May 26, 2009.
-
-
-
diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf
deleted file mode 100644
index 864f3b6..0000000
--- a/general/datasets/Eye_AXBXA_1008_RankInv/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The AXB/BXA genetic reference panel of recombinant inbred strains consists of just about 26 fully independent strains. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf
deleted file mode 100644
index 23268bc..0000000
--- a/general/datasets/Eye_AXBXA_1008_RankInv/platform.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-Illumina Sentrix MouseWG-6 v2 BeadChip: This array consists of 45,281 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-ANNOTATION: In the summer of 2008, Xusheng Wang and Robert W. Williams reannotated all three Illumina Mouse 6 BeadChips, including the array used to process the AXB/BXA eye samples. This new annotation is now incorporated into GeneNetwork. The annotation file can be accessed at http://www.genenetwork.org/share/annotations/, by selecting "Illumina Mouse WG-6 v2.0 (GPL6887)".
-
-Position data for the 50-mer Illumina probe sequences were aligned to the mm8 mouse genome build by Xusheng Wang as part of his master annotation of all Illumina mouse arrays. Manual annotation of this array was usually done by RW Williams.
-
diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf
deleted file mode 100644
index 7d79970..0000000
--- a/general/datasets/Eye_AXBXA_1008_RankInv/processing.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between August 2008 and September 2008. All processing steps were performed by Dr. David Li. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (approximately 10% failed and new RNA samples had to be acquired and processed) were immediately used on BeadChips. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from 25 of the 28 strains. Three strains are represented by samples from a single sex.
-
diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf
deleted file mode 100644
index 0cf2818..0000000
--- a/general/datasets/Eye_AXBXA_1008_RankInv/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-AXB/BXA
\ No newline at end of file
diff --git a/general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf b/general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf
deleted file mode 100644
index 0bf1369..0000000
--- a/general/datasets/Eye_AXBXA_1008_RankInv/summary.rtf
+++ /dev/null
@@ -1,769 +0,0 @@
-
-FINAL RECOMMENDED AXB/BXA EYE DATA SET. The Eye AXBXA Illumina Illumina V6.2 (Oct08) data set provides estimates of mRNA expression for whole eyes of 28 strains of mice, including 26 AXB/BXA recombinant inbred strains, and two parental strains, A/J and C57BL/6J. All eye samples were obtained from normal adult control animals raised in a standard laboratory environment at the Jackson Laboratory. We used the Illumina Sentrix MouseWG-6 v2 BeadChip (despite the nomenclature, this is actually the third version of the Illumina Mouse-6 platform).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
-
-
- About the cases used to generate this set of data:
-
-
-
-
-A total of 54 pooled whole eye samples were processed using approximately 10 Illumina Sentrix Mouse WG-6 v2 oligomer BeadChip slides. All 10 slides and a total of 54 samples passed stringent quality control and error checking. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed. Variance of each array was stabilized to 4 units (SD of 2 units) and recentered to a mean of 8. values range from a low of 6.3 (e.g., ILMN_1225143, no expression) to a high of about 19.7 for ILMN_2772482 (Crygd, extremely highly expressed). Data were entered by Arthur Centeno, Hongqiang Li, Robert W. Williams, and Lu Lu, October 1, 2008.
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10. In this data set, 255 probes have LRS values >46 (LOD >10). The maximum LOD score achieved in this data set is 27.7 for Zfp330 (LRS of 127.9 using ILMN_2825109).
-
-The probe ILMN_2475156 can be used to check sex assignment. With three exceptions, all 28 strains are represented by one male sample and one female sample. The three exceptions are are follows: both AXB13/14 cases are males, BXA25 is represented by a single male sample or a mixed sex sample, and BXA11 is represented by a single female sample.
-
-
-
-Legend: Bar chart of the expression of Xist probe ILMN_2475156 in the AXB/BXA eye data set. This probe is used to check sex. Strains represented by equal numbers of male and female arrays (usually one of each) should have intermediate values and a high error term. Strains represented only by males will have very low values (for example, AXB13/14 is represented by only one male) and strains represented by only females will have very high expression (for example, BXA11 is represented by only one female).
-
- About the animals and tissue used to generate this set of data:
-
-
-AXB/BXA animals were obtained directly from The Jackson Laboratory. Animals were housed at UTHSC before sacrifice. Mice were killed by cervical dislocation and eyes and brains were removed and placed in RNAlater.
-
-Animals used in this study were between 51 and 90 days of age (see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-
-Experimental Design and Batch Structure: This data set consists arrays processed September 2008 and all arrays in this data set were processed using a single protocol by a single operator. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute in September 2008. Details on sample assignment to slides and batches is provide in the table below.
-
-
- Data Table 1:
-
-
-
-This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, number of animals in each sample pool (pool size), slide ID, slide position (A through F), batch by slide number (1 or 2), and Source of animals.
-
-
-
-
-
-
-
-
-
- | Index |
- Tube ID |
- Strain |
- Age |
- Sex |
- Pool size |
- Slide Id |
- Slide Position |
- Batch Id |
- Source |
-
-
- | 1 |
- R4893E1 |
- A/J |
- 59 |
- F |
- 0 |
- 4252491010 |
- A |
- 1 |
- JAX |
-
-
- | 2 |
- R4982E1 |
- A/J |
- 79 |
- M |
- 2 |
- 4252491006 |
- A |
- 1 |
- JAX |
-
-
- | 3 |
- R4894E1 |
- A/J |
- 59 |
- M |
- 0 |
- 4252491011 |
- A |
- 1 |
- JAX |
-
-
- | 4 |
- R3655E1 |
- A/J |
- 86 |
- M |
- 0 |
- 4252491031 |
- A |
- 2 |
- JAX |
-
-
- | 5 |
- R4897E1 |
- AXB1 |
- 90 |
- F |
- 0 |
- 4252491005 |
- C |
- 1 |
- JAX |
-
-
- | 6 |
- R5005E1 |
- AXB1 |
- 56 |
- M |
- 0 |
- 4252491008 |
- A |
- 1 |
- JAX |
-
-
- | 7 |
- R5001E1 |
- AXB10 |
- 63 |
- F |
- 2 |
- 4252491008 |
- B |
- 1 |
- JAX |
-
-
- | 8 |
- R5002E1 |
- AXB10 |
- 63 |
- M |
- 2 |
- 4252491021 |
- B |
- 1 |
- JAX |
-
-
- | 9 |
- R4891E1 |
- AXB12 |
- 63 |
- F |
- 0 |
- 4252491009 |
- A |
- 1 |
- JAX |
-
-
- | 10 |
- R4999E1 |
- AXB12 |
- 57 |
- M |
- 2 |
- 4252491005 |
- D |
- 1 |
- JAX |
-
-
- | 11 |
- R5000E1 |
- AXB13 |
- 57 |
- M |
- 2 |
- 4252491008 |
- C |
- 1 |
- JAX |
-
-
- | 12 |
- R5003E1 |
- AXB15 |
- 63 |
- F |
- 2 |
- 4252491005 |
- E |
- 1 |
- JAX |
-
-
- | 13 |
- R4963E1 |
- AXB15 |
- 63 |
- M |
- 2 |
- 4252491031 |
- B |
- 1 |
- JAX |
-
-
- | 14 |
- R3661E1 |
- AXB19 |
- 89 |
- F |
- 0 |
- 4252491008 |
- D |
- 1 |
- JAX |
-
-
- | 15 |
- R4962E1 |
- AXB19 |
- 62 |
- M |
- 0 |
- 4252491005 |
- F |
- 1 |
- JAX |
-
-
- | 16 |
- R4975E1 |
- AXB2 |
- 79 |
- F |
- 2 |
- 4252491006 |
- C |
- 1 |
- JAX |
-
-
- | 17 |
- R4976E1 |
- AXB2 |
- 79 |
- M |
- 2 |
- 4252491021 |
- C |
- 1 |
- JAX |
-
-
- | 18 |
- R4973E1 |
- AXB23 |
- 66 |
- F |
- 2 |
- 4252491009 |
- E |
- 1 |
- JAX |
-
-
- | 19 |
- R4972E1 |
- AXB23 |
- 66 |
- M |
- 2 |
- 4252491006 |
- D |
- 1 |
- JAX |
-
-
- | 20 |
- R4959E1 |
- AXB24 |
- 100 |
- F |
- 2 |
- 4252491006 |
- E |
- 1 |
- JAX |
-
-
- | 21 |
- R4960E1 |
- AXB24 |
- 100 |
- M |
- 2 |
- 4252491019 |
- A |
- 1 |
- JAX |
-
-
- | 22 |
- R4994E1 |
- AXB4 |
- 54 |
- F |
- 2 |
- 4252491031 |
- C |
- 1 |
- JAX |
-
-
- | 23 |
- R5007E1 |
- AXB4 |
- 54 |
- M |
- 2 |
- 4252491006 |
- F |
- 1 |
- JAX |
-
-
- | 24 |
- R4995E1 |
- AXB5 |
- 61 |
- F |
- 2 |
- 4252491021 |
- F |
- 1 |
- JAX |
-
-
- | 25 |
- R4996E1 |
- AXB5 |
- 61 |
- M |
- 2 |
- 4252491009 |
- F |
- 1 |
- JAX |
-
-
- | 26 |
- R4997E1 |
- AXB6 |
- 60 |
- F |
- 2 |
- 4252491010 |
- C |
- 1 |
- JAX |
-
-
- | 27 |
- R4998E1 |
- AXB6 |
- 60 |
- M |
- 2 |
- 4252491021 |
- D |
- 1 |
- JAX |
-
-
- | 28 |
- R4958E1 |
- AXB8 |
- 52 |
- F |
- 2 |
- 4252491019 |
- D |
- 1 |
- JAX |
-
-
- | 29 |
- R4957E1 |
- AXB8 |
- 52 |
- M |
- 2 |
- 4252491010 |
- D |
- 1 |
- JAX |
-
-
- | 30 |
- R4991E1 |
- BXA1 |
- 54 |
- F |
- 2 |
- 4252491010 |
- E |
- 1 |
- JAX |
-
-
- | 31 |
- R4990E1 |
- BXA1 |
- 54 |
- M |
- 2 |
- 4252491009 |
- B |
- 1 |
- JAX |
-
-
- | 32 |
- R4980E1 |
- BXA11 |
- 52 |
- F |
- 0 |
- 4252491020 |
- A |
- 1 |
- JAX |
-
-
- | 33 |
- R5006E1 |
- BXA12 |
- 48 |
- F |
- 2 |
- 4252491011 |
- C |
- 2 |
- JAX |
-
-
- | 34 |
- R4993E1 |
- BXA12 |
- 48 |
- M |
- 2 |
- 4252491031 |
- D |
- 1 |
- JAX |
-
-
- | 35 |
- R4968E1 |
- BXA13 |
- 61 |
- F |
- 2 |
- 4252491011 |
- D |
- 1 |
- JAX |
-
-
- | 36 |
- R4969E1 |
- BXA13 |
- 61 |
- M |
- 2 |
- 4252491008 |
- E |
- 1 |
- JAX |
-
-
- | 37 |
- R4966E1 |
- BXA14 |
- 56 |
- F |
- 2 |
- 4252491031 |
- E |
- 1 |
- JAX |
-
-
- | 38 |
- R4967E1 |
- BXA14 |
- 56 |
- M |
- 2 |
- 4252491011 |
- E |
- 1 |
- JAX |
-
-
- | 39 |
- R4970E1 |
- BXA16 |
- 51 |
- F |
- 2 |
- 4252491011 |
- F |
- 1 |
- JAX |
-
-
- | 40 |
- R5004E1 |
- BXA16 |
- 51 |
- M |
- 2 |
- 4252491031 |
- F |
- 1 |
- JAX |
-
-
- | 41 |
- R4981E1 |
- BXA2 |
- 50 |
- F |
- 2 |
- 4252491008 |
- F |
- 1 |
- JAX |
-
-
- | 42 |
- R4965E1 |
- BXA2 |
- 54 |
- M |
- 0 |
- 4252491020 |
- B |
- 1 |
- JAX |
-
-
- | 43 |
- R4984E1 |
- BXA24 |
- 54 |
- F |
- 2 |
- 4252491021 |
- E |
- 1 |
- JAX |
-
-
- | 44 |
- R4974E1 |
- BXA24 |
- 54 |
- M |
- 2 |
- 4252491019 |
- C |
- 1 |
- JAX |
-
-
- | 45 |
- R4988E1 |
- BXA25 |
- 70 |
- M |
- 0 |
- 4252491020 |
- F |
- 1 |
- JAX |
-
-
- | 46 |
- R4964E1 |
- BXA26 |
- 54 |
- F |
- 0 |
- 4252491019 |
- B |
- 1 |
- JAX |
-
-
- | 47 |
- R3636E1 |
- BXA26 |
- 87 |
- M |
- 0 |
- 4252491009 |
- D |
- 1 |
- JAX |
-
-
- | 48 |
- R4977E1 |
- BXA4 |
- 65 |
- F |
- 0 |
- 4252491020 |
- C |
- 1 |
- JAX |
-
-
- | 49 |
- R3638E1 |
- BXA4 |
- 87 |
- M |
- 0 |
- 4252491019 |
- E |
- 1 |
- JAX |
-
-
- | 50 |
- R4978E1 |
- BXA7 |
- 65 |
- F |
- 2 |
- 4252491019 |
- F |
- 1 |
- JAX |
-
-
- | 51 |
- R4979E1 |
- BXA7 |
- 65 |
- M |
- 2 |
- 4252491021 |
- A |
- 1 |
- JAX |
-
-
- | 52 |
- R5008E1 |
- BXA8 |
- 52 |
- F |
- 2 |
- 4252491020 |
- E |
- 1 |
- JAX |
-
-
- | 53 |
- R4983E1 |
- BXA8 |
- 52 |
- M |
- 2 |
- 4252491020 |
- D |
- 1 |
- JAX |
-
-
- | 54 |
- R5012E1 |
- C57BL/6J |
- 87 |
- F |
- 2 |
- 4252491006 |
- B |
- 1 |
- UTHSC RW |
-
-
- | 55 |
- R5010E1 |
- C57BL/6J |
- 87 |
- F |
- 2 |
- 4252491011 |
- B |
- 1 |
- UTHSC RW |
-
-
- | 56 |
- R5011E1 |
- C57BL/6J |
- 79 |
- M |
- 2 |
- 4252491005 |
- B |
- 1 |
- UTHSC RW |
-
-
- | 57 |
- R5009E1 |
- C57BL/6J |
- 79 |
- M |
- 2 |
- 4252491010 |
- B |
- 1 |
- UTHSC RW |
-
-
-
-
- Downloading all data:
-
-
- All data links (right-most column above) will be made active as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact RW Williams if you have any questions on the use of these open data.
-
-
- About data processing:
-
-
- This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
- |
-
-
-
-
-
-
diff --git a/general/datasets/Eye_M2_0406_M/acknowledgment.rtf b/general/datasets/Eye_M2_0406_M/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/Eye_M2_0406_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/Eye_M2_0406_M/cases.rtf b/general/datasets/Eye_M2_0406_M/cases.rtf
deleted file mode 100644
index 5cb5539..0000000
--- a/general/datasets/Eye_M2_0406_M/cases.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-We used a set of 55 BXD recombinant inbred strains, 14 conventional inbred strains including C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1s. BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D2). Physical maps in WebQTL incorporate approximately 2 million B6 vs D2 SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) have been included in the MDP. Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J. These reciprocal F1 can be used to detect some imprinted genes.
-
diff --git a/general/datasets/Eye_M2_0406_M/notes.rtf b/general/datasets/Eye_M2_0406_M/notes.rtf
deleted file mode 100644
index 39475ab..0000000
--- a/general/datasets/Eye_M2_0406_M/notes.rtf
+++ /dev/null
@@ -1,18 +0,0 @@
-This study includes the following datasets:
-
-
- -
-
Eye M430v2 (Apr06) RMA
-
- -
-
Eye M430v2 (Apr06) PDNN
-
- -
-
Eye M430v2 (Apr06) MAS5
-
- -
-
Eye M430v2 (Sep06) RMA
-
-
-
-This text file originally generated by RWW, May 26, 2006. Updated by RWW, May 27, 2006.
diff --git a/general/datasets/Eye_M2_0406_M/platform.rtf b/general/datasets/Eye_M2_0406_M/platform.rtf
deleted file mode 100644
index ac743ee..0000000
--- a/general/datasets/Eye_M2_0406_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/Eye_M2_0406_M/processing.rtf b/general/datasets/Eye_M2_0406_M/processing.rtf
deleted file mode 100644
index d23bc47..0000000
--- a/general/datasets/Eye_M2_0406_M/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the two batches together in RMA.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing all arrays were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (C3H/HeJ and BXD24) and samples from wild subspecies such as CAST/Ei, PWD/Ph, and PWK/Ph. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. We tended to keep arrays that "conformed" to the expectation. The assumption in these cases is that anomolous data are much more likely due to experimental problem and errors than to informative biological variation. Approximately 8 arrays total were discarded in batches 1 and 2 combined.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We then categorized arrays into XXX major "technical groups" depending on expression patterns as noted in scatterplots. This process of defining technical groups was done in DataDesk by manually "typing" arrays. These technical groups are apparently due to subtle within-batch effect that we do not yet understand and that cannot be corrected by quantile normalization. These XXX major technical groups are not obviously related to strain, sex, age, or any other known biological effect or variable. They are also not obviously related to any of the Affymetrix QC data types (3'/5' ratios, gain, etc.). Once the technical groups were defined, we forced the means of each probe set in the XX technical groups to the same value. This simple process partially removes a technical error of unknown origin in large expression array data sets.
-
-We reviewed the final data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of 140 arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g. 1000) represented the QTL harvest for the full data set. We then dropped a single array from the data set (n = 139 arrays), recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 950 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs (1000-950). Values ranged from -90 (good0 to +38 (bad). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a final method to polish a data set. By applying this procedure we discovered that a set of XX (7?) arrays could be excluded while simultaneously improving the total number of QTLs with values above 50.
-
-During this final process we discovered that nearly XX arrays in the second batch had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of very high quality.
-
diff --git a/general/datasets/Eye_M2_0406_M/summary.rtf b/general/datasets/Eye_M2_0406_M/summary.rtf
deleted file mode 100644
index 68a4484..0000000
--- a/general/datasets/Eye_M2_0406_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATA SET. The HEIMED April 2006 data set provides estimates of mRNA expression in whole eyes of 71 lines of young adult mice generated using 132 Affymetrix M430 2.0 arrays. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools; one male, one female, for each straion. This data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/Eye_M2_0406_M/tissue.rtf b/general/datasets/Eye_M2_0406_M/tissue.rtf
deleted file mode 100644
index d8d345f..0000000
--- a/general/datasets/Eye_M2_0406_M/tissue.rtf
+++ /dev/null
@@ -1,7112 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 4 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2) in the first batch of arrays (the November 05 data set) of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table). This same protocol was used for all samples in the second batch added in April 2006.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The first and second batches of array data, collectively represents a reasonably well balanced sample of males and females belonging to 62 strains, but without within-strain-by-sex replication. Six strains are represented only by male sample pools (BXD15, 28, 29, 55, 98, and DBA/2J. Four strains are represented only by a female pool sample (BXD1, 27, 73 and 86). Please use the probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males) as quantitative surrogates for the sex balance in this data set.
-
-Batch Structure: This data set consists of a two batches: the original batch that makes up the November 2005 data set and a new batch of 63 arrays (R0857E through R2649E, and R2682E through R2742E, non-consecutive identifiers) run in January 2006 by Dr. Yan Jiao. The arrays in the two batches are from two different lots. All arrays in the second batch were from Lot 4016879 (expiration date 12.28.06). We started working with a total of 140 arrays that passed initial crude quality control based on RNA quality and initial Affymetrix report file information such as 3'/5' ratio, scale factor, and percent present calls. A total of 130 arrays were finally approved for inclusion in this April 2006 data set. The complex normalization procedure is described below.
-
-The table below summarizes information on strain, age, sex, original CEL filename, Affymetrix quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-IN PROGRESS: PLEASE NOTE THAT THIS TABLE IS NOW BEING UPDATED TO INCLUDE BATCH 2 OF EARLY 2006.
-
-
-
-
-
- | ID |
-
- tube ID
- |
-
- group_type
- |
-
- Strain
- |
-
- age
- |
-
- Sex
- |
-
- original
-
- CEL
-
- filename
- |
-
- PDNN
-
- 2Z
-
- outlier
- |
-
- RMA
-
- 2Z
-
- outlier
- |
-
- scale
-
- factor
- |
-
- background
-
- average
- |
-
- present
- |
-
- absent
- |
-
- marginal
- |
-
- AFFX-b-
-
- ActinMur(3'/5')
- |
-
- AFFX-
-
- GapdhMur(3'/5')
- |
-
- Source
- |
-
-
- |
- 1
- |
-
- R2533E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 60
- |
-
- M
- |
-
- R2533E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.11
- |
-
- 94
- |
-
- 57.90%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 2
- |
-
- R2595E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 59
- |
-
- F
- |
-
- R2595E.CEL
- |
-
- 0.033
- |
-
- 0.036
- |
-
- 1.79
- |
-
- 115
- |
-
- 61.00%
- |
-
- 37.50%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 3
- |
-
- R0754E2
- |
-
- GDP
- |
-
- A/J
- |
-
- 60
- |
-
- M
- |
-
- R0754E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.72
- |
-
- 86
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.36
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 4
- |
-
- R2546E1
- |
-
- GDP
- |
-
- A/J
- |
-
- 66
- |
-
- F
- |
-
- R2545E.CEL
- |
-
- 0.024
- |
-
- 0.029
- |
-
- 1.99
- |
-
- 96
- |
-
- 58.60%
- |
-
- 39.70%
- |
-
- 1.70%
- |
-
- 1.47
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 5
- |
-
- R2601E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- F
- |
-
- R2601E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 2.55
- |
-
- 92
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 6
- |
-
- R2602E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- M
- |
-
- R2602E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 2.60
- |
-
- 84
- |
-
- 59.70%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 7
- |
-
- R1672E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- M
- |
-
- R1672E.CEL
- |
-
- 0.043
- |
-
- 0.039
- |
-
- 2.22
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 8
- |
-
- R1676E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- F
- |
-
- R1676E.CEL
- |
-
- 0.083
- |
-
- 0.085
- |
-
- 2.69
- |
-
- 98
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.74
- |
-
- JAX
- |
-
-
- |
- 9
- |
-
- R2581E1
- |
-
- BXD
- |
-
- BXD11
- |
-
- 65
- |
-
- F
- |
-
- R2581E.CEL
- |
-
- 0.009
- |
-
- 0.021
- |
-
- 1.94
- |
-
- 89
- |
-
- 62.10%
- |
-
- 36.40%
- |
-
- 1.60%
- |
-
- 1.55
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 10
- |
-
- R2543E1
- |
-
- BXD
- |
-
- BXD12
- |
-
- 63
- |
-
- M
- |
-
- R2543E.CEL
- |
-
- 0.018
- |
-
- 0.017
- |
-
- 1.61
- |
-
- 118
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 11
- |
-
- R2586E1
- |
-
- BXD
- |
-
- BXD13
- |
-
- 60
- |
-
- F
- |
-
- R2586E.CEL
- |
-
- 0.259
- |
-
- 0.258
- |
-
- 2.01
- |
-
- 74
- |
-
- 56.40%
- |
-
- 42.00%
- |
-
- 1.60%
- |
-
- 2.85
- |
-
- 3.81
- |
-
- Glenn
- |
-
-
- |
- 12
- |
-
- R2557E1
- |
-
- BXD
- |
-
- BXD14
- |
-
- 60
- |
-
- F
- |
-
- R2557E.CEL
- |
-
- 0.012
- |
-
- 0.027
- |
-
- 1.83
- |
-
- 99
- |
-
- 62.50%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 13
- |
-
- R2567E1
- |
-
- BXD
- |
-
- BXD16
- |
-
- 60
- |
-
- M
- |
-
- R2567E.CEL
- |
-
- 0.048
- |
-
- 0.058
- |
-
- 2.24
- |
-
- 82
- |
-
- 56.70%
- |
-
- 41.60%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.75
- |
-
- Glenn
- |
-
-
- |
- 14
- |
-
- R2559E1
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- M
- |
-
- R2559E.CEL
- |
-
- 0.01
- |
-
- 0.012
- |
-
- 1.65
- |
-
- 104
- |
-
- 60.80%
- |
-
- 37.70%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 15
- |
-
- R2560E1
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- F
- |
-
- R2560E.CEL
- |
-
- 0.009
- |
-
- 0.012
- |
-
- 1.79
- |
-
- 98
- |
-
- 60.90%
- |
-
- 37.50%
- |
-
- 1.60%
- |
-
- 1.35
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 16
- |
-
- R2597E1
- |
-
- BXD
- |
-
- BXD2
- |
-
- 61
- |
-
- M
- |
-
- R2597E.CEL
- |
-
- 0.005
- |
-
- 0.012
- |
-
- 2.37
- |
-
- 94
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 17
- |
-
- R2584E1
- |
-
- BXD
- |
-
- BXD20
- |
-
- 59
- |
-
- F
- |
-
- R2584E.CEL
- |
-
- 0.011
- |
-
- 0.017
- |
-
- 2.07
- |
-
- 84
- |
-
- 59.30%
- |
-
- 39.10%
- |
-
- 1.60%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 18
- |
-
- R2541E2
- |
-
- BXD
- |
-
- BXD21
- |
-
- 61
- |
-
- M
- |
-
- R2541E2.CEL
- |
-
- 0.049
- |
-
- 0.084
- |
-
- 2.63
- |
-
- 125
- |
-
- 56.00%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.29
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 19
- |
-
- R2553E1
- |
-
- BXD
- |
-
- BXD22
- |
-
- 58
- |
-
- F
- |
-
- R2553E.CEL
- |
-
- 0.004
- |
-
- 0.01
- |
-
- 1.95
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.50%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 20
- |
-
- R2558E1
- |
-
- BXD
- |
-
- BXD23
- |
-
- 60
- |
-
- F
- |
-
- R2558E-2.CEL
- |
-
- 0.018
- |
-
- 0.027
- |
-
- 1.91
- |
-
- 115
- |
-
- 59.90%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.20
- |
-
- 0.82
- |
-
- Glenn
- |
-
-
- |
- 21
- |
-
- R2589E2
- |
-
- BXD
- |
-
- BXD24
- |
-
- 59
- |
-
- M
- |
-
- R2589E2.CEL
- |
-
- 0.132
- |
-
- 0.176
- |
-
- 2.61
- |
-
- 112
- |
-
- 57.50%
- |
-
- 40.90%
- |
-
- 1.60%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 22
- |
-
- R2573E1
- |
-
- BXD
- |
-
- BXD25
- |
-
- 67
- |
-
- F
- |
-
- R2573E-2.CEL
- |
-
- 0.055
- |
-
- 0.063
- |
-
- 3.15
- |
-
- 72
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.77
- |
-
- 0.97
- |
-
- UAB
- |
-
-
- |
- 23
- |
-
- R2562E1
- |
-
- BXD
- |
-
- BXD29
- |
-
- 60
- |
-
- M
- |
-
- R2562E.CEL
- |
-
- 0.007
- |
-
- 0.01
- |
-
- 1.65
- |
-
- 116
- |
-
- 59.90%
- |
-
- 38.40%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- Glenn
- |
-
-
- |
- 24
- |
-
- R2598E1
- |
-
- BXD
- |
-
- BXD31
- |
-
- 61
- |
-
- M
- |
-
- R2598E.CEL
- |
-
- 0.006
- |
-
- 0.013
- |
-
- 1.99
- |
-
- 106
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 25
- |
-
- R2563E1
- |
-
- BXD
- |
-
- BXD32
- |
-
- 63
- |
-
- F
- |
-
- R2563E.CEL
- |
-
- 0.023
- |
-
- 0.025
- |
-
- 1.55
- |
-
- 102
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.40%
- |
-
- 1.50
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 26
- |
-
- R2542E1
- |
-
- BXD
- |
-
- BXD33
- |
-
- 67
- |
-
- F
- |
-
- R2542E.CEL
- |
-
- 0.058
- |
-
- 0.062
- |
-
- 2.13
- |
-
- 97
- |
-
- 56.50%
- |
-
- 41.80%
- |
-
- 1.60%
- |
-
- 1.91
- |
-
- 0.93
- |
-
- UTM RW
- |
-
-
- |
- 27
- |
-
- R2585E1
- |
-
- BXD
- |
-
- BXD34
- |
-
- 60
- |
-
- M
- |
-
- R2585E.CEL
- |
-
- 0.024
- |
-
- 0.032
- |
-
- 2.64
- |
-
- 75
- |
-
- 58.30%
- |
-
- 40.00%
- |
-
- 1.70%
- |
-
- 1.25
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 28
- |
-
- R2532E1
- |
-
- BXD
- |
-
- BXD38
- |
-
- 62
- |
-
- M
- |
-
- R2532E.CEL
- |
-
- 0.002
- |
-
- 0.006
- |
-
- 2.04
- |
-
- 94
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 29
- |
-
- R2574E1
- |
-
- BXD
- |
-
- BXD39
- |
-
- 70
- |
-
- F
- |
-
- R2574E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 1.98
- |
-
- 91
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 30
- |
-
- R2590E1
- |
-
- BXD
- |
-
- BXD40
- |
-
- 60
- |
-
- M
- |
-
- R2590E.CEL
- |
-
- 0.007
- |
-
- 0.012
- |
-
- 2.71
- |
-
- 77
- |
-
- 59.10%
- |
-
- 39.30%
- |
-
- 1.50%
- |
-
- 1.40
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 31
- |
-
- R2596E1
- |
-
- BXD
- |
-
- BXD42
- |
-
- 59
- |
-
- M
- |
-
- R2596E.CEL
- |
-
- 0.016
- |
-
- 0.03
- |
-
- 2.63
- |
-
- 108
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 32
- |
-
- R2605E1
- |
-
- BXD
- |
-
- BXD43
- |
-
- 79
- |
-
- M
- |
-
- R2607E.CEL
- |
-
- 0.006
- |
-
- 0.01
- |
-
- 1.82
- |
-
- 131
- |
-
- 60.50%
- |
-
- 38.20%
- |
-
- 1.30%
- |
-
- 1.32
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 33
- |
-
- R2594E1
- |
-
- BXD
- |
-
- BXD44
- |
-
- 63
- |
-
- F
- |
-
- R2594E.CEL
- |
-
- 0.014
- |
-
- 0.024
- |
-
- 1.77
- |
-
- 117
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 34
- |
-
- R2592E1
- |
-
- BXD
- |
-
- BXD45
- |
-
- 62
- |
-
- M
- |
-
- R2592E.CEL
- |
-
- 0.005
- |
-
- 0.011
- |
-
- 1.85
- |
-
- 106
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.43
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 35
- |
-
- R2606E1
- |
-
- BXD
- |
-
- BXD48
- |
-
- 78
- |
-
- M
- |
-
- R2606E.CEL
- |
-
- 0.007
- |
-
- 0.015
- |
-
- 2.56
- |
-
- 106
- |
-
- 58.90%
- |
-
- 39.70%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.83
- |
-
- UTM RW
- |
-
-
- |
- 36
- |
-
- R2591E1
- |
-
- BXD
- |
-
- BXD5
- |
-
- 60
- |
-
- F
- |
-
- R2591E.CEL
- |
-
- 0.052
- |
-
- 0.014
- |
-
- 1.70
- |
-
- 136
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 37
- |
-
- R2603E1
- |
-
- BXD
- |
-
- BXD51
- |
-
- 66
- |
-
- F
- |
-
- R2603E.CEL
- |
-
- 0.007
- |
-
- 0.02
- |
-
- 2.49
- |
-
- 115
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 38
- |
-
- R2570E1
- |
-
- BXD
- |
-
- BXD6
- |
-
- 65
- |
-
- F
- |
-
- R2570E.CEL
- |
-
- 0.013
- |
-
- 0.017
- |
-
- 1.99
- |
-
- 87
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 39
- |
-
- R2534E2
- |
-
- BXD
- |
-
- BXD61
- |
-
- 70
- |
-
- F
- |
-
- R2534E2.CEL
- |
-
- 0.03
- |
-
- 0.058
- |
-
- 2.47
- |
-
- 118
- |
-
- 57.90%
- |
-
- 40.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 40
- |
-
- R2611E1
- |
-
- BXD
- |
-
- BXD64
- |
-
- 68
- |
-
- M
- |
-
- R2611E.CEL
- |
-
- 0.067
- |
-
- 0.068
- |
-
- 2.29
- |
-
- 92
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 1.06
- |
-
- UTM RW
- |
-
-
- |
- 41
- |
-
- R2583E1
- |
-
- BXD
- |
-
- BXD65
- |
-
- 60
- |
-
- M
- |
-
- R2583E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.49
- |
-
- 70
- |
-
- 56.90%
- |
-
- 41.50%
- |
-
- 1.60%
- |
-
- 1.67
- |
-
- 1.01
- |
-
- UTM RW
- |
-
-
- |
- 42
- |
-
- R2536E2
- |
-
- BXD
- |
-
- BXD66
- |
-
- 64
- |
-
- F
- |
-
- R2536E2.CEL
- |
-
- 0.067
- |
-
- 0.139
- |
-
- 2.74
- |
-
- 109
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.70%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 43
- |
-
- R2551E1
- |
-
- BXD
- |
-
- BXD68
- |
-
- 67
- |
-
- F
- |
-
- R2551E.CEL
- |
-
- 0.294
- |
-
- 0.291
- |
-
- 2.49
- |
-
- 92
- |
-
- 54.30%
- |
-
- 44.10%
- |
-
- 1.60%
- |
-
- 2.91
- |
-
- 1.55
- |
-
- UTM RW
- |
-
-
- |
- 44
- |
-
- R2593E1
- |
-
- BXD
- |
-
- BXD69
- |
-
- 59
- |
-
- F
- |
-
- R2593E.CEL
- |
-
- 0.027
- |
-
- 0.038
- |
-
- 1.67
- |
-
- 128
- |
-
- 59.20%
- |
-
- 39.50%
- |
-
- 1.30%
- |
-
- 1.47
- |
-
- 0.92
- |
-
- UTM RW
- |
-
-
- |
- 45
- |
-
- R2537E2
- |
-
- BXD
- |
-
- BXD70
- |
-
- 59
- |
-
- M
- |
-
- R2537E2.CEL
- |
-
- 0.049
- |
-
- 0.092
- |
-
- 2.93
- |
-
- 99
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.29
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 46
- |
-
- R2565E1
- |
-
- BXD
- |
-
- BXD75
- |
-
- 61
- |
-
- F
- |
-
- R2565E.CEL
- |
-
- 0.118
- |
-
- 0.124
- |
-
- 1.79
- |
-
- 102
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 2.31
- |
-
- 3.47
- |
-
- UTM RW
- |
-
-
- |
- 47
- |
-
- R2538E1
- |
-
- BXD
- |
-
- BXD8
- |
-
- 77
- |
-
- F
- |
-
- R2538E.CEL
- |
-
- 0.033
- |
-
- 0.056
- |
-
- 1.91
- |
-
- 102
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 48
- |
-
- R2579E1
- |
-
- BXD
- |
-
- BXD80
- |
-
- 65
- |
-
- F
- |
-
- R2579E.CEL
- |
-
- 0.013
- |
-
- 0.026
- |
-
- 2.42
- |
-
- 72
- |
-
- 59.20%
- |
-
- 39.40%
- |
-
- 1.50%
- |
-
- 1.73
- |
-
- 0.82
- |
-
- UTM RW
- |
-
-
- |
- 49
- |
-
- R2540E1
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- M
- |
-
- R2540E.CEL
- |
-
- 0.014
- |
-
- 0.034
- |
-
- 2.33
- |
-
- 93
- |
-
- 61.10%
- |
-
- 37.40%
- |
-
- 1.40%
- |
-
- 1.22
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 50
- |
-
- R2545E1
- |
-
- BXD
- |
-
- BXD89
- |
-
- 67
- |
-
- M
- |
-
- R2546E.CEL
- |
-
- 0.266
- |
-
- 0.257
- |
-
- 1.67
- |
-
- 105
- |
-
- 56.20%
- |
-
- 42.30%
- |
-
- 1.50%
- |
-
- 3.60
- |
-
- 9.84
- |
-
- UTM RW
- |
-
-
- |
- 51
- |
-
- R2569E1
- |
-
- BXD
- |
-
- BXD9
- |
-
- 67
- |
-
- M
- |
-
- R2569E.CEL
- |
-
- 0.256
- |
-
- 0.239
- |
-
- 1.75
- |
-
- 87
- |
-
- 55.10%
- |
-
- 43.40%
- |
-
- 1.50%
- |
-
- 2.82
- |
-
- 3.14
- |
-
- UTM RW
- |
-
-
- |
- 52
- |
-
- R2578E2
- |
-
- BXD
- |
-
- BXD90
- |
-
- 61
- |
-
- F
- |
-
- R2578E2.CEL
- |
-
- 0.041
- |
-
- 0.062
- |
-
- 2.79
- |
-
- 92
- |
-
- 58.60%
- |
-
- 39.80%
- |
-
- 1.60%
- |
-
- 1.52
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 53
- |
-
- R2554E1
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- M
- |
-
- R2554E.CEL
- |
-
- 0.005
- |
-
- 0.008
- |
-
- 2.18
- |
-
- 93
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 54
- |
-
- R2577E1
- |
-
- BXD
- |
-
- BXD97
- |
-
- 55
- |
-
- M
- |
-
- R2577E.CEL
- |
-
- 0.065
- |
-
- 0.069
- |
-
- 2.07
- |
-
- 77
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.87
- |
-
- 1.29
- |
-
- UTM RW
- |
-
-
- |
- 55
- |
-
- R1700E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- F
- |
-
- R1700E.CEL
- |
-
- 0.152
- |
-
- 0.168
- |
-
- 2.98
- |
-
- 69
- |
-
- 60.80%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.48
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 56
- |
-
- R1704E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- M
- |
-
- R1704E.CEL
- |
-
- 0.154
- |
-
- 0.165
- |
-
- 2.58
- |
-
- 88
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.84
- |
-
- UTM RW
- |
-
-
- |
- 57
- |
-
- R0872E2
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 66
- |
-
- M
- |
-
- R0872E.CEL
- |
-
- 0.014
- |
-
- 0.023
- |
-
- 3.13
- |
-
- 89
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 58
- |
-
- R2607E1
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 67
- |
-
- F
- |
-
- R2605E.CEL
- |
-
- 0.008
- |
-
- 0.018
- |
-
- 2.43
- |
-
- 115
- |
-
- 58.60%
- |
-
- 40.00%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 59
- |
-
- R2564E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- F
- |
-
- R2564E.CEL
- |
-
- 0.124
- |
-
- 0.105
- |
-
- 1.94
- |
-
- 89
- |
-
- 58.50%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.60
- |
-
- 0.77
- |
-
- JAX
- |
-
-
- |
- 60
- |
-
- R2580E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- M
- |
-
- R2580E.CEL
- |
-
- 0.123
- |
-
- 0.109
- |
-
- 2.09
- |
-
- 95
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.70%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 61
- |
-
- R2600E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 72
- |
-
- F
- |
-
- R2600E.CEL
- |
-
- 0.008
- |
-
- 0.02
- |
-
- 2.47
- |
-
- 95
- |
-
- 58.10%
- |
-
- 40.20%
- |
-
- 1.70%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 62
- |
-
- R2604E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 69
- |
-
- M
- |
-
- R2604E.CEL
- |
-
- 0.005
- |
-
- 0.014
- |
-
- 2.66
- |
-
- 90
- |
-
- 59.40%
- |
-
- 39.20%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 63
- |
-
- R2572E1
- |
-
- GDP BXD
- |
-
- DBA/2J
- |
-
- 65
- |
-
- M
- |
-
- R2572E.CEL
- |
-
- 0.091
- |
-
- 0.106
- |
-
- 2.41
- |
-
- 79
- |
-
- 55.50%
- |
-
- 42.90%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 64
- |
-
- R2636E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- F
- |
-
- R2636E.CEL
- |
-
- 0.044
- |
-
- 0.043
- |
-
- 2.61
- |
-
- 93
- |
-
- 58.90%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 65
- |
-
- R2637E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- M
- |
-
- R2637E.CEL
- |
-
- 0.056
- |
-
- 0.036
- |
-
- 2.19
- |
-
- 103
- |
-
- 59.40%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 66
- |
-
- R0999E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 57
- |
-
- F
- |
-
- R0999E.CEL
- |
-
- 0.021
- |
-
- 0.023
- |
-
- 2.45
- |
-
- 82
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 67
- |
-
- R1004E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 65
- |
-
- M
- |
-
- R1004E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.44
- |
-
- 92
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 68
- |
-
- R1688E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 66
- |
-
- F
- |
-
- R1688E.CEL
- |
-
- 0.028
- |
-
- 0.033
- |
-
- 2.66
- |
-
- 98
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 69
- |
-
- R2566E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 76
- |
-
- M
- |
-
- R2566E-2.CEL
- |
-
- 0.036
- |
-
- 0.04
- |
-
- 3.03
- |
-
- 69
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 70
- |
-
- R2535E1
- |
-
- GDP
- |
-
- NZO/H1LtJ
- |
-
- 62
- |
-
- F
- |
-
- R2535E.CEL
- |
-
- 0.037
- |
-
- 0.062
- |
-
- 1.89
- |
-
- 86
- |
-
- 60.40%
- |
-
- 38.20%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 71
- |
-
- R2550E1
- |
-
- GDP
- |
-
- NZO/HILtJ
- |
-
- 96
- |
-
- M
- |
-
- R2550E.CEL
- |
-
- 0.025
- |
-
- 0.029
- |
-
- 1.79
- |
-
- 87
- |
-
- 60.70%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 72
- |
-
- R2634E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- F
- |
-
- R2635E.CEL
- |
-
- 0.126
- |
-
- 0.114
- |
-
- 3.29
- |
-
- 90
- |
-
- 55.90%
- |
-
- 42.50%
- |
-
- 1.60%
- |
-
- 1.57
- |
-
- 0.81
- |
-
- JAX
- |
-
-
- |
- 73
- |
-
- R2635E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- M
- |
-
- R2634E.CEL
- |
-
- 0.15
- |
-
- 0.137
- |
-
- 3.72
- |
-
- 80
- |
-
- 54.20%
- |
-
- 44.10%
- |
-
- 1.70%
- |
-
- 1.53
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 74
- |
-
- R2544E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 63
- |
-
- F
- |
-
- R2544E.CEL
- |
-
- 0.174
- |
-
- 0.175
- |
-
- 2.20
- |
-
- 108
- |
-
- 54.90%
- |
-
- 43.50%
- |
-
- 1.70%
- |
-
- 1.36
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 75
- |
-
- R2549E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 83
- |
-
- M
- |
-
- R2549E.CEL
- |
-
- 0.103
- |
-
- 0.087
- |
-
- 2.28
- |
-
- 84
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 0.83
- |
-
- JAX
- |
-
-
- |
- 76
- |
-
- R2368E1
- |
-
- GDP
- |
-
- WSB/EI
- |
-
- 67
- |
-
- F
- |
-
- R2368E.CEL
- |
-
- 0.041
- |
-
- 0.047
- |
-
- 2.57
- |
-
- 86
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.29
- |
-
- 0.74
- |
-
- UTM RW
- |
-
-
- |
- 77
- |
-
- R2704E
- |
-
- BXD
- |
-
- BXD1
- |
-
- 59
- |
-
- F
- |
-
- R2704E.CEL
- |
-
- 0.029
- |
-
- 0.03
- |
-
- 2.066
- |
-
- 139.61
- |
-
- 56.60%
- |
-
- 41.90%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 78
- |
-
- R2612E
- |
-
- BXD
- |
-
- BXD11
- |
-
- 70
- |
-
- M
- |
-
- R2612E.CEL
- |
-
- 0.101
- |
-
- 0.112
- |
-
- 1.83
- |
-
- 142.03
- |
-
- 58.20%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.78
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 79
- |
-
- R2742E
- |
-
- BXD
- |
-
- BXD12
- |
-
- 71
- |
-
- F
- |
-
- R2742E.CEL
- |
-
- 0.073
- |
-
- 0.077
- |
-
- 2.127
- |
-
- 134.14
- |
-
- 57.00%
- |
-
- 41.60%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 80
- |
-
- R1086E
- |
-
- BXD
- |
-
- BXD23
- |
-
- 55
- |
-
- M
- |
-
- R1086E.CEL
- |
-
- 0.043
- |
-
- 0.034
- |
-
- 2.233
- |
-
- 125.05
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 81
- |
-
- R2716E
- |
-
- BXD
- |
-
- BXD15
- |
-
- 60
- |
-
- M
- |
-
- R2716E.CEL
- |
-
- 0.035
- |
-
- 0.037
- |
-
- 2.015
- |
-
- 150.83
- |
-
- 56.40%
- |
-
- 42.10%
- |
-
- 1.60%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 82
- |
-
- R2711E
- |
-
- BXD
- |
-
- BXD16
- |
-
- 61
- |
-
- F
- |
-
- R2711E.CEL
- |
-
- 0.032
- |
-
- 0.021
- |
-
- 1.953
- |
-
- 118.53
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 83
- |
-
- R2720E
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- F
- |
-
- R2720E.CEL
- |
-
- 0.014
- |
-
- 0.019
- |
-
- 2.32
- |
-
- 99.93
- |
-
- 59.50%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 84
- |
-
- R2713E
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- M
- |
-
- R2713E.CEL
- |
-
- 0.055
- |
-
- 0.021
- |
-
- 1.67
- |
-
- 120.82
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 85
- |
-
- R1231E
- |
-
- BXD
- |
-
- BXD2
- |
-
- 64
- |
-
- F
- |
-
- R1231E.CEL
- |
-
- 0.044
- |
-
- 0.037
- |
-
- 2.197
- |
-
- 138.73
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 86
- |
-
- R2731E
- |
-
- BXD
- |
-
- BXD20
- |
-
- 60
- |
-
- M
- |
-
- R2731E.CEL
- |
-
- 0.017
- |
-
- 0.019
- |
-
- 1.825
- |
-
- 147
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 87
- |
-
- R2702E
- |
-
- BXD
- |
-
- BXD21
- |
-
- 59
- |
-
- F
- |
-
- R2702E.CEL
- |
-
- 0.009
- |
-
- 0.008
- |
-
- 1.811
- |
-
- 128.65
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.26
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 88
- |
-
- R2700E
- |
-
- BXD
- |
-
- BXD22
- |
-
- 59
- |
-
- M
- |
-
- R2700E.CEL
- |
-
- 0.01
- |
-
- 0.015
- |
-
- 1.858
- |
-
- 102.96
- |
-
- 61.50%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.48
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 89
- |
-
- R1128E
- |
-
- BXD
- |
-
- BXD14
- |
-
- 65
- |
-
- M
- |
-
- R1128E.CEL
- |
-
- 0.037
- |
-
- 0.038
- |
-
- 2.366
- |
-
- 118.39
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 90
- |
-
- R2719E
- |
-
- BXD
- |
-
- BXD24
- |
-
- 123
- |
-
- F
- |
-
- R2719E.CEL
- |
-
- 0.112
- |
-
- 0.111
- |
-
- 1.47
- |
-
- 140.38
- |
-
- 61.50%
- |
-
- 37.20%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 91
- |
-
- R2683E
- |
-
- BXD
- |
-
- BXD25
- |
-
- 58
- |
-
- M
- |
-
- R2683E.CEL
- |
-
- 0.068
- |
-
- 0.068
- |
-
- 1.777
- |
-
- 115.64
- |
-
- 58.30%
- |
-
- 40.30%
- |
-
- 1.40%
- |
-
- 2.01
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 92
- |
-
- R2703E
- |
-
- BXD
- |
-
- BXD27
- |
-
- 60
- |
-
- F
- |
-
- R2703E.CEL
- |
-
- 0.008
- |
-
- 0.012
- |
-
- 1.263
- |
-
- 134.78
- |
-
- 62.60%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 93
- |
-
- R2721E
- |
-
- BXD
- |
-
- BXD28
- |
-
- 60
- |
-
- M
- |
-
- R2721E.CEL
- |
-
- 0.04
- |
-
- 0.048
- |
-
- 2.065
- |
-
- 157.39
- |
-
- 56.10%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 94
- |
-
- R1258E
- |
-
- BXD
- |
-
- BXD31
- |
-
- 57
- |
-
- F
- |
-
- R1258E.CEL
- |
-
- 0.037
- |
-
- 0.036
- |
-
- 2.063
- |
-
- 117.09
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.54
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 95
- |
-
- R1216E
- |
-
- BXD
- |
-
- BXD32
- |
-
- 76
- |
-
- M
- |
-
- R1216E.CEL
- |
-
- 0.05
- |
-
- 0.049
- |
-
- 2.23
- |
-
- 111.99
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 96
- |
-
- R857E
- |
-
- BXD
- |
-
- BXD33
- |
-
- 77
- |
-
- M
- |
-
- R857E.CEL
- |
-
- 0.078
- |
-
- 0.108
- |
-
- 1.737
- |
-
- 113.98
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.30%
- |
-
- 1.6
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 97
- |
-
- R859E
- |
-
- BXD
- |
-
- BXD90
- |
-
- 72
- |
-
- M
- |
-
- R859E.CEL
- |
-
- 0.028
- |
-
- 0.02
- |
-
- 1.847
- |
-
- 152.22
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 98
- |
-
- R1207E
- |
-
- BXD
- |
-
- BXD66
- |
-
- 83
- |
-
- M
- |
-
- R1207E.CEL
- |
-
- 0.017
- |
-
- 0.012
- |
-
- 1.681
- |
-
- 136.86
- |
-
- 60.40%
- |
-
- 38.10%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 99
- |
-
- R2710E
- |
-
- BXD
- |
-
- BXD38
- |
-
- 55
- |
-
- F
- |
-
- R2710E.CEL
- |
-
- 0.033
- |
-
- 0.031
- |
-
- 2.112
- |
-
- 122.1
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 100
- |
-
- R2695E
- |
-
- BXD
- |
-
- BXD39
- |
-
- 59
- |
-
- M
- |
-
- R2695E.CEL
- |
-
- 0.018
- |
-
- 0.016
- |
-
- 1.638
- |
-
- 122.7
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 101
- |
-
- R2699E
- |
-
- BXD
- |
-
- BXD40
- |
-
- 59
- |
-
- F
- |
-
- R2699E.CEL
- |
-
- 0.014
- |
-
- 0.015
- |
-
- 1.827
- |
-
- 105.23
- |
-
- 61.70%
- |
-
- 36.90%
- |
-
- 1.40%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 102
- |
-
- R2696E
- |
-
- BXD
- |
-
- BXD42
- |
-
- 58
- |
-
- F
- |
-
- R2696E.CEL
- |
-
- 0.01
- |
-
- 0.017
- |
-
- 1.622
- |
-
- 118.95
- |
-
- 62.00%
- |
-
- 36.60%
- |
-
- 1.50%
- |
-
- 1.53
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 103
- |
-
- R943E-2
- |
-
- BXD
- |
-
- BXD64
- |
-
- 56
- |
-
- F
- |
-
- R943E-2.CEL
- |
-
- 0.024
- |
-
- 0.021
- |
-
- 1.591
- |
-
- 141.34
- |
-
- 60.10%
- |
-
- 38.40%
- |
-
- 1.50%
- |
-
- 1.32
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 104
- |
-
- R967E
- |
-
- BXD
- |
-
- BXD48
- |
-
- 64
- |
-
- F
- |
-
- R967E.CEL
- |
-
- 0.101
- |
-
- 0.052
- |
-
- 1.948
- |
-
- 130.95
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.63
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 105
- |
-
- R2714E
- |
-
- BXD
- |
-
- BXD5
- |
-
- 58
- |
-
- M
- |
-
- R2714E.CEL
- |
-
- 0.047
- |
-
- 0.014
- |
-
- 1.404
- |
-
- 144.35
- |
-
- 60.60%
- |
-
- 37.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 106
- |
-
- R1042E
- |
-
- BXD
- |
-
- BXD51
- |
-
- 62
- |
-
- M
- |
-
- R1042E.CEL
- |
-
- 0.028
- |
-
- 0.027
- |
-
- 2.352
- |
-
- 104.12
- |
-
- 58.70%
- |
-
- 39.90%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 107
- |
-
- R2690E
- |
-
- BXD
- |
-
- BXD55
- |
-
- 65
- |
-
- M
- |
-
- R2690E.CEL
- |
-
- 0.081
- |
-
- 0.067
- |
-
- 1.887
- |
-
- 164.01
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 108
- |
-
- R2694E
- |
-
- BXD
- |
-
- BXD6
- |
-
- 58
- |
-
- M
- |
-
- R2694E.CEL
- |
-
- 0.012
- |
-
- 0.018
- |
-
- 1.983
- |
-
- 97.23
- |
-
- 61.60%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 109
- |
-
- R975E
- |
-
- BXD
- |
-
- BXD70
- |
-
- 64
- |
-
- F
- |
-
- R975E.CEL
- |
-
- 0.028
- |
-
- 0.024
- |
-
- 1.841
- |
-
- 137.97
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 110
- |
-
- R2684E
- |
-
- BXD
- |
-
- BXD61
- |
-
- 62
- |
-
- M
- |
-
- R2684E.CEL
- |
-
- 0.031
- |
-
- 0.032
- |
-
- 2.01
- |
-
- 131.03
- |
-
- 57.00%
- |
-
- 41.50%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 111
- |
-
- R994E
- |
-
- BXD
- |
-
- BXD43
- |
-
- 60
- |
-
- F
- |
-
- R994E.CEL
- |
-
- 0.013
- |
-
- 0.014
- |
-
- 1.966
- |
-
- 113.12
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.40%
- |
-
- 1.66
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 112
- |
-
- R2610E
- |
-
- BXD
- |
-
- BXD44
- |
-
- 68
- |
-
- M
- |
-
- R2610E.CEL
- |
-
- 0.013
- |
-
- 0.009
- |
-
- 1.814
- |
-
- 142.91
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.35
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 113
- |
-
- R2689E
- |
-
- BXD
- |
-
- BXD65
- |
-
- 63
- |
-
- F
- |
-
- R2689E.CEL
- |
-
- 0.008
- |
-
- 0.008
- |
-
- 1.721
- |
-
- 142.44
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 114
- |
-
- R2727E
- |
-
- BXD
- |
-
- BXD69
- |
-
- 65
- |
-
- M
- |
-
- R2727E.CEL
- |
-
- 0.01
- |
-
- 0.008
- |
-
- 1.578
- |
-
- 143.86
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 115
- |
-
- R2726E
- |
-
- BXD
- |
-
- BXD68
- |
-
- 64
- |
-
- M
- |
-
- R2726E.CEL
- |
-
- 0.125
- |
-
- 0.025
- |
-
- 1.811
- |
-
- 153.09
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 116
- |
-
- R2732E
- |
-
- BXD
- |
-
- BXD45
- |
-
- 63
- |
-
- F
- |
-
- R2732E.CEL
- |
-
- 0.039
- |
-
- 0.036
- |
-
- 2.154
- |
-
- 122.45
- |
-
- 56.50%
- |
-
- 42.10%
- |
-
- 1.40%
- |
-
- 1.8
- |
-
- 0.83
- |
-
- GU
- |
-
-
- |
- 117
- |
-
- R2709E
- |
-
- BXD
- |
-
- BXD8
- |
-
- 61
- |
-
- M
- |
-
- R2709E.CEL
- |
-
- 0.012
- |
-
- 0.011
- |
-
- 1.99
- |
-
- 99.79
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 118
- |
-
- R2686E
- |
-
- BXD
- |
-
- BXD80
- |
-
- 61
- |
-
- M
- |
-
- R2686E.CEL
- |
-
- 0.046
- |
-
- 0.05
- |
-
- 2.342
- |
-
- 119.63
- |
-
- 56.00%
- |
-
- 42.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 119
- |
-
- R2692E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 63
- |
-
- F
- |
-
- R2692E.CEL
- |
-
- 0.006
- |
-
- 0.007
- |
-
- 1.423
- |
-
- 160.87
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.46
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 120
- |
-
- R2715E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 91
- |
-
- M
- |
-
- R2715E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 1.488
- |
-
- 142.6
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 121
- |
-
- R1405E
- |
-
- BXD
- |
-
- BXD86
- |
-
- 58
- |
-
- F
- |
-
- R1405E.CEL
- |
-
- 0.053
- |
-
- 0.052
- |
-
- 2.351
- |
-
- 119.34
- |
-
- 56.40%
- |
-
- 42.20%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 122
- |
-
- R2724E
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- F
- |
-
- R2724E.CEL
- |
-
- 0.013
- |
-
- 0.019
- |
-
- 1.906
- |
-
- 113.71
- |
-
- 60.70%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 123
- |
-
- R1451E
- |
-
- BXD
- |
-
- BXD34
- |
-
- 61
- |
-
- F
- |
-
- R1451E.CEL
- |
-
- 0.01
- |
-
- 0.009
- |
-
- 1.843
- |
-
- 140.05
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 124
- |
-
- R1433E
- |
-
- BXD
- |
-
- BXD89
- |
-
- 63
- |
-
- F
- |
-
- R1433E.CEL
- |
-
- 0.029
- |
-
- 0.026
- |
-
- 2.241
- |
-
- 115.86
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 125
- |
-
- R2733E
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- F
- |
-
- R2733E.CEL
- |
-
- 0.024
- |
-
- 0.054
- |
-
- 1.7
- |
-
- 113.99
- |
-
- 62.10%
- |
-
- 36.60%
- |
-
- 1.30%
- |
-
- 1.4
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 126
- |
-
- R2649E
- |
-
- BXD
- |
-
- BXD97
- |
-
- 74
- |
-
- F
- |
-
- R2649E.CEL
- |
-
- 0.029
- |
-
- 0.032
- |
-
- 2.343
- |
-
- 119.04
- |
-
- 57.50%
- |
-
- 41.20%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 127
- |
-
- R2688E
- |
-
- BXD
- |
-
- BXD98
- |
-
- 67
- |
-
- M
- |
-
- R2688E.CEL
- |
-
- 0.032
- |
-
- 0.03
- |
-
- 1.772
- |
-
- 145.24
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.48
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 128
- |
-
- R877E
- |
-
- BXD
- |
-
- BXD13
- |
-
- 76
- |
-
- M
- |
-
- R877E.CEL
- |
-
- 0.026
- |
-
- 0.067
- |
-
- 1.558
- |
-
- 125.63
- |
-
- 61.20%
- |
-
- 37.50%
- |
-
- 1.20%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 129
- |
-
- R1397E-re
- |
-
- BXD
- |
-
- BXD75
- |
-
- 58
- |
-
- M
- |
-
- R1397E-re.CEL
- |
-
- 0.032
- |
-
- 0.01
- |
-
- 1.449
- |
-
- 189.71
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 130
- |
-
- R2779E
- |
-
- BXD
- |
-
- BXD73
- |
-
- 64
- |
-
- F
- |
-
- R2779E.CEL
- |
-
- 0.012
- |
-
- 0.038
- |
-
- 1.746
- |
-
- 121.11
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 131
- |
-
- R2708E
- |
-
- BXD
- |
-
- BXD9
- |
-
- 60
- |
-
- F
- |
-
- R2708E.CEL
- |
-
- 0.024
- |
-
- 0.045
- |
-
- 1.966
- |
-
- 126.46
- |
-
- 57.70%
- |
-
- 40.70%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.84
- |
-
- GU
- |
-
-
- |
- 132
- |
-
- R2547E1
- |
-
- GDP
- |
-
- WSB/Ei
- |
-
- 67
- |
-
- M
- |
-
- R2547E.CEL
- |
-
- 0.041
- |
-
- 0.039
- |
-
- 2.14
- |
-
- 90
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.60%
- |
-
- 1.32
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0406_P/acknowledgment.rtf b/general/datasets/Eye_M2_0406_P/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/Eye_M2_0406_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/Eye_M2_0406_P/cases.rtf b/general/datasets/Eye_M2_0406_P/cases.rtf
deleted file mode 100644
index 5cb5539..0000000
--- a/general/datasets/Eye_M2_0406_P/cases.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-We used a set of 55 BXD recombinant inbred strains, 14 conventional inbred strains including C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1s. BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D2). Physical maps in WebQTL incorporate approximately 2 million B6 vs D2 SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) have been included in the MDP. Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J. These reciprocal F1 can be used to detect some imprinted genes.
-
diff --git a/general/datasets/Eye_M2_0406_P/notes.rtf b/general/datasets/Eye_M2_0406_P/notes.rtf
deleted file mode 100644
index 39475ab..0000000
--- a/general/datasets/Eye_M2_0406_P/notes.rtf
+++ /dev/null
@@ -1,18 +0,0 @@
-This study includes the following datasets:
-
-
- -
-
Eye M430v2 (Apr06) RMA
-
- -
-
Eye M430v2 (Apr06) PDNN
-
- -
-
Eye M430v2 (Apr06) MAS5
-
- -
-
Eye M430v2 (Sep06) RMA
-
-
-
-This text file originally generated by RWW, May 26, 2006. Updated by RWW, May 27, 2006.
diff --git a/general/datasets/Eye_M2_0406_P/platform.rtf b/general/datasets/Eye_M2_0406_P/platform.rtf
deleted file mode 100644
index ac743ee..0000000
--- a/general/datasets/Eye_M2_0406_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/Eye_M2_0406_P/processing.rtf b/general/datasets/Eye_M2_0406_P/processing.rtf
deleted file mode 100644
index d23bc47..0000000
--- a/general/datasets/Eye_M2_0406_P/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the two batches together in RMA.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing all arrays were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (C3H/HeJ and BXD24) and samples from wild subspecies such as CAST/Ei, PWD/Ph, and PWK/Ph. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. We tended to keep arrays that "conformed" to the expectation. The assumption in these cases is that anomolous data are much more likely due to experimental problem and errors than to informative biological variation. Approximately 8 arrays total were discarded in batches 1 and 2 combined.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We then categorized arrays into XXX major "technical groups" depending on expression patterns as noted in scatterplots. This process of defining technical groups was done in DataDesk by manually "typing" arrays. These technical groups are apparently due to subtle within-batch effect that we do not yet understand and that cannot be corrected by quantile normalization. These XXX major technical groups are not obviously related to strain, sex, age, or any other known biological effect or variable. They are also not obviously related to any of the Affymetrix QC data types (3'/5' ratios, gain, etc.). Once the technical groups were defined, we forced the means of each probe set in the XX technical groups to the same value. This simple process partially removes a technical error of unknown origin in large expression array data sets.
-
-We reviewed the final data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of 140 arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g. 1000) represented the QTL harvest for the full data set. We then dropped a single array from the data set (n = 139 arrays), recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 950 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs (1000-950). Values ranged from -90 (good0 to +38 (bad). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a final method to polish a data set. By applying this procedure we discovered that a set of XX (7?) arrays could be excluded while simultaneously improving the total number of QTLs with values above 50.
-
-During this final process we discovered that nearly XX arrays in the second batch had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of very high quality.
-
diff --git a/general/datasets/Eye_M2_0406_P/summary.rtf b/general/datasets/Eye_M2_0406_P/summary.rtf
deleted file mode 100644
index 68a4484..0000000
--- a/general/datasets/Eye_M2_0406_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATA SET. The HEIMED April 2006 data set provides estimates of mRNA expression in whole eyes of 71 lines of young adult mice generated using 132 Affymetrix M430 2.0 arrays. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools; one male, one female, for each straion. This data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/Eye_M2_0406_P/tissue.rtf b/general/datasets/Eye_M2_0406_P/tissue.rtf
deleted file mode 100644
index d8d345f..0000000
--- a/general/datasets/Eye_M2_0406_P/tissue.rtf
+++ /dev/null
@@ -1,7112 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 4 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2) in the first batch of arrays (the November 05 data set) of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table). This same protocol was used for all samples in the second batch added in April 2006.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The first and second batches of array data, collectively represents a reasonably well balanced sample of males and females belonging to 62 strains, but without within-strain-by-sex replication. Six strains are represented only by male sample pools (BXD15, 28, 29, 55, 98, and DBA/2J. Four strains are represented only by a female pool sample (BXD1, 27, 73 and 86). Please use the probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males) as quantitative surrogates for the sex balance in this data set.
-
-Batch Structure: This data set consists of a two batches: the original batch that makes up the November 2005 data set and a new batch of 63 arrays (R0857E through R2649E, and R2682E through R2742E, non-consecutive identifiers) run in January 2006 by Dr. Yan Jiao. The arrays in the two batches are from two different lots. All arrays in the second batch were from Lot 4016879 (expiration date 12.28.06). We started working with a total of 140 arrays that passed initial crude quality control based on RNA quality and initial Affymetrix report file information such as 3'/5' ratio, scale factor, and percent present calls. A total of 130 arrays were finally approved for inclusion in this April 2006 data set. The complex normalization procedure is described below.
-
-The table below summarizes information on strain, age, sex, original CEL filename, Affymetrix quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-IN PROGRESS: PLEASE NOTE THAT THIS TABLE IS NOW BEING UPDATED TO INCLUDE BATCH 2 OF EARLY 2006.
-
-
-
-
-
- | ID |
-
- tube ID
- |
-
- group_type
- |
-
- Strain
- |
-
- age
- |
-
- Sex
- |
-
- original
-
- CEL
-
- filename
- |
-
- PDNN
-
- 2Z
-
- outlier
- |
-
- RMA
-
- 2Z
-
- outlier
- |
-
- scale
-
- factor
- |
-
- background
-
- average
- |
-
- present
- |
-
- absent
- |
-
- marginal
- |
-
- AFFX-b-
-
- ActinMur(3'/5')
- |
-
- AFFX-
-
- GapdhMur(3'/5')
- |
-
- Source
- |
-
-
- |
- 1
- |
-
- R2533E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 60
- |
-
- M
- |
-
- R2533E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.11
- |
-
- 94
- |
-
- 57.90%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 2
- |
-
- R2595E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 59
- |
-
- F
- |
-
- R2595E.CEL
- |
-
- 0.033
- |
-
- 0.036
- |
-
- 1.79
- |
-
- 115
- |
-
- 61.00%
- |
-
- 37.50%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 3
- |
-
- R0754E2
- |
-
- GDP
- |
-
- A/J
- |
-
- 60
- |
-
- M
- |
-
- R0754E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.72
- |
-
- 86
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.36
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 4
- |
-
- R2546E1
- |
-
- GDP
- |
-
- A/J
- |
-
- 66
- |
-
- F
- |
-
- R2545E.CEL
- |
-
- 0.024
- |
-
- 0.029
- |
-
- 1.99
- |
-
- 96
- |
-
- 58.60%
- |
-
- 39.70%
- |
-
- 1.70%
- |
-
- 1.47
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 5
- |
-
- R2601E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- F
- |
-
- R2601E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 2.55
- |
-
- 92
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 6
- |
-
- R2602E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- M
- |
-
- R2602E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 2.60
- |
-
- 84
- |
-
- 59.70%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 7
- |
-
- R1672E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- M
- |
-
- R1672E.CEL
- |
-
- 0.043
- |
-
- 0.039
- |
-
- 2.22
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 8
- |
-
- R1676E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- F
- |
-
- R1676E.CEL
- |
-
- 0.083
- |
-
- 0.085
- |
-
- 2.69
- |
-
- 98
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.74
- |
-
- JAX
- |
-
-
- |
- 9
- |
-
- R2581E1
- |
-
- BXD
- |
-
- BXD11
- |
-
- 65
- |
-
- F
- |
-
- R2581E.CEL
- |
-
- 0.009
- |
-
- 0.021
- |
-
- 1.94
- |
-
- 89
- |
-
- 62.10%
- |
-
- 36.40%
- |
-
- 1.60%
- |
-
- 1.55
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 10
- |
-
- R2543E1
- |
-
- BXD
- |
-
- BXD12
- |
-
- 63
- |
-
- M
- |
-
- R2543E.CEL
- |
-
- 0.018
- |
-
- 0.017
- |
-
- 1.61
- |
-
- 118
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 11
- |
-
- R2586E1
- |
-
- BXD
- |
-
- BXD13
- |
-
- 60
- |
-
- F
- |
-
- R2586E.CEL
- |
-
- 0.259
- |
-
- 0.258
- |
-
- 2.01
- |
-
- 74
- |
-
- 56.40%
- |
-
- 42.00%
- |
-
- 1.60%
- |
-
- 2.85
- |
-
- 3.81
- |
-
- Glenn
- |
-
-
- |
- 12
- |
-
- R2557E1
- |
-
- BXD
- |
-
- BXD14
- |
-
- 60
- |
-
- F
- |
-
- R2557E.CEL
- |
-
- 0.012
- |
-
- 0.027
- |
-
- 1.83
- |
-
- 99
- |
-
- 62.50%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 13
- |
-
- R2567E1
- |
-
- BXD
- |
-
- BXD16
- |
-
- 60
- |
-
- M
- |
-
- R2567E.CEL
- |
-
- 0.048
- |
-
- 0.058
- |
-
- 2.24
- |
-
- 82
- |
-
- 56.70%
- |
-
- 41.60%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.75
- |
-
- Glenn
- |
-
-
- |
- 14
- |
-
- R2559E1
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- M
- |
-
- R2559E.CEL
- |
-
- 0.01
- |
-
- 0.012
- |
-
- 1.65
- |
-
- 104
- |
-
- 60.80%
- |
-
- 37.70%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 15
- |
-
- R2560E1
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- F
- |
-
- R2560E.CEL
- |
-
- 0.009
- |
-
- 0.012
- |
-
- 1.79
- |
-
- 98
- |
-
- 60.90%
- |
-
- 37.50%
- |
-
- 1.60%
- |
-
- 1.35
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 16
- |
-
- R2597E1
- |
-
- BXD
- |
-
- BXD2
- |
-
- 61
- |
-
- M
- |
-
- R2597E.CEL
- |
-
- 0.005
- |
-
- 0.012
- |
-
- 2.37
- |
-
- 94
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 17
- |
-
- R2584E1
- |
-
- BXD
- |
-
- BXD20
- |
-
- 59
- |
-
- F
- |
-
- R2584E.CEL
- |
-
- 0.011
- |
-
- 0.017
- |
-
- 2.07
- |
-
- 84
- |
-
- 59.30%
- |
-
- 39.10%
- |
-
- 1.60%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 18
- |
-
- R2541E2
- |
-
- BXD
- |
-
- BXD21
- |
-
- 61
- |
-
- M
- |
-
- R2541E2.CEL
- |
-
- 0.049
- |
-
- 0.084
- |
-
- 2.63
- |
-
- 125
- |
-
- 56.00%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.29
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 19
- |
-
- R2553E1
- |
-
- BXD
- |
-
- BXD22
- |
-
- 58
- |
-
- F
- |
-
- R2553E.CEL
- |
-
- 0.004
- |
-
- 0.01
- |
-
- 1.95
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.50%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 20
- |
-
- R2558E1
- |
-
- BXD
- |
-
- BXD23
- |
-
- 60
- |
-
- F
- |
-
- R2558E-2.CEL
- |
-
- 0.018
- |
-
- 0.027
- |
-
- 1.91
- |
-
- 115
- |
-
- 59.90%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.20
- |
-
- 0.82
- |
-
- Glenn
- |
-
-
- |
- 21
- |
-
- R2589E2
- |
-
- BXD
- |
-
- BXD24
- |
-
- 59
- |
-
- M
- |
-
- R2589E2.CEL
- |
-
- 0.132
- |
-
- 0.176
- |
-
- 2.61
- |
-
- 112
- |
-
- 57.50%
- |
-
- 40.90%
- |
-
- 1.60%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 22
- |
-
- R2573E1
- |
-
- BXD
- |
-
- BXD25
- |
-
- 67
- |
-
- F
- |
-
- R2573E-2.CEL
- |
-
- 0.055
- |
-
- 0.063
- |
-
- 3.15
- |
-
- 72
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.77
- |
-
- 0.97
- |
-
- UAB
- |
-
-
- |
- 23
- |
-
- R2562E1
- |
-
- BXD
- |
-
- BXD29
- |
-
- 60
- |
-
- M
- |
-
- R2562E.CEL
- |
-
- 0.007
- |
-
- 0.01
- |
-
- 1.65
- |
-
- 116
- |
-
- 59.90%
- |
-
- 38.40%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- Glenn
- |
-
-
- |
- 24
- |
-
- R2598E1
- |
-
- BXD
- |
-
- BXD31
- |
-
- 61
- |
-
- M
- |
-
- R2598E.CEL
- |
-
- 0.006
- |
-
- 0.013
- |
-
- 1.99
- |
-
- 106
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 25
- |
-
- R2563E1
- |
-
- BXD
- |
-
- BXD32
- |
-
- 63
- |
-
- F
- |
-
- R2563E.CEL
- |
-
- 0.023
- |
-
- 0.025
- |
-
- 1.55
- |
-
- 102
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.40%
- |
-
- 1.50
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 26
- |
-
- R2542E1
- |
-
- BXD
- |
-
- BXD33
- |
-
- 67
- |
-
- F
- |
-
- R2542E.CEL
- |
-
- 0.058
- |
-
- 0.062
- |
-
- 2.13
- |
-
- 97
- |
-
- 56.50%
- |
-
- 41.80%
- |
-
- 1.60%
- |
-
- 1.91
- |
-
- 0.93
- |
-
- UTM RW
- |
-
-
- |
- 27
- |
-
- R2585E1
- |
-
- BXD
- |
-
- BXD34
- |
-
- 60
- |
-
- M
- |
-
- R2585E.CEL
- |
-
- 0.024
- |
-
- 0.032
- |
-
- 2.64
- |
-
- 75
- |
-
- 58.30%
- |
-
- 40.00%
- |
-
- 1.70%
- |
-
- 1.25
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 28
- |
-
- R2532E1
- |
-
- BXD
- |
-
- BXD38
- |
-
- 62
- |
-
- M
- |
-
- R2532E.CEL
- |
-
- 0.002
- |
-
- 0.006
- |
-
- 2.04
- |
-
- 94
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 29
- |
-
- R2574E1
- |
-
- BXD
- |
-
- BXD39
- |
-
- 70
- |
-
- F
- |
-
- R2574E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 1.98
- |
-
- 91
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 30
- |
-
- R2590E1
- |
-
- BXD
- |
-
- BXD40
- |
-
- 60
- |
-
- M
- |
-
- R2590E.CEL
- |
-
- 0.007
- |
-
- 0.012
- |
-
- 2.71
- |
-
- 77
- |
-
- 59.10%
- |
-
- 39.30%
- |
-
- 1.50%
- |
-
- 1.40
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 31
- |
-
- R2596E1
- |
-
- BXD
- |
-
- BXD42
- |
-
- 59
- |
-
- M
- |
-
- R2596E.CEL
- |
-
- 0.016
- |
-
- 0.03
- |
-
- 2.63
- |
-
- 108
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 32
- |
-
- R2605E1
- |
-
- BXD
- |
-
- BXD43
- |
-
- 79
- |
-
- M
- |
-
- R2607E.CEL
- |
-
- 0.006
- |
-
- 0.01
- |
-
- 1.82
- |
-
- 131
- |
-
- 60.50%
- |
-
- 38.20%
- |
-
- 1.30%
- |
-
- 1.32
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 33
- |
-
- R2594E1
- |
-
- BXD
- |
-
- BXD44
- |
-
- 63
- |
-
- F
- |
-
- R2594E.CEL
- |
-
- 0.014
- |
-
- 0.024
- |
-
- 1.77
- |
-
- 117
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 34
- |
-
- R2592E1
- |
-
- BXD
- |
-
- BXD45
- |
-
- 62
- |
-
- M
- |
-
- R2592E.CEL
- |
-
- 0.005
- |
-
- 0.011
- |
-
- 1.85
- |
-
- 106
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.43
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 35
- |
-
- R2606E1
- |
-
- BXD
- |
-
- BXD48
- |
-
- 78
- |
-
- M
- |
-
- R2606E.CEL
- |
-
- 0.007
- |
-
- 0.015
- |
-
- 2.56
- |
-
- 106
- |
-
- 58.90%
- |
-
- 39.70%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.83
- |
-
- UTM RW
- |
-
-
- |
- 36
- |
-
- R2591E1
- |
-
- BXD
- |
-
- BXD5
- |
-
- 60
- |
-
- F
- |
-
- R2591E.CEL
- |
-
- 0.052
- |
-
- 0.014
- |
-
- 1.70
- |
-
- 136
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 37
- |
-
- R2603E1
- |
-
- BXD
- |
-
- BXD51
- |
-
- 66
- |
-
- F
- |
-
- R2603E.CEL
- |
-
- 0.007
- |
-
- 0.02
- |
-
- 2.49
- |
-
- 115
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 38
- |
-
- R2570E1
- |
-
- BXD
- |
-
- BXD6
- |
-
- 65
- |
-
- F
- |
-
- R2570E.CEL
- |
-
- 0.013
- |
-
- 0.017
- |
-
- 1.99
- |
-
- 87
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 39
- |
-
- R2534E2
- |
-
- BXD
- |
-
- BXD61
- |
-
- 70
- |
-
- F
- |
-
- R2534E2.CEL
- |
-
- 0.03
- |
-
- 0.058
- |
-
- 2.47
- |
-
- 118
- |
-
- 57.90%
- |
-
- 40.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 40
- |
-
- R2611E1
- |
-
- BXD
- |
-
- BXD64
- |
-
- 68
- |
-
- M
- |
-
- R2611E.CEL
- |
-
- 0.067
- |
-
- 0.068
- |
-
- 2.29
- |
-
- 92
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 1.06
- |
-
- UTM RW
- |
-
-
- |
- 41
- |
-
- R2583E1
- |
-
- BXD
- |
-
- BXD65
- |
-
- 60
- |
-
- M
- |
-
- R2583E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.49
- |
-
- 70
- |
-
- 56.90%
- |
-
- 41.50%
- |
-
- 1.60%
- |
-
- 1.67
- |
-
- 1.01
- |
-
- UTM RW
- |
-
-
- |
- 42
- |
-
- R2536E2
- |
-
- BXD
- |
-
- BXD66
- |
-
- 64
- |
-
- F
- |
-
- R2536E2.CEL
- |
-
- 0.067
- |
-
- 0.139
- |
-
- 2.74
- |
-
- 109
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.70%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 43
- |
-
- R2551E1
- |
-
- BXD
- |
-
- BXD68
- |
-
- 67
- |
-
- F
- |
-
- R2551E.CEL
- |
-
- 0.294
- |
-
- 0.291
- |
-
- 2.49
- |
-
- 92
- |
-
- 54.30%
- |
-
- 44.10%
- |
-
- 1.60%
- |
-
- 2.91
- |
-
- 1.55
- |
-
- UTM RW
- |
-
-
- |
- 44
- |
-
- R2593E1
- |
-
- BXD
- |
-
- BXD69
- |
-
- 59
- |
-
- F
- |
-
- R2593E.CEL
- |
-
- 0.027
- |
-
- 0.038
- |
-
- 1.67
- |
-
- 128
- |
-
- 59.20%
- |
-
- 39.50%
- |
-
- 1.30%
- |
-
- 1.47
- |
-
- 0.92
- |
-
- UTM RW
- |
-
-
- |
- 45
- |
-
- R2537E2
- |
-
- BXD
- |
-
- BXD70
- |
-
- 59
- |
-
- M
- |
-
- R2537E2.CEL
- |
-
- 0.049
- |
-
- 0.092
- |
-
- 2.93
- |
-
- 99
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.29
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 46
- |
-
- R2565E1
- |
-
- BXD
- |
-
- BXD75
- |
-
- 61
- |
-
- F
- |
-
- R2565E.CEL
- |
-
- 0.118
- |
-
- 0.124
- |
-
- 1.79
- |
-
- 102
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 2.31
- |
-
- 3.47
- |
-
- UTM RW
- |
-
-
- |
- 47
- |
-
- R2538E1
- |
-
- BXD
- |
-
- BXD8
- |
-
- 77
- |
-
- F
- |
-
- R2538E.CEL
- |
-
- 0.033
- |
-
- 0.056
- |
-
- 1.91
- |
-
- 102
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 48
- |
-
- R2579E1
- |
-
- BXD
- |
-
- BXD80
- |
-
- 65
- |
-
- F
- |
-
- R2579E.CEL
- |
-
- 0.013
- |
-
- 0.026
- |
-
- 2.42
- |
-
- 72
- |
-
- 59.20%
- |
-
- 39.40%
- |
-
- 1.50%
- |
-
- 1.73
- |
-
- 0.82
- |
-
- UTM RW
- |
-
-
- |
- 49
- |
-
- R2540E1
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- M
- |
-
- R2540E.CEL
- |
-
- 0.014
- |
-
- 0.034
- |
-
- 2.33
- |
-
- 93
- |
-
- 61.10%
- |
-
- 37.40%
- |
-
- 1.40%
- |
-
- 1.22
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 50
- |
-
- R2545E1
- |
-
- BXD
- |
-
- BXD89
- |
-
- 67
- |
-
- M
- |
-
- R2546E.CEL
- |
-
- 0.266
- |
-
- 0.257
- |
-
- 1.67
- |
-
- 105
- |
-
- 56.20%
- |
-
- 42.30%
- |
-
- 1.50%
- |
-
- 3.60
- |
-
- 9.84
- |
-
- UTM RW
- |
-
-
- |
- 51
- |
-
- R2569E1
- |
-
- BXD
- |
-
- BXD9
- |
-
- 67
- |
-
- M
- |
-
- R2569E.CEL
- |
-
- 0.256
- |
-
- 0.239
- |
-
- 1.75
- |
-
- 87
- |
-
- 55.10%
- |
-
- 43.40%
- |
-
- 1.50%
- |
-
- 2.82
- |
-
- 3.14
- |
-
- UTM RW
- |
-
-
- |
- 52
- |
-
- R2578E2
- |
-
- BXD
- |
-
- BXD90
- |
-
- 61
- |
-
- F
- |
-
- R2578E2.CEL
- |
-
- 0.041
- |
-
- 0.062
- |
-
- 2.79
- |
-
- 92
- |
-
- 58.60%
- |
-
- 39.80%
- |
-
- 1.60%
- |
-
- 1.52
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 53
- |
-
- R2554E1
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- M
- |
-
- R2554E.CEL
- |
-
- 0.005
- |
-
- 0.008
- |
-
- 2.18
- |
-
- 93
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 54
- |
-
- R2577E1
- |
-
- BXD
- |
-
- BXD97
- |
-
- 55
- |
-
- M
- |
-
- R2577E.CEL
- |
-
- 0.065
- |
-
- 0.069
- |
-
- 2.07
- |
-
- 77
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.87
- |
-
- 1.29
- |
-
- UTM RW
- |
-
-
- |
- 55
- |
-
- R1700E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- F
- |
-
- R1700E.CEL
- |
-
- 0.152
- |
-
- 0.168
- |
-
- 2.98
- |
-
- 69
- |
-
- 60.80%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.48
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 56
- |
-
- R1704E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- M
- |
-
- R1704E.CEL
- |
-
- 0.154
- |
-
- 0.165
- |
-
- 2.58
- |
-
- 88
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.84
- |
-
- UTM RW
- |
-
-
- |
- 57
- |
-
- R0872E2
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 66
- |
-
- M
- |
-
- R0872E.CEL
- |
-
- 0.014
- |
-
- 0.023
- |
-
- 3.13
- |
-
- 89
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 58
- |
-
- R2607E1
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 67
- |
-
- F
- |
-
- R2605E.CEL
- |
-
- 0.008
- |
-
- 0.018
- |
-
- 2.43
- |
-
- 115
- |
-
- 58.60%
- |
-
- 40.00%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 59
- |
-
- R2564E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- F
- |
-
- R2564E.CEL
- |
-
- 0.124
- |
-
- 0.105
- |
-
- 1.94
- |
-
- 89
- |
-
- 58.50%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.60
- |
-
- 0.77
- |
-
- JAX
- |
-
-
- |
- 60
- |
-
- R2580E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- M
- |
-
- R2580E.CEL
- |
-
- 0.123
- |
-
- 0.109
- |
-
- 2.09
- |
-
- 95
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.70%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 61
- |
-
- R2600E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 72
- |
-
- F
- |
-
- R2600E.CEL
- |
-
- 0.008
- |
-
- 0.02
- |
-
- 2.47
- |
-
- 95
- |
-
- 58.10%
- |
-
- 40.20%
- |
-
- 1.70%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 62
- |
-
- R2604E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 69
- |
-
- M
- |
-
- R2604E.CEL
- |
-
- 0.005
- |
-
- 0.014
- |
-
- 2.66
- |
-
- 90
- |
-
- 59.40%
- |
-
- 39.20%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 63
- |
-
- R2572E1
- |
-
- GDP BXD
- |
-
- DBA/2J
- |
-
- 65
- |
-
- M
- |
-
- R2572E.CEL
- |
-
- 0.091
- |
-
- 0.106
- |
-
- 2.41
- |
-
- 79
- |
-
- 55.50%
- |
-
- 42.90%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 64
- |
-
- R2636E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- F
- |
-
- R2636E.CEL
- |
-
- 0.044
- |
-
- 0.043
- |
-
- 2.61
- |
-
- 93
- |
-
- 58.90%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 65
- |
-
- R2637E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- M
- |
-
- R2637E.CEL
- |
-
- 0.056
- |
-
- 0.036
- |
-
- 2.19
- |
-
- 103
- |
-
- 59.40%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 66
- |
-
- R0999E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 57
- |
-
- F
- |
-
- R0999E.CEL
- |
-
- 0.021
- |
-
- 0.023
- |
-
- 2.45
- |
-
- 82
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 67
- |
-
- R1004E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 65
- |
-
- M
- |
-
- R1004E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.44
- |
-
- 92
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 68
- |
-
- R1688E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 66
- |
-
- F
- |
-
- R1688E.CEL
- |
-
- 0.028
- |
-
- 0.033
- |
-
- 2.66
- |
-
- 98
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 69
- |
-
- R2566E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 76
- |
-
- M
- |
-
- R2566E-2.CEL
- |
-
- 0.036
- |
-
- 0.04
- |
-
- 3.03
- |
-
- 69
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 70
- |
-
- R2535E1
- |
-
- GDP
- |
-
- NZO/H1LtJ
- |
-
- 62
- |
-
- F
- |
-
- R2535E.CEL
- |
-
- 0.037
- |
-
- 0.062
- |
-
- 1.89
- |
-
- 86
- |
-
- 60.40%
- |
-
- 38.20%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 71
- |
-
- R2550E1
- |
-
- GDP
- |
-
- NZO/HILtJ
- |
-
- 96
- |
-
- M
- |
-
- R2550E.CEL
- |
-
- 0.025
- |
-
- 0.029
- |
-
- 1.79
- |
-
- 87
- |
-
- 60.70%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 72
- |
-
- R2634E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- F
- |
-
- R2635E.CEL
- |
-
- 0.126
- |
-
- 0.114
- |
-
- 3.29
- |
-
- 90
- |
-
- 55.90%
- |
-
- 42.50%
- |
-
- 1.60%
- |
-
- 1.57
- |
-
- 0.81
- |
-
- JAX
- |
-
-
- |
- 73
- |
-
- R2635E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- M
- |
-
- R2634E.CEL
- |
-
- 0.15
- |
-
- 0.137
- |
-
- 3.72
- |
-
- 80
- |
-
- 54.20%
- |
-
- 44.10%
- |
-
- 1.70%
- |
-
- 1.53
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 74
- |
-
- R2544E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 63
- |
-
- F
- |
-
- R2544E.CEL
- |
-
- 0.174
- |
-
- 0.175
- |
-
- 2.20
- |
-
- 108
- |
-
- 54.90%
- |
-
- 43.50%
- |
-
- 1.70%
- |
-
- 1.36
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 75
- |
-
- R2549E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 83
- |
-
- M
- |
-
- R2549E.CEL
- |
-
- 0.103
- |
-
- 0.087
- |
-
- 2.28
- |
-
- 84
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 0.83
- |
-
- JAX
- |
-
-
- |
- 76
- |
-
- R2368E1
- |
-
- GDP
- |
-
- WSB/EI
- |
-
- 67
- |
-
- F
- |
-
- R2368E.CEL
- |
-
- 0.041
- |
-
- 0.047
- |
-
- 2.57
- |
-
- 86
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.29
- |
-
- 0.74
- |
-
- UTM RW
- |
-
-
- |
- 77
- |
-
- R2704E
- |
-
- BXD
- |
-
- BXD1
- |
-
- 59
- |
-
- F
- |
-
- R2704E.CEL
- |
-
- 0.029
- |
-
- 0.03
- |
-
- 2.066
- |
-
- 139.61
- |
-
- 56.60%
- |
-
- 41.90%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 78
- |
-
- R2612E
- |
-
- BXD
- |
-
- BXD11
- |
-
- 70
- |
-
- M
- |
-
- R2612E.CEL
- |
-
- 0.101
- |
-
- 0.112
- |
-
- 1.83
- |
-
- 142.03
- |
-
- 58.20%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.78
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 79
- |
-
- R2742E
- |
-
- BXD
- |
-
- BXD12
- |
-
- 71
- |
-
- F
- |
-
- R2742E.CEL
- |
-
- 0.073
- |
-
- 0.077
- |
-
- 2.127
- |
-
- 134.14
- |
-
- 57.00%
- |
-
- 41.60%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 80
- |
-
- R1086E
- |
-
- BXD
- |
-
- BXD23
- |
-
- 55
- |
-
- M
- |
-
- R1086E.CEL
- |
-
- 0.043
- |
-
- 0.034
- |
-
- 2.233
- |
-
- 125.05
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 81
- |
-
- R2716E
- |
-
- BXD
- |
-
- BXD15
- |
-
- 60
- |
-
- M
- |
-
- R2716E.CEL
- |
-
- 0.035
- |
-
- 0.037
- |
-
- 2.015
- |
-
- 150.83
- |
-
- 56.40%
- |
-
- 42.10%
- |
-
- 1.60%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 82
- |
-
- R2711E
- |
-
- BXD
- |
-
- BXD16
- |
-
- 61
- |
-
- F
- |
-
- R2711E.CEL
- |
-
- 0.032
- |
-
- 0.021
- |
-
- 1.953
- |
-
- 118.53
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 83
- |
-
- R2720E
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- F
- |
-
- R2720E.CEL
- |
-
- 0.014
- |
-
- 0.019
- |
-
- 2.32
- |
-
- 99.93
- |
-
- 59.50%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 84
- |
-
- R2713E
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- M
- |
-
- R2713E.CEL
- |
-
- 0.055
- |
-
- 0.021
- |
-
- 1.67
- |
-
- 120.82
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 85
- |
-
- R1231E
- |
-
- BXD
- |
-
- BXD2
- |
-
- 64
- |
-
- F
- |
-
- R1231E.CEL
- |
-
- 0.044
- |
-
- 0.037
- |
-
- 2.197
- |
-
- 138.73
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 86
- |
-
- R2731E
- |
-
- BXD
- |
-
- BXD20
- |
-
- 60
- |
-
- M
- |
-
- R2731E.CEL
- |
-
- 0.017
- |
-
- 0.019
- |
-
- 1.825
- |
-
- 147
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 87
- |
-
- R2702E
- |
-
- BXD
- |
-
- BXD21
- |
-
- 59
- |
-
- F
- |
-
- R2702E.CEL
- |
-
- 0.009
- |
-
- 0.008
- |
-
- 1.811
- |
-
- 128.65
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.26
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 88
- |
-
- R2700E
- |
-
- BXD
- |
-
- BXD22
- |
-
- 59
- |
-
- M
- |
-
- R2700E.CEL
- |
-
- 0.01
- |
-
- 0.015
- |
-
- 1.858
- |
-
- 102.96
- |
-
- 61.50%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.48
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 89
- |
-
- R1128E
- |
-
- BXD
- |
-
- BXD14
- |
-
- 65
- |
-
- M
- |
-
- R1128E.CEL
- |
-
- 0.037
- |
-
- 0.038
- |
-
- 2.366
- |
-
- 118.39
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 90
- |
-
- R2719E
- |
-
- BXD
- |
-
- BXD24
- |
-
- 123
- |
-
- F
- |
-
- R2719E.CEL
- |
-
- 0.112
- |
-
- 0.111
- |
-
- 1.47
- |
-
- 140.38
- |
-
- 61.50%
- |
-
- 37.20%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 91
- |
-
- R2683E
- |
-
- BXD
- |
-
- BXD25
- |
-
- 58
- |
-
- M
- |
-
- R2683E.CEL
- |
-
- 0.068
- |
-
- 0.068
- |
-
- 1.777
- |
-
- 115.64
- |
-
- 58.30%
- |
-
- 40.30%
- |
-
- 1.40%
- |
-
- 2.01
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 92
- |
-
- R2703E
- |
-
- BXD
- |
-
- BXD27
- |
-
- 60
- |
-
- F
- |
-
- R2703E.CEL
- |
-
- 0.008
- |
-
- 0.012
- |
-
- 1.263
- |
-
- 134.78
- |
-
- 62.60%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 93
- |
-
- R2721E
- |
-
- BXD
- |
-
- BXD28
- |
-
- 60
- |
-
- M
- |
-
- R2721E.CEL
- |
-
- 0.04
- |
-
- 0.048
- |
-
- 2.065
- |
-
- 157.39
- |
-
- 56.10%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 94
- |
-
- R1258E
- |
-
- BXD
- |
-
- BXD31
- |
-
- 57
- |
-
- F
- |
-
- R1258E.CEL
- |
-
- 0.037
- |
-
- 0.036
- |
-
- 2.063
- |
-
- 117.09
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.54
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 95
- |
-
- R1216E
- |
-
- BXD
- |
-
- BXD32
- |
-
- 76
- |
-
- M
- |
-
- R1216E.CEL
- |
-
- 0.05
- |
-
- 0.049
- |
-
- 2.23
- |
-
- 111.99
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 96
- |
-
- R857E
- |
-
- BXD
- |
-
- BXD33
- |
-
- 77
- |
-
- M
- |
-
- R857E.CEL
- |
-
- 0.078
- |
-
- 0.108
- |
-
- 1.737
- |
-
- 113.98
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.30%
- |
-
- 1.6
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 97
- |
-
- R859E
- |
-
- BXD
- |
-
- BXD90
- |
-
- 72
- |
-
- M
- |
-
- R859E.CEL
- |
-
- 0.028
- |
-
- 0.02
- |
-
- 1.847
- |
-
- 152.22
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 98
- |
-
- R1207E
- |
-
- BXD
- |
-
- BXD66
- |
-
- 83
- |
-
- M
- |
-
- R1207E.CEL
- |
-
- 0.017
- |
-
- 0.012
- |
-
- 1.681
- |
-
- 136.86
- |
-
- 60.40%
- |
-
- 38.10%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 99
- |
-
- R2710E
- |
-
- BXD
- |
-
- BXD38
- |
-
- 55
- |
-
- F
- |
-
- R2710E.CEL
- |
-
- 0.033
- |
-
- 0.031
- |
-
- 2.112
- |
-
- 122.1
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 100
- |
-
- R2695E
- |
-
- BXD
- |
-
- BXD39
- |
-
- 59
- |
-
- M
- |
-
- R2695E.CEL
- |
-
- 0.018
- |
-
- 0.016
- |
-
- 1.638
- |
-
- 122.7
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 101
- |
-
- R2699E
- |
-
- BXD
- |
-
- BXD40
- |
-
- 59
- |
-
- F
- |
-
- R2699E.CEL
- |
-
- 0.014
- |
-
- 0.015
- |
-
- 1.827
- |
-
- 105.23
- |
-
- 61.70%
- |
-
- 36.90%
- |
-
- 1.40%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 102
- |
-
- R2696E
- |
-
- BXD
- |
-
- BXD42
- |
-
- 58
- |
-
- F
- |
-
- R2696E.CEL
- |
-
- 0.01
- |
-
- 0.017
- |
-
- 1.622
- |
-
- 118.95
- |
-
- 62.00%
- |
-
- 36.60%
- |
-
- 1.50%
- |
-
- 1.53
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 103
- |
-
- R943E-2
- |
-
- BXD
- |
-
- BXD64
- |
-
- 56
- |
-
- F
- |
-
- R943E-2.CEL
- |
-
- 0.024
- |
-
- 0.021
- |
-
- 1.591
- |
-
- 141.34
- |
-
- 60.10%
- |
-
- 38.40%
- |
-
- 1.50%
- |
-
- 1.32
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 104
- |
-
- R967E
- |
-
- BXD
- |
-
- BXD48
- |
-
- 64
- |
-
- F
- |
-
- R967E.CEL
- |
-
- 0.101
- |
-
- 0.052
- |
-
- 1.948
- |
-
- 130.95
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.63
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 105
- |
-
- R2714E
- |
-
- BXD
- |
-
- BXD5
- |
-
- 58
- |
-
- M
- |
-
- R2714E.CEL
- |
-
- 0.047
- |
-
- 0.014
- |
-
- 1.404
- |
-
- 144.35
- |
-
- 60.60%
- |
-
- 37.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 106
- |
-
- R1042E
- |
-
- BXD
- |
-
- BXD51
- |
-
- 62
- |
-
- M
- |
-
- R1042E.CEL
- |
-
- 0.028
- |
-
- 0.027
- |
-
- 2.352
- |
-
- 104.12
- |
-
- 58.70%
- |
-
- 39.90%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 107
- |
-
- R2690E
- |
-
- BXD
- |
-
- BXD55
- |
-
- 65
- |
-
- M
- |
-
- R2690E.CEL
- |
-
- 0.081
- |
-
- 0.067
- |
-
- 1.887
- |
-
- 164.01
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 108
- |
-
- R2694E
- |
-
- BXD
- |
-
- BXD6
- |
-
- 58
- |
-
- M
- |
-
- R2694E.CEL
- |
-
- 0.012
- |
-
- 0.018
- |
-
- 1.983
- |
-
- 97.23
- |
-
- 61.60%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 109
- |
-
- R975E
- |
-
- BXD
- |
-
- BXD70
- |
-
- 64
- |
-
- F
- |
-
- R975E.CEL
- |
-
- 0.028
- |
-
- 0.024
- |
-
- 1.841
- |
-
- 137.97
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 110
- |
-
- R2684E
- |
-
- BXD
- |
-
- BXD61
- |
-
- 62
- |
-
- M
- |
-
- R2684E.CEL
- |
-
- 0.031
- |
-
- 0.032
- |
-
- 2.01
- |
-
- 131.03
- |
-
- 57.00%
- |
-
- 41.50%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 111
- |
-
- R994E
- |
-
- BXD
- |
-
- BXD43
- |
-
- 60
- |
-
- F
- |
-
- R994E.CEL
- |
-
- 0.013
- |
-
- 0.014
- |
-
- 1.966
- |
-
- 113.12
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.40%
- |
-
- 1.66
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 112
- |
-
- R2610E
- |
-
- BXD
- |
-
- BXD44
- |
-
- 68
- |
-
- M
- |
-
- R2610E.CEL
- |
-
- 0.013
- |
-
- 0.009
- |
-
- 1.814
- |
-
- 142.91
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.35
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 113
- |
-
- R2689E
- |
-
- BXD
- |
-
- BXD65
- |
-
- 63
- |
-
- F
- |
-
- R2689E.CEL
- |
-
- 0.008
- |
-
- 0.008
- |
-
- 1.721
- |
-
- 142.44
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 114
- |
-
- R2727E
- |
-
- BXD
- |
-
- BXD69
- |
-
- 65
- |
-
- M
- |
-
- R2727E.CEL
- |
-
- 0.01
- |
-
- 0.008
- |
-
- 1.578
- |
-
- 143.86
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 115
- |
-
- R2726E
- |
-
- BXD
- |
-
- BXD68
- |
-
- 64
- |
-
- M
- |
-
- R2726E.CEL
- |
-
- 0.125
- |
-
- 0.025
- |
-
- 1.811
- |
-
- 153.09
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 116
- |
-
- R2732E
- |
-
- BXD
- |
-
- BXD45
- |
-
- 63
- |
-
- F
- |
-
- R2732E.CEL
- |
-
- 0.039
- |
-
- 0.036
- |
-
- 2.154
- |
-
- 122.45
- |
-
- 56.50%
- |
-
- 42.10%
- |
-
- 1.40%
- |
-
- 1.8
- |
-
- 0.83
- |
-
- GU
- |
-
-
- |
- 117
- |
-
- R2709E
- |
-
- BXD
- |
-
- BXD8
- |
-
- 61
- |
-
- M
- |
-
- R2709E.CEL
- |
-
- 0.012
- |
-
- 0.011
- |
-
- 1.99
- |
-
- 99.79
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 118
- |
-
- R2686E
- |
-
- BXD
- |
-
- BXD80
- |
-
- 61
- |
-
- M
- |
-
- R2686E.CEL
- |
-
- 0.046
- |
-
- 0.05
- |
-
- 2.342
- |
-
- 119.63
- |
-
- 56.00%
- |
-
- 42.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 119
- |
-
- R2692E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 63
- |
-
- F
- |
-
- R2692E.CEL
- |
-
- 0.006
- |
-
- 0.007
- |
-
- 1.423
- |
-
- 160.87
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.46
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 120
- |
-
- R2715E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 91
- |
-
- M
- |
-
- R2715E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 1.488
- |
-
- 142.6
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 121
- |
-
- R1405E
- |
-
- BXD
- |
-
- BXD86
- |
-
- 58
- |
-
- F
- |
-
- R1405E.CEL
- |
-
- 0.053
- |
-
- 0.052
- |
-
- 2.351
- |
-
- 119.34
- |
-
- 56.40%
- |
-
- 42.20%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 122
- |
-
- R2724E
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- F
- |
-
- R2724E.CEL
- |
-
- 0.013
- |
-
- 0.019
- |
-
- 1.906
- |
-
- 113.71
- |
-
- 60.70%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 123
- |
-
- R1451E
- |
-
- BXD
- |
-
- BXD34
- |
-
- 61
- |
-
- F
- |
-
- R1451E.CEL
- |
-
- 0.01
- |
-
- 0.009
- |
-
- 1.843
- |
-
- 140.05
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 124
- |
-
- R1433E
- |
-
- BXD
- |
-
- BXD89
- |
-
- 63
- |
-
- F
- |
-
- R1433E.CEL
- |
-
- 0.029
- |
-
- 0.026
- |
-
- 2.241
- |
-
- 115.86
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 125
- |
-
- R2733E
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- F
- |
-
- R2733E.CEL
- |
-
- 0.024
- |
-
- 0.054
- |
-
- 1.7
- |
-
- 113.99
- |
-
- 62.10%
- |
-
- 36.60%
- |
-
- 1.30%
- |
-
- 1.4
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 126
- |
-
- R2649E
- |
-
- BXD
- |
-
- BXD97
- |
-
- 74
- |
-
- F
- |
-
- R2649E.CEL
- |
-
- 0.029
- |
-
- 0.032
- |
-
- 2.343
- |
-
- 119.04
- |
-
- 57.50%
- |
-
- 41.20%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 127
- |
-
- R2688E
- |
-
- BXD
- |
-
- BXD98
- |
-
- 67
- |
-
- M
- |
-
- R2688E.CEL
- |
-
- 0.032
- |
-
- 0.03
- |
-
- 1.772
- |
-
- 145.24
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.48
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 128
- |
-
- R877E
- |
-
- BXD
- |
-
- BXD13
- |
-
- 76
- |
-
- M
- |
-
- R877E.CEL
- |
-
- 0.026
- |
-
- 0.067
- |
-
- 1.558
- |
-
- 125.63
- |
-
- 61.20%
- |
-
- 37.50%
- |
-
- 1.20%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 129
- |
-
- R1397E-re
- |
-
- BXD
- |
-
- BXD75
- |
-
- 58
- |
-
- M
- |
-
- R1397E-re.CEL
- |
-
- 0.032
- |
-
- 0.01
- |
-
- 1.449
- |
-
- 189.71
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 130
- |
-
- R2779E
- |
-
- BXD
- |
-
- BXD73
- |
-
- 64
- |
-
- F
- |
-
- R2779E.CEL
- |
-
- 0.012
- |
-
- 0.038
- |
-
- 1.746
- |
-
- 121.11
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 131
- |
-
- R2708E
- |
-
- BXD
- |
-
- BXD9
- |
-
- 60
- |
-
- F
- |
-
- R2708E.CEL
- |
-
- 0.024
- |
-
- 0.045
- |
-
- 1.966
- |
-
- 126.46
- |
-
- 57.70%
- |
-
- 40.70%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.84
- |
-
- GU
- |
-
-
- |
- 132
- |
-
- R2547E1
- |
-
- GDP
- |
-
- WSB/Ei
- |
-
- 67
- |
-
- M
- |
-
- R2547E.CEL
- |
-
- 0.041
- |
-
- 0.039
- |
-
- 2.14
- |
-
- 90
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.60%
- |
-
- 1.32
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0608_R/summary.rtf b/general/datasets/Eye_M2_0608_R/summary.rtf
deleted file mode 100644
index 58d1226..0000000
--- a/general/datasets/Eye_M2_0608_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 61, Name: Eye M430v2 (Sep08) RMA
\ No newline at end of file
diff --git a/general/datasets/Eye_M2_0906_R/acknowledgment.rtf b/general/datasets/Eye_M2_0906_R/acknowledgment.rtf
deleted file mode 100644
index 3f040d2..0000000
--- a/general/datasets/Eye_M2_0906_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant. All arrays were processed at the VA Medical Center, Memphis by Weikuan Gu.
diff --git a/general/datasets/Eye_M2_0906_R/cases.rtf b/general/datasets/Eye_M2_0906_R/cases.rtf
deleted file mode 100644
index 5cb5539..0000000
--- a/general/datasets/Eye_M2_0906_R/cases.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-We used a set of 55 BXD recombinant inbred strains, 14 conventional inbred strains including C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1s. BXD strains were generated by crossing C57BL/6J with DBA/2J. The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D2). Physical maps in WebQTL incorporate approximately 2 million B6 vs D2 SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD1 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-Please note that BXD24/TyJ (JAX stock number 000031) used in this study is also known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 stock that has now been rederived, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control.
-
-BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
-
-Mouse Diversity Panel (MDP). In addition to the BXD strains, we have profiled a MDP consisting 14 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) have been included in the MDP. Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) also carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene.
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase-negative albino (c) mutant
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list. A tyrosinase-negative albino (c) mutant
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list. Important to note for this Eye dataset, C3H/HeJ is a Pdeb6 mutant with near total photoreceptor loss at maturity.
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1, aka F1 in some graphs and tables
- F1 hybrids generated by crossing C57BL/6J with DBA/2J. These reciprocal F1 can be used to detect some imprinted genes.
-
diff --git a/general/datasets/Eye_M2_0906_R/notes.rtf b/general/datasets/Eye_M2_0906_R/notes.rtf
deleted file mode 100644
index 39475ab..0000000
--- a/general/datasets/Eye_M2_0906_R/notes.rtf
+++ /dev/null
@@ -1,18 +0,0 @@
-This study includes the following datasets:
-
-
- -
-
Eye M430v2 (Apr06) RMA
-
- -
-
Eye M430v2 (Apr06) PDNN
-
- -
-
Eye M430v2 (Apr06) MAS5
-
- -
-
Eye M430v2 (Sep06) RMA
-
-
-
-This text file originally generated by RWW, May 26, 2006. Updated by RWW, May 27, 2006.
diff --git a/general/datasets/Eye_M2_0906_R/platform.rtf b/general/datasets/Eye_M2_0906_R/platform.rtf
deleted file mode 100644
index ac743ee..0000000
--- a/general/datasets/Eye_M2_0906_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
diff --git a/general/datasets/Eye_M2_0906_R/processing.rtf b/general/datasets/Eye_M2_0906_R/processing.rtf
deleted file mode 100644
index d23bc47..0000000
--- a/general/datasets/Eye_M2_0906_R/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the two batches together in RMA.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 7: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing all arrays were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (C3H/HeJ and BXD24) and samples from wild subspecies such as CAST/Ei, PWD/Ph, and PWK/Ph. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. We tended to keep arrays that "conformed" to the expectation. The assumption in these cases is that anomolous data are much more likely due to experimental problem and errors than to informative biological variation. Approximately 8 arrays total were discarded in batches 1 and 2 combined.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We then categorized arrays into XXX major "technical groups" depending on expression patterns as noted in scatterplots. This process of defining technical groups was done in DataDesk by manually "typing" arrays. These technical groups are apparently due to subtle within-batch effect that we do not yet understand and that cannot be corrected by quantile normalization. These XXX major technical groups are not obviously related to strain, sex, age, or any other known biological effect or variable. They are also not obviously related to any of the Affymetrix QC data types (3'/5' ratios, gain, etc.). Once the technical groups were defined, we forced the means of each probe set in the XX technical groups to the same value. This simple process partially removes a technical error of unknown origin in large expression array data sets.
-
-We reviewed the final data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of 140 arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g. 1000) represented the QTL harvest for the full data set. We then dropped a single array from the data set (n = 139 arrays), recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 950 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs (1000-950). Values ranged from -90 (good0 to +38 (bad). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a final method to polish a data set. By applying this procedure we discovered that a set of XX (7?) arrays could be excluded while simultaneously improving the total number of QTLs with values above 50.
-
-During this final process we discovered that nearly XX arrays in the second batch had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of very high quality.
-
diff --git a/general/datasets/Eye_M2_0906_R/summary.rtf b/general/datasets/Eye_M2_0906_R/summary.rtf
deleted file mode 100644
index 68a4484..0000000
--- a/general/datasets/Eye_M2_0906_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-SUPERCEDED EYE DATA SET. The HEIMED April 2006 data set provides estimates of mRNA expression in whole eyes of 71 lines of young adult mice generated using 132 Affymetrix M430 2.0 arrays. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools; one male, one female, for each straion. This data set was processed using the RMA protocol. To simplify comparison among different transforms, RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/Eye_M2_0906_R/tissue.rtf b/general/datasets/Eye_M2_0906_R/tissue.rtf
deleted file mode 100644
index d8d345f..0000000
--- a/general/datasets/Eye_M2_0906_R/tissue.rtf
+++ /dev/null
@@ -1,7112 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of RNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. Samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center lead by Drs. John Stuart and Weikuan Gu. All processing steps were performed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use (one third roughly) or were immediately used for hybridization.
-
-Dealing with Ocular Pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. The key determinant of this interesting effect is the Tyrp1 (brown) locus on Chr 4 at about 80 Mb. Loci on Chr 4 that map at this location should be considered with skepticism and reviewed carefully. To address this problem Yan Jiao purified total RNA a second time using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204). This was done for 8 colored samples (R2534E2, R2578E2, R1441E2, R2537E2, R2536E2, R2589E2, R2539E2) in the first batch of arrays (the November 05 data set) of which 5 were finally included in this data set (cases in which the strain ID is labeled with asterisks in the table). This same protocol was used for all samples in the second batch added in April 2006.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. The first and second batches of array data, collectively represents a reasonably well balanced sample of males and females belonging to 62 strains, but without within-strain-by-sex replication. Six strains are represented only by male sample pools (BXD15, 28, 29, 55, 98, and DBA/2J. Four strains are represented only by a female pool sample (BXD1, 27, 73 and 86). Please use the probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males) as quantitative surrogates for the sex balance in this data set.
-
-Batch Structure: This data set consists of a two batches: the original batch that makes up the November 2005 data set and a new batch of 63 arrays (R0857E through R2649E, and R2682E through R2742E, non-consecutive identifiers) run in January 2006 by Dr. Yan Jiao. The arrays in the two batches are from two different lots. All arrays in the second batch were from Lot 4016879 (expiration date 12.28.06). We started working with a total of 140 arrays that passed initial crude quality control based on RNA quality and initial Affymetrix report file information such as 3'/5' ratio, scale factor, and percent present calls. A total of 130 arrays were finally approved for inclusion in this April 2006 data set. The complex normalization procedure is described below.
-
-The table below summarizes information on strain, age, sex, original CEL filename, Affymetrix quality control values, and source of mice. Columns labeled "PDNN 2Z outlier" and "RMA 2Z outlier" list the fraction of probe sets with values that deviated more than 2 z units from the mean. Scale factor, background average, present, absent, marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-IN PROGRESS: PLEASE NOTE THAT THIS TABLE IS NOW BEING UPDATED TO INCLUDE BATCH 2 OF EARLY 2006.
-
-
-
-
-
- | ID |
-
- tube ID
- |
-
- group_type
- |
-
- Strain
- |
-
- age
- |
-
- Sex
- |
-
- original
-
- CEL
-
- filename
- |
-
- PDNN
-
- 2Z
-
- outlier
- |
-
- RMA
-
- 2Z
-
- outlier
- |
-
- scale
-
- factor
- |
-
- background
-
- average
- |
-
- present
- |
-
- absent
- |
-
- marginal
- |
-
- AFFX-b-
-
- ActinMur(3'/5')
- |
-
- AFFX-
-
- GapdhMur(3'/5')
- |
-
- Source
- |
-
-
- |
- 1
- |
-
- R2533E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 60
- |
-
- M
- |
-
- R2533E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.11
- |
-
- 94
- |
-
- 57.90%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 2
- |
-
- R2595E1
- |
-
- GDP
- |
-
- 129S1/SvImJ
- |
-
- 59
- |
-
- F
- |
-
- R2595E.CEL
- |
-
- 0.033
- |
-
- 0.036
- |
-
- 1.79
- |
-
- 115
- |
-
- 61.00%
- |
-
- 37.50%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 3
- |
-
- R0754E2
- |
-
- GDP
- |
-
- A/J
- |
-
- 60
- |
-
- M
- |
-
- R0754E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.72
- |
-
- 86
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.36
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 4
- |
-
- R2546E1
- |
-
- GDP
- |
-
- A/J
- |
-
- 66
- |
-
- F
- |
-
- R2545E.CEL
- |
-
- 0.024
- |
-
- 0.029
- |
-
- 1.99
- |
-
- 96
- |
-
- 58.60%
- |
-
- 39.70%
- |
-
- 1.70%
- |
-
- 1.47
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 5
- |
-
- R2601E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- F
- |
-
- R2601E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 2.55
- |
-
- 92
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 6
- |
-
- R2602E1
- |
-
- GDP BXD
- |
-
- B6D2F1
- |
-
- 73
- |
-
- M
- |
-
- R2602E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 2.60
- |
-
- 84
- |
-
- 59.70%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 7
- |
-
- R1672E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- M
- |
-
- R1672E.CEL
- |
-
- 0.043
- |
-
- 0.039
- |
-
- 2.22
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 8
- |
-
- R1676E1
- |
-
- GDP
- |
-
- BALB/cByJ
- |
-
- 83
- |
-
- F
- |
-
- R1676E.CEL
- |
-
- 0.083
- |
-
- 0.085
- |
-
- 2.69
- |
-
- 98
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.74
- |
-
- JAX
- |
-
-
- |
- 9
- |
-
- R2581E1
- |
-
- BXD
- |
-
- BXD11
- |
-
- 65
- |
-
- F
- |
-
- R2581E.CEL
- |
-
- 0.009
- |
-
- 0.021
- |
-
- 1.94
- |
-
- 89
- |
-
- 62.10%
- |
-
- 36.40%
- |
-
- 1.60%
- |
-
- 1.55
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 10
- |
-
- R2543E1
- |
-
- BXD
- |
-
- BXD12
- |
-
- 63
- |
-
- M
- |
-
- R2543E.CEL
- |
-
- 0.018
- |
-
- 0.017
- |
-
- 1.61
- |
-
- 118
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 11
- |
-
- R2586E1
- |
-
- BXD
- |
-
- BXD13
- |
-
- 60
- |
-
- F
- |
-
- R2586E.CEL
- |
-
- 0.259
- |
-
- 0.258
- |
-
- 2.01
- |
-
- 74
- |
-
- 56.40%
- |
-
- 42.00%
- |
-
- 1.60%
- |
-
- 2.85
- |
-
- 3.81
- |
-
- Glenn
- |
-
-
- |
- 12
- |
-
- R2557E1
- |
-
- BXD
- |
-
- BXD14
- |
-
- 60
- |
-
- F
- |
-
- R2557E.CEL
- |
-
- 0.012
- |
-
- 0.027
- |
-
- 1.83
- |
-
- 99
- |
-
- 62.50%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 13
- |
-
- R2567E1
- |
-
- BXD
- |
-
- BXD16
- |
-
- 60
- |
-
- M
- |
-
- R2567E.CEL
- |
-
- 0.048
- |
-
- 0.058
- |
-
- 2.24
- |
-
- 82
- |
-
- 56.70%
- |
-
- 41.60%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.75
- |
-
- Glenn
- |
-
-
- |
- 14
- |
-
- R2559E1
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- M
- |
-
- R2559E.CEL
- |
-
- 0.01
- |
-
- 0.012
- |
-
- 1.65
- |
-
- 104
- |
-
- 60.80%
- |
-
- 37.70%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 15
- |
-
- R2560E1
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- F
- |
-
- R2560E.CEL
- |
-
- 0.009
- |
-
- 0.012
- |
-
- 1.79
- |
-
- 98
- |
-
- 60.90%
- |
-
- 37.50%
- |
-
- 1.60%
- |
-
- 1.35
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 16
- |
-
- R2597E1
- |
-
- BXD
- |
-
- BXD2
- |
-
- 61
- |
-
- M
- |
-
- R2597E.CEL
- |
-
- 0.005
- |
-
- 0.012
- |
-
- 2.37
- |
-
- 94
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 17
- |
-
- R2584E1
- |
-
- BXD
- |
-
- BXD20
- |
-
- 59
- |
-
- F
- |
-
- R2584E.CEL
- |
-
- 0.011
- |
-
- 0.017
- |
-
- 2.07
- |
-
- 84
- |
-
- 59.30%
- |
-
- 39.10%
- |
-
- 1.60%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 18
- |
-
- R2541E2
- |
-
- BXD
- |
-
- BXD21
- |
-
- 61
- |
-
- M
- |
-
- R2541E2.CEL
- |
-
- 0.049
- |
-
- 0.084
- |
-
- 2.63
- |
-
- 125
- |
-
- 56.00%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.29
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 19
- |
-
- R2553E1
- |
-
- BXD
- |
-
- BXD22
- |
-
- 58
- |
-
- F
- |
-
- R2553E.CEL
- |
-
- 0.004
- |
-
- 0.01
- |
-
- 1.95
- |
-
- 111
- |
-
- 59.90%
- |
-
- 38.50%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.76
- |
-
- Glenn
- |
-
-
- |
- 20
- |
-
- R2558E1
- |
-
- BXD
- |
-
- BXD23
- |
-
- 60
- |
-
- F
- |
-
- R2558E-2.CEL
- |
-
- 0.018
- |
-
- 0.027
- |
-
- 1.91
- |
-
- 115
- |
-
- 59.90%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.20
- |
-
- 0.82
- |
-
- Glenn
- |
-
-
- |
- 21
- |
-
- R2589E2
- |
-
- BXD
- |
-
- BXD24
- |
-
- 59
- |
-
- M
- |
-
- R2589E2.CEL
- |
-
- 0.132
- |
-
- 0.176
- |
-
- 2.61
- |
-
- 112
- |
-
- 57.50%
- |
-
- 40.90%
- |
-
- 1.60%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 22
- |
-
- R2573E1
- |
-
- BXD
- |
-
- BXD25
- |
-
- 67
- |
-
- F
- |
-
- R2573E-2.CEL
- |
-
- 0.055
- |
-
- 0.063
- |
-
- 3.15
- |
-
- 72
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.77
- |
-
- 0.97
- |
-
- UAB
- |
-
-
- |
- 23
- |
-
- R2562E1
- |
-
- BXD
- |
-
- BXD29
- |
-
- 60
- |
-
- M
- |
-
- R2562E.CEL
- |
-
- 0.007
- |
-
- 0.01
- |
-
- 1.65
- |
-
- 116
- |
-
- 59.90%
- |
-
- 38.40%
- |
-
- 1.70%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- Glenn
- |
-
-
- |
- 24
- |
-
- R2598E1
- |
-
- BXD
- |
-
- BXD31
- |
-
- 61
- |
-
- M
- |
-
- R2598E.CEL
- |
-
- 0.006
- |
-
- 0.013
- |
-
- 1.99
- |
-
- 106
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.27
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 25
- |
-
- R2563E1
- |
-
- BXD
- |
-
- BXD32
- |
-
- 63
- |
-
- F
- |
-
- R2563E.CEL
- |
-
- 0.023
- |
-
- 0.025
- |
-
- 1.55
- |
-
- 102
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.40%
- |
-
- 1.50
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 26
- |
-
- R2542E1
- |
-
- BXD
- |
-
- BXD33
- |
-
- 67
- |
-
- F
- |
-
- R2542E.CEL
- |
-
- 0.058
- |
-
- 0.062
- |
-
- 2.13
- |
-
- 97
- |
-
- 56.50%
- |
-
- 41.80%
- |
-
- 1.60%
- |
-
- 1.91
- |
-
- 0.93
- |
-
- UTM RW
- |
-
-
- |
- 27
- |
-
- R2585E1
- |
-
- BXD
- |
-
- BXD34
- |
-
- 60
- |
-
- M
- |
-
- R2585E.CEL
- |
-
- 0.024
- |
-
- 0.032
- |
-
- 2.64
- |
-
- 75
- |
-
- 58.30%
- |
-
- 40.00%
- |
-
- 1.70%
- |
-
- 1.25
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 28
- |
-
- R2532E1
- |
-
- BXD
- |
-
- BXD38
- |
-
- 62
- |
-
- M
- |
-
- R2532E.CEL
- |
-
- 0.002
- |
-
- 0.006
- |
-
- 2.04
- |
-
- 94
- |
-
- 59.80%
- |
-
- 38.70%
- |
-
- 1.50%
- |
-
- 1.37
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 29
- |
-
- R2574E1
- |
-
- BXD
- |
-
- BXD39
- |
-
- 70
- |
-
- F
- |
-
- R2574E.CEL
- |
-
- 0.003
- |
-
- 0.008
- |
-
- 1.98
- |
-
- 91
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 30
- |
-
- R2590E1
- |
-
- BXD
- |
-
- BXD40
- |
-
- 60
- |
-
- M
- |
-
- R2590E.CEL
- |
-
- 0.007
- |
-
- 0.012
- |
-
- 2.71
- |
-
- 77
- |
-
- 59.10%
- |
-
- 39.30%
- |
-
- 1.50%
- |
-
- 1.40
- |
-
- 0.77
- |
-
- Glenn
- |
-
-
- |
- 31
- |
-
- R2596E1
- |
-
- BXD
- |
-
- BXD42
- |
-
- 59
- |
-
- M
- |
-
- R2596E.CEL
- |
-
- 0.016
- |
-
- 0.03
- |
-
- 2.63
- |
-
- 108
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.80
- |
-
- Glenn
- |
-
-
- |
- 32
- |
-
- R2605E1
- |
-
- BXD
- |
-
- BXD43
- |
-
- 79
- |
-
- M
- |
-
- R2607E.CEL
- |
-
- 0.006
- |
-
- 0.01
- |
-
- 1.82
- |
-
- 131
- |
-
- 60.50%
- |
-
- 38.20%
- |
-
- 1.30%
- |
-
- 1.32
- |
-
- 0.80
- |
-
- UTM RW
- |
-
-
- |
- 33
- |
-
- R2594E1
- |
-
- BXD
- |
-
- BXD44
- |
-
- 63
- |
-
- F
- |
-
- R2594E.CEL
- |
-
- 0.014
- |
-
- 0.024
- |
-
- 1.77
- |
-
- 117
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 34
- |
-
- R2592E1
- |
-
- BXD
- |
-
- BXD45
- |
-
- 62
- |
-
- M
- |
-
- R2592E.CEL
- |
-
- 0.005
- |
-
- 0.011
- |
-
- 1.85
- |
-
- 106
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.43
- |
-
- 0.85
- |
-
- UTM RW
- |
-
-
- |
- 35
- |
-
- R2606E1
- |
-
- BXD
- |
-
- BXD48
- |
-
- 78
- |
-
- M
- |
-
- R2606E.CEL
- |
-
- 0.007
- |
-
- 0.015
- |
-
- 2.56
- |
-
- 106
- |
-
- 58.90%
- |
-
- 39.70%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.83
- |
-
- UTM RW
- |
-
-
- |
- 36
- |
-
- R2591E1
- |
-
- BXD
- |
-
- BXD5
- |
-
- 60
- |
-
- F
- |
-
- R2591E.CEL
- |
-
- 0.052
- |
-
- 0.014
- |
-
- 1.70
- |
-
- 136
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.78
- |
-
- Glenn
- |
-
-
- |
- 37
- |
-
- R2603E1
- |
-
- BXD
- |
-
- BXD51
- |
-
- 66
- |
-
- F
- |
-
- R2603E.CEL
- |
-
- 0.007
- |
-
- 0.02
- |
-
- 2.49
- |
-
- 115
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.24
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 38
- |
-
- R2570E1
- |
-
- BXD
- |
-
- BXD6
- |
-
- 65
- |
-
- F
- |
-
- R2570E.CEL
- |
-
- 0.013
- |
-
- 0.017
- |
-
- 1.99
- |
-
- 87
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 39
- |
-
- R2534E2
- |
-
- BXD
- |
-
- BXD61
- |
-
- 70
- |
-
- F
- |
-
- R2534E2.CEL
- |
-
- 0.03
- |
-
- 0.058
- |
-
- 2.47
- |
-
- 118
- |
-
- 57.90%
- |
-
- 40.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 40
- |
-
- R2611E1
- |
-
- BXD
- |
-
- BXD64
- |
-
- 68
- |
-
- M
- |
-
- R2611E.CEL
- |
-
- 0.067
- |
-
- 0.068
- |
-
- 2.29
- |
-
- 92
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 1.06
- |
-
- UTM RW
- |
-
-
- |
- 41
- |
-
- R2583E1
- |
-
- BXD
- |
-
- BXD65
- |
-
- 60
- |
-
- M
- |
-
- R2583E.CEL
- |
-
- 0.027
- |
-
- 0.03
- |
-
- 2.49
- |
-
- 70
- |
-
- 56.90%
- |
-
- 41.50%
- |
-
- 1.60%
- |
-
- 1.67
- |
-
- 1.01
- |
-
- UTM RW
- |
-
-
- |
- 42
- |
-
- R2536E2
- |
-
- BXD
- |
-
- BXD66
- |
-
- 64
- |
-
- F
- |
-
- R2536E2.CEL
- |
-
- 0.067
- |
-
- 0.139
- |
-
- 2.74
- |
-
- 109
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.70%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 43
- |
-
- R2551E1
- |
-
- BXD
- |
-
- BXD68
- |
-
- 67
- |
-
- F
- |
-
- R2551E.CEL
- |
-
- 0.294
- |
-
- 0.291
- |
-
- 2.49
- |
-
- 92
- |
-
- 54.30%
- |
-
- 44.10%
- |
-
- 1.60%
- |
-
- 2.91
- |
-
- 1.55
- |
-
- UTM RW
- |
-
-
- |
- 44
- |
-
- R2593E1
- |
-
- BXD
- |
-
- BXD69
- |
-
- 59
- |
-
- F
- |
-
- R2593E.CEL
- |
-
- 0.027
- |
-
- 0.038
- |
-
- 1.67
- |
-
- 128
- |
-
- 59.20%
- |
-
- 39.50%
- |
-
- 1.30%
- |
-
- 1.47
- |
-
- 0.92
- |
-
- UTM RW
- |
-
-
- |
- 45
- |
-
- R2537E2
- |
-
- BXD
- |
-
- BXD70
- |
-
- 59
- |
-
- M
- |
-
- R2537E2.CEL
- |
-
- 0.049
- |
-
- 0.092
- |
-
- 2.93
- |
-
- 99
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.60%
- |
-
- 1.29
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 46
- |
-
- R2565E1
- |
-
- BXD
- |
-
- BXD75
- |
-
- 61
- |
-
- F
- |
-
- R2565E.CEL
- |
-
- 0.118
- |
-
- 0.124
- |
-
- 1.79
- |
-
- 102
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.50%
- |
-
- 2.31
- |
-
- 3.47
- |
-
- UTM RW
- |
-
-
- |
- 47
- |
-
- R2538E1
- |
-
- BXD
- |
-
- BXD8
- |
-
- 77
- |
-
- F
- |
-
- R2538E.CEL
- |
-
- 0.033
- |
-
- 0.056
- |
-
- 1.91
- |
-
- 102
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 48
- |
-
- R2579E1
- |
-
- BXD
- |
-
- BXD80
- |
-
- 65
- |
-
- F
- |
-
- R2579E.CEL
- |
-
- 0.013
- |
-
- 0.026
- |
-
- 2.42
- |
-
- 72
- |
-
- 59.20%
- |
-
- 39.40%
- |
-
- 1.50%
- |
-
- 1.73
- |
-
- 0.82
- |
-
- UTM RW
- |
-
-
- |
- 49
- |
-
- R2540E1
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- M
- |
-
- R2540E.CEL
- |
-
- 0.014
- |
-
- 0.034
- |
-
- 2.33
- |
-
- 93
- |
-
- 61.10%
- |
-
- 37.40%
- |
-
- 1.40%
- |
-
- 1.22
- |
-
- 0.81
- |
-
- UTM RW
- |
-
-
- |
- 50
- |
-
- R2545E1
- |
-
- BXD
- |
-
- BXD89
- |
-
- 67
- |
-
- M
- |
-
- R2546E.CEL
- |
-
- 0.266
- |
-
- 0.257
- |
-
- 1.67
- |
-
- 105
- |
-
- 56.20%
- |
-
- 42.30%
- |
-
- 1.50%
- |
-
- 3.60
- |
-
- 9.84
- |
-
- UTM RW
- |
-
-
- |
- 51
- |
-
- R2569E1
- |
-
- BXD
- |
-
- BXD9
- |
-
- 67
- |
-
- M
- |
-
- R2569E.CEL
- |
-
- 0.256
- |
-
- 0.239
- |
-
- 1.75
- |
-
- 87
- |
-
- 55.10%
- |
-
- 43.40%
- |
-
- 1.50%
- |
-
- 2.82
- |
-
- 3.14
- |
-
- UTM RW
- |
-
-
- |
- 52
- |
-
- R2578E2
- |
-
- BXD
- |
-
- BXD90
- |
-
- 61
- |
-
- F
- |
-
- R2578E2.CEL
- |
-
- 0.041
- |
-
- 0.062
- |
-
- 2.79
- |
-
- 92
- |
-
- 58.60%
- |
-
- 39.80%
- |
-
- 1.60%
- |
-
- 1.52
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 53
- |
-
- R2554E1
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- M
- |
-
- R2554E.CEL
- |
-
- 0.005
- |
-
- 0.008
- |
-
- 2.18
- |
-
- 93
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.46
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
- |
- 54
- |
-
- R2577E1
- |
-
- BXD
- |
-
- BXD97
- |
-
- 55
- |
-
- M
- |
-
- R2577E.CEL
- |
-
- 0.065
- |
-
- 0.069
- |
-
- 2.07
- |
-
- 77
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.87
- |
-
- 1.29
- |
-
- UTM RW
- |
-
-
- |
- 55
- |
-
- R1700E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- F
- |
-
- R1700E.CEL
- |
-
- 0.152
- |
-
- 0.168
- |
-
- 2.98
- |
-
- 69
- |
-
- 60.80%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.48
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 56
- |
-
- R1704E1
- |
-
- GDP
- |
-
- C3H/HeJ
- |
-
- 83
- |
-
- M
- |
-
- R1704E.CEL
- |
-
- 0.154
- |
-
- 0.165
- |
-
- 2.58
- |
-
- 88
- |
-
- 60.10%
- |
-
- 38.60%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.84
- |
-
- UTM RW
- |
-
-
- |
- 57
- |
-
- R0872E2
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 66
- |
-
- M
- |
-
- R0872E.CEL
- |
-
- 0.014
- |
-
- 0.023
- |
-
- 3.13
- |
-
- 89
- |
-
- 58.90%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 58
- |
-
- R2607E1
- |
-
- GDP BXD
- |
-
- C57BL/6J
- |
-
- 67
- |
-
- F
- |
-
- R2605E.CEL
- |
-
- 0.008
- |
-
- 0.018
- |
-
- 2.43
- |
-
- 115
- |
-
- 58.60%
- |
-
- 40.00%
- |
-
- 1.40%
- |
-
- 1.31
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 59
- |
-
- R2564E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- F
- |
-
- R2564E.CEL
- |
-
- 0.124
- |
-
- 0.105
- |
-
- 1.94
- |
-
- 89
- |
-
- 58.50%
- |
-
- 39.90%
- |
-
- 1.60%
- |
-
- 1.60
- |
-
- 0.77
- |
-
- JAX
- |
-
-
- |
- 60
- |
-
- R2580E1
- |
-
- GDP
- |
-
- CAST/Ei
- |
-
- 64
- |
-
- M
- |
-
- R2580E.CEL
- |
-
- 0.123
- |
-
- 0.109
- |
-
- 2.09
- |
-
- 95
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.70%
- |
-
- 1.40
- |
-
- 0.76
- |
-
- JAX
- |
-
-
- |
- 61
- |
-
- R2600E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 72
- |
-
- F
- |
-
- R2600E.CEL
- |
-
- 0.008
- |
-
- 0.02
- |
-
- 2.47
- |
-
- 95
- |
-
- 58.10%
- |
-
- 40.20%
- |
-
- 1.70%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- UTM RW
- |
-
-
- |
- 62
- |
-
- R2604E1
- |
-
- GDP BXD
- |
-
- D2B6F1
- |
-
- 69
- |
-
- M
- |
-
- R2604E.CEL
- |
-
- 0.005
- |
-
- 0.014
- |
-
- 2.66
- |
-
- 90
- |
-
- 59.40%
- |
-
- 39.20%
- |
-
- 1.50%
- |
-
- 1.28
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 63
- |
-
- R2572E1
- |
-
- GDP BXD
- |
-
- DBA/2J
- |
-
- 65
- |
-
- M
- |
-
- R2572E.CEL
- |
-
- 0.091
- |
-
- 0.106
- |
-
- 2.41
- |
-
- 79
- |
-
- 55.50%
- |
-
- 42.90%
- |
-
- 1.60%
- |
-
- 1.37
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 64
- |
-
- R2636E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- F
- |
-
- R2636E.CEL
- |
-
- 0.044
- |
-
- 0.043
- |
-
- 2.61
- |
-
- 93
- |
-
- 58.90%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.76
- |
-
- UTM RW
- |
-
-
- |
- 65
- |
-
- R2637E1
- |
-
- GDP
- |
-
- KK/HIJ
- |
-
- 64
- |
-
- M
- |
-
- R2637E.CEL
- |
-
- 0.056
- |
-
- 0.036
- |
-
- 2.19
- |
-
- 103
- |
-
- 59.40%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.30
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 66
- |
-
- R0999E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 57
- |
-
- F
- |
-
- R0999E.CEL
- |
-
- 0.021
- |
-
- 0.023
- |
-
- 2.45
- |
-
- 82
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 67
- |
-
- R1004E1
- |
-
- GDP
- |
-
- LG/J
- |
-
- 65
- |
-
- M
- |
-
- R1004E.CEL
- |
-
- 0.025
- |
-
- 0.028
- |
-
- 2.44
- |
-
- 92
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- UTM RW
- |
-
-
- |
- 68
- |
-
- R1688E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 66
- |
-
- F
- |
-
- R1688E.CEL
- |
-
- 0.028
- |
-
- 0.033
- |
-
- 2.66
- |
-
- 98
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.26
- |
-
- 0.80
- |
-
- JAX
- |
-
-
- |
- 69
- |
-
- R2566E1
- |
-
- GDP
- |
-
- NOD/LtJ
- |
-
- 76
- |
-
- M
- |
-
- R2566E-2.CEL
- |
-
- 0.036
- |
-
- 0.04
- |
-
- 3.03
- |
-
- 69
- |
-
- 59.80%
- |
-
- 38.80%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.75
- |
-
- UTM RW
- |
-
-
- |
- 70
- |
-
- R2535E1
- |
-
- GDP
- |
-
- NZO/H1LtJ
- |
-
- 62
- |
-
- F
- |
-
- R2535E.CEL
- |
-
- 0.037
- |
-
- 0.062
- |
-
- 1.89
- |
-
- 86
- |
-
- 60.40%
- |
-
- 38.20%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 71
- |
-
- R2550E1
- |
-
- GDP
- |
-
- NZO/HILtJ
- |
-
- 96
- |
-
- M
- |
-
- R2550E.CEL
- |
-
- 0.025
- |
-
- 0.029
- |
-
- 1.79
- |
-
- 87
- |
-
- 60.70%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.52
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 72
- |
-
- R2634E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- F
- |
-
- R2635E.CEL
- |
-
- 0.126
- |
-
- 0.114
- |
-
- 3.29
- |
-
- 90
- |
-
- 55.90%
- |
-
- 42.50%
- |
-
- 1.60%
- |
-
- 1.57
- |
-
- 0.81
- |
-
- JAX
- |
-
-
- |
- 73
- |
-
- R2635E1
- |
-
- GDP
- |
-
- PWD/PhJ
- |
-
- 62
- |
-
- M
- |
-
- R2634E.CEL
- |
-
- 0.15
- |
-
- 0.137
- |
-
- 3.72
- |
-
- 80
- |
-
- 54.20%
- |
-
- 44.10%
- |
-
- 1.70%
- |
-
- 1.53
- |
-
- 0.85
- |
-
- JAX
- |
-
-
- |
- 74
- |
-
- R2544E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 63
- |
-
- F
- |
-
- R2544E.CEL
- |
-
- 0.174
- |
-
- 0.175
- |
-
- 2.20
- |
-
- 108
- |
-
- 54.90%
- |
-
- 43.50%
- |
-
- 1.70%
- |
-
- 1.36
- |
-
- 0.82
- |
-
- JAX
- |
-
-
- |
- 75
- |
-
- R2549E1
- |
-
- GDP
- |
-
- PWK/PhJ
- |
-
- 83
- |
-
- M
- |
-
- R2549E.CEL
- |
-
- 0.103
- |
-
- 0.087
- |
-
- 2.28
- |
-
- 84
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.57
- |
-
- 0.83
- |
-
- JAX
- |
-
-
- |
- 76
- |
-
- R2368E1
- |
-
- GDP
- |
-
- WSB/EI
- |
-
- 67
- |
-
- F
- |
-
- R2368E.CEL
- |
-
- 0.041
- |
-
- 0.047
- |
-
- 2.57
- |
-
- 86
- |
-
- 59.50%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.29
- |
-
- 0.74
- |
-
- UTM RW
- |
-
-
- |
- 77
- |
-
- R2704E
- |
-
- BXD
- |
-
- BXD1
- |
-
- 59
- |
-
- F
- |
-
- R2704E.CEL
- |
-
- 0.029
- |
-
- 0.03
- |
-
- 2.066
- |
-
- 139.61
- |
-
- 56.60%
- |
-
- 41.90%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 78
- |
-
- R2612E
- |
-
- BXD
- |
-
- BXD11
- |
-
- 70
- |
-
- M
- |
-
- R2612E.CEL
- |
-
- 0.101
- |
-
- 0.112
- |
-
- 1.83
- |
-
- 142.03
- |
-
- 58.20%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.78
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 79
- |
-
- R2742E
- |
-
- BXD
- |
-
- BXD12
- |
-
- 71
- |
-
- F
- |
-
- R2742E.CEL
- |
-
- 0.073
- |
-
- 0.077
- |
-
- 2.127
- |
-
- 134.14
- |
-
- 57.00%
- |
-
- 41.60%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 80
- |
-
- R1086E
- |
-
- BXD
- |
-
- BXD23
- |
-
- 55
- |
-
- M
- |
-
- R1086E.CEL
- |
-
- 0.043
- |
-
- 0.034
- |
-
- 2.233
- |
-
- 125.05
- |
-
- 58.60%
- |
-
- 39.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 81
- |
-
- R2716E
- |
-
- BXD
- |
-
- BXD15
- |
-
- 60
- |
-
- M
- |
-
- R2716E.CEL
- |
-
- 0.035
- |
-
- 0.037
- |
-
- 2.015
- |
-
- 150.83
- |
-
- 56.40%
- |
-
- 42.10%
- |
-
- 1.60%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 82
- |
-
- R2711E
- |
-
- BXD
- |
-
- BXD16
- |
-
- 61
- |
-
- F
- |
-
- R2711E.CEL
- |
-
- 0.032
- |
-
- 0.021
- |
-
- 1.953
- |
-
- 118.53
- |
-
- 59.00%
- |
-
- 39.60%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 83
- |
-
- R2720E
- |
-
- BXD
- |
-
- BXD18
- |
-
- 59
- |
-
- F
- |
-
- R2720E.CEL
- |
-
- 0.014
- |
-
- 0.019
- |
-
- 2.32
- |
-
- 99.93
- |
-
- 59.50%
- |
-
- 39.00%
- |
-
- 1.50%
- |
-
- 1.33
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 84
- |
-
- R2713E
- |
-
- BXD
- |
-
- BXD19
- |
-
- 60
- |
-
- M
- |
-
- R2713E.CEL
- |
-
- 0.055
- |
-
- 0.021
- |
-
- 1.67
- |
-
- 120.82
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 85
- |
-
- R1231E
- |
-
- BXD
- |
-
- BXD2
- |
-
- 64
- |
-
- F
- |
-
- R1231E.CEL
- |
-
- 0.044
- |
-
- 0.037
- |
-
- 2.197
- |
-
- 138.73
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.41
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 86
- |
-
- R2731E
- |
-
- BXD
- |
-
- BXD20
- |
-
- 60
- |
-
- M
- |
-
- R2731E.CEL
- |
-
- 0.017
- |
-
- 0.019
- |
-
- 1.825
- |
-
- 147
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 87
- |
-
- R2702E
- |
-
- BXD
- |
-
- BXD21
- |
-
- 59
- |
-
- F
- |
-
- R2702E.CEL
- |
-
- 0.009
- |
-
- 0.008
- |
-
- 1.811
- |
-
- 128.65
- |
-
- 59.40%
- |
-
- 39.10%
- |
-
- 1.40%
- |
-
- 1.26
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 88
- |
-
- R2700E
- |
-
- BXD
- |
-
- BXD22
- |
-
- 59
- |
-
- M
- |
-
- R2700E.CEL
- |
-
- 0.01
- |
-
- 0.015
- |
-
- 1.858
- |
-
- 102.96
- |
-
- 61.50%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.48
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 89
- |
-
- R1128E
- |
-
- BXD
- |
-
- BXD14
- |
-
- 65
- |
-
- M
- |
-
- R1128E.CEL
- |
-
- 0.037
- |
-
- 0.038
- |
-
- 2.366
- |
-
- 118.39
- |
-
- 57.30%
- |
-
- 41.30%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 90
- |
-
- R2719E
- |
-
- BXD
- |
-
- BXD24
- |
-
- 123
- |
-
- F
- |
-
- R2719E.CEL
- |
-
- 0.112
- |
-
- 0.111
- |
-
- 1.47
- |
-
- 140.38
- |
-
- 61.50%
- |
-
- 37.20%
- |
-
- 1.30%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 91
- |
-
- R2683E
- |
-
- BXD
- |
-
- BXD25
- |
-
- 58
- |
-
- M
- |
-
- R2683E.CEL
- |
-
- 0.068
- |
-
- 0.068
- |
-
- 1.777
- |
-
- 115.64
- |
-
- 58.30%
- |
-
- 40.30%
- |
-
- 1.40%
- |
-
- 2.01
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 92
- |
-
- R2703E
- |
-
- BXD
- |
-
- BXD27
- |
-
- 60
- |
-
- F
- |
-
- R2703E.CEL
- |
-
- 0.008
- |
-
- 0.012
- |
-
- 1.263
- |
-
- 134.78
- |
-
- 62.60%
- |
-
- 36.10%
- |
-
- 1.40%
- |
-
- 1.44
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 93
- |
-
- R2721E
- |
-
- BXD
- |
-
- BXD28
- |
-
- 60
- |
-
- M
- |
-
- R2721E.CEL
- |
-
- 0.04
- |
-
- 0.048
- |
-
- 2.065
- |
-
- 157.39
- |
-
- 56.10%
- |
-
- 42.40%
- |
-
- 1.50%
- |
-
- 1.31
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 94
- |
-
- R1258E
- |
-
- BXD
- |
-
- BXD31
- |
-
- 57
- |
-
- F
- |
-
- R1258E.CEL
- |
-
- 0.037
- |
-
- 0.036
- |
-
- 2.063
- |
-
- 117.09
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.54
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 95
- |
-
- R1216E
- |
-
- BXD
- |
-
- BXD32
- |
-
- 76
- |
-
- M
- |
-
- R1216E.CEL
- |
-
- 0.05
- |
-
- 0.049
- |
-
- 2.23
- |
-
- 111.99
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.35
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 96
- |
-
- R857E
- |
-
- BXD
- |
-
- BXD33
- |
-
- 77
- |
-
- M
- |
-
- R857E.CEL
- |
-
- 0.078
- |
-
- 0.108
- |
-
- 1.737
- |
-
- 113.98
- |
-
- 61.90%
- |
-
- 36.70%
- |
-
- 1.30%
- |
-
- 1.6
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 97
- |
-
- R859E
- |
-
- BXD
- |
-
- BXD90
- |
-
- 72
- |
-
- M
- |
-
- R859E.CEL
- |
-
- 0.028
- |
-
- 0.02
- |
-
- 1.847
- |
-
- 152.22
- |
-
- 57.90%
- |
-
- 40.70%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 98
- |
-
- R1207E
- |
-
- BXD
- |
-
- BXD66
- |
-
- 83
- |
-
- M
- |
-
- R1207E.CEL
- |
-
- 0.017
- |
-
- 0.012
- |
-
- 1.681
- |
-
- 136.86
- |
-
- 60.40%
- |
-
- 38.10%
- |
-
- 1.50%
- |
-
- 1.45
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 99
- |
-
- R2710E
- |
-
- BXD
- |
-
- BXD38
- |
-
- 55
- |
-
- F
- |
-
- R2710E.CEL
- |
-
- 0.033
- |
-
- 0.031
- |
-
- 2.112
- |
-
- 122.1
- |
-
- 58.80%
- |
-
- 39.80%
- |
-
- 1.40%
- |
-
- 1.37
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 100
- |
-
- R2695E
- |
-
- BXD
- |
-
- BXD39
- |
-
- 59
- |
-
- M
- |
-
- R2695E.CEL
- |
-
- 0.018
- |
-
- 0.016
- |
-
- 1.638
- |
-
- 122.7
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 101
- |
-
- R2699E
- |
-
- BXD
- |
-
- BXD40
- |
-
- 59
- |
-
- F
- |
-
- R2699E.CEL
- |
-
- 0.014
- |
-
- 0.015
- |
-
- 1.827
- |
-
- 105.23
- |
-
- 61.70%
- |
-
- 36.90%
- |
-
- 1.40%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 102
- |
-
- R2696E
- |
-
- BXD
- |
-
- BXD42
- |
-
- 58
- |
-
- F
- |
-
- R2696E.CEL
- |
-
- 0.01
- |
-
- 0.017
- |
-
- 1.622
- |
-
- 118.95
- |
-
- 62.00%
- |
-
- 36.60%
- |
-
- 1.50%
- |
-
- 1.53
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 103
- |
-
- R943E-2
- |
-
- BXD
- |
-
- BXD64
- |
-
- 56
- |
-
- F
- |
-
- R943E-2.CEL
- |
-
- 0.024
- |
-
- 0.021
- |
-
- 1.591
- |
-
- 141.34
- |
-
- 60.10%
- |
-
- 38.40%
- |
-
- 1.50%
- |
-
- 1.32
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 104
- |
-
- R967E
- |
-
- BXD
- |
-
- BXD48
- |
-
- 64
- |
-
- F
- |
-
- R967E.CEL
- |
-
- 0.101
- |
-
- 0.052
- |
-
- 1.948
- |
-
- 130.95
- |
-
- 57.30%
- |
-
- 41.20%
- |
-
- 1.50%
- |
-
- 1.63
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 105
- |
-
- R2714E
- |
-
- BXD
- |
-
- BXD5
- |
-
- 58
- |
-
- M
- |
-
- R2714E.CEL
- |
-
- 0.047
- |
-
- 0.014
- |
-
- 1.404
- |
-
- 144.35
- |
-
- 60.60%
- |
-
- 37.90%
- |
-
- 1.50%
- |
-
- 1.43
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 106
- |
-
- R1042E
- |
-
- BXD
- |
-
- BXD51
- |
-
- 62
- |
-
- M
- |
-
- R1042E.CEL
- |
-
- 0.028
- |
-
- 0.027
- |
-
- 2.352
- |
-
- 104.12
- |
-
- 58.70%
- |
-
- 39.90%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 107
- |
-
- R2690E
- |
-
- BXD
- |
-
- BXD55
- |
-
- 65
- |
-
- M
- |
-
- R2690E.CEL
- |
-
- 0.081
- |
-
- 0.067
- |
-
- 1.887
- |
-
- 164.01
- |
-
- 56.10%
- |
-
- 42.30%
- |
-
- 1.60%
- |
-
- 1.43
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 108
- |
-
- R2694E
- |
-
- BXD
- |
-
- BXD6
- |
-
- 58
- |
-
- M
- |
-
- R2694E.CEL
- |
-
- 0.012
- |
-
- 0.018
- |
-
- 1.983
- |
-
- 97.23
- |
-
- 61.60%
- |
-
- 37.10%
- |
-
- 1.30%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 109
- |
-
- R975E
- |
-
- BXD
- |
-
- BXD70
- |
-
- 64
- |
-
- F
- |
-
- R975E.CEL
- |
-
- 0.028
- |
-
- 0.024
- |
-
- 1.841
- |
-
- 137.97
- |
-
- 58.00%
- |
-
- 40.50%
- |
-
- 1.40%
- |
-
- 1.36
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 110
- |
-
- R2684E
- |
-
- BXD
- |
-
- BXD61
- |
-
- 62
- |
-
- M
- |
-
- R2684E.CEL
- |
-
- 0.031
- |
-
- 0.032
- |
-
- 2.01
- |
-
- 131.03
- |
-
- 57.00%
- |
-
- 41.50%
- |
-
- 1.50%
- |
-
- 1.34
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 111
- |
-
- R994E
- |
-
- BXD
- |
-
- BXD43
- |
-
- 60
- |
-
- F
- |
-
- R994E.CEL
- |
-
- 0.013
- |
-
- 0.014
- |
-
- 1.966
- |
-
- 113.12
- |
-
- 60.80%
- |
-
- 37.80%
- |
-
- 1.40%
- |
-
- 1.66
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 112
- |
-
- R2610E
- |
-
- BXD
- |
-
- BXD44
- |
-
- 68
- |
-
- M
- |
-
- R2610E.CEL
- |
-
- 0.013
- |
-
- 0.009
- |
-
- 1.814
- |
-
- 142.91
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.35
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 113
- |
-
- R2689E
- |
-
- BXD
- |
-
- BXD65
- |
-
- 63
- |
-
- F
- |
-
- R2689E.CEL
- |
-
- 0.008
- |
-
- 0.008
- |
-
- 1.721
- |
-
- 142.44
- |
-
- 59.90%
- |
-
- 38.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 114
- |
-
- R2727E
- |
-
- BXD
- |
-
- BXD69
- |
-
- 65
- |
-
- M
- |
-
- R2727E.CEL
- |
-
- 0.01
- |
-
- 0.008
- |
-
- 1.578
- |
-
- 143.86
- |
-
- 60.30%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.34
- |
-
- 0.77
- |
-
- GU
- |
-
-
- |
- 115
- |
-
- R2726E
- |
-
- BXD
- |
-
- BXD68
- |
-
- 64
- |
-
- M
- |
-
- R2726E.CEL
- |
-
- 0.125
- |
-
- 0.025
- |
-
- 1.811
- |
-
- 153.09
- |
-
- 58.70%
- |
-
- 39.80%
- |
-
- 1.50%
- |
-
- 1.39
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 116
- |
-
- R2732E
- |
-
- BXD
- |
-
- BXD45
- |
-
- 63
- |
-
- F
- |
-
- R2732E.CEL
- |
-
- 0.039
- |
-
- 0.036
- |
-
- 2.154
- |
-
- 122.45
- |
-
- 56.50%
- |
-
- 42.10%
- |
-
- 1.40%
- |
-
- 1.8
- |
-
- 0.83
- |
-
- GU
- |
-
-
- |
- 117
- |
-
- R2709E
- |
-
- BXD
- |
-
- BXD8
- |
-
- 61
- |
-
- M
- |
-
- R2709E.CEL
- |
-
- 0.012
- |
-
- 0.011
- |
-
- 1.99
- |
-
- 99.79
- |
-
- 60.90%
- |
-
- 37.60%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.76
- |
-
- GU
- |
-
-
- |
- 118
- |
-
- R2686E
- |
-
- BXD
- |
-
- BXD80
- |
-
- 61
- |
-
- M
- |
-
- R2686E.CEL
- |
-
- 0.046
- |
-
- 0.05
- |
-
- 2.342
- |
-
- 119.63
- |
-
- 56.00%
- |
-
- 42.60%
- |
-
- 1.50%
- |
-
- 1.38
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 119
- |
-
- R2692E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 63
- |
-
- F
- |
-
- R2692E.CEL
- |
-
- 0.006
- |
-
- 0.007
- |
-
- 1.423
- |
-
- 160.87
- |
-
- 60.20%
- |
-
- 38.30%
- |
-
- 1.40%
- |
-
- 1.46
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 120
- |
-
- R2715E
- |
-
- BXD
- |
-
- BXD85
- |
-
- 91
- |
-
- M
- |
-
- R2715E.CEL
- |
-
- 0.007
- |
-
- 0.008
- |
-
- 1.488
- |
-
- 142.6
- |
-
- 61.20%
- |
-
- 37.30%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 121
- |
-
- R1405E
- |
-
- BXD
- |
-
- BXD86
- |
-
- 58
- |
-
- F
- |
-
- R1405E.CEL
- |
-
- 0.053
- |
-
- 0.052
- |
-
- 2.351
- |
-
- 119.34
- |
-
- 56.40%
- |
-
- 42.20%
- |
-
- 1.40%
- |
-
- 1.64
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 122
- |
-
- R2724E
- |
-
- BXD
- |
-
- BXD87
- |
-
- 63
- |
-
- F
- |
-
- R2724E.CEL
- |
-
- 0.013
- |
-
- 0.019
- |
-
- 1.906
- |
-
- 113.71
- |
-
- 60.70%
- |
-
- 37.90%
- |
-
- 1.40%
- |
-
- 1.45
- |
-
- 0.79
- |
-
- GU
- |
-
-
- |
- 123
- |
-
- R1451E
- |
-
- BXD
- |
-
- BXD34
- |
-
- 61
- |
-
- F
- |
-
- R1451E.CEL
- |
-
- 0.01
- |
-
- 0.009
- |
-
- 1.843
- |
-
- 140.05
- |
-
- 59.00%
- |
-
- 39.50%
- |
-
- 1.50%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 124
- |
-
- R1433E
- |
-
- BXD
- |
-
- BXD89
- |
-
- 63
- |
-
- F
- |
-
- R1433E.CEL
- |
-
- 0.029
- |
-
- 0.026
- |
-
- 2.241
- |
-
- 115.86
- |
-
- 57.70%
- |
-
- 40.80%
- |
-
- 1.50%
- |
-
- 1.41
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 125
- |
-
- R2733E
- |
-
- BXD
- |
-
- BXD96
- |
-
- 67
- |
-
- F
- |
-
- R2733E.CEL
- |
-
- 0.024
- |
-
- 0.054
- |
-
- 1.7
- |
-
- 113.99
- |
-
- 62.10%
- |
-
- 36.60%
- |
-
- 1.30%
- |
-
- 1.4
- |
-
- 0.78
- |
-
- GU
- |
-
-
- |
- 126
- |
-
- R2649E
- |
-
- BXD
- |
-
- BXD97
- |
-
- 74
- |
-
- F
- |
-
- R2649E.CEL
- |
-
- 0.029
- |
-
- 0.032
- |
-
- 2.343
- |
-
- 119.04
- |
-
- 57.50%
- |
-
- 41.20%
- |
-
- 1.40%
- |
-
- 1.53
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 127
- |
-
- R2688E
- |
-
- BXD
- |
-
- BXD98
- |
-
- 67
- |
-
- M
- |
-
- R2688E.CEL
- |
-
- 0.032
- |
-
- 0.03
- |
-
- 1.772
- |
-
- 145.24
- |
-
- 58.50%
- |
-
- 40.00%
- |
-
- 1.50%
- |
-
- 1.48
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 128
- |
-
- R877E
- |
-
- BXD
- |
-
- BXD13
- |
-
- 76
- |
-
- M
- |
-
- R877E.CEL
- |
-
- 0.026
- |
-
- 0.067
- |
-
- 1.558
- |
-
- 125.63
- |
-
- 61.20%
- |
-
- 37.50%
- |
-
- 1.20%
- |
-
- 1.42
- |
-
- 0.81
- |
-
- GU
- |
-
-
- |
- 129
- |
-
- R1397E-re
- |
-
- BXD
- |
-
- BXD75
- |
-
- 58
- |
-
- M
- |
-
- R1397E-re.CEL
- |
-
- 0.032
- |
-
- 0.01
- |
-
- 1.449
- |
-
- 189.71
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.39
- |
-
- 0.82
- |
-
- GU
- |
-
-
- |
- 130
- |
-
- R2779E
- |
-
- BXD
- |
-
- BXD73
- |
-
- 64
- |
-
- F
- |
-
- R2779E.CEL
- |
-
- 0.012
- |
-
- 0.038
- |
-
- 1.746
- |
-
- 121.11
- |
-
- 59.60%
- |
-
- 39.00%
- |
-
- 1.40%
- |
-
- 1.5
- |
-
- 0.8
- |
-
- GU
- |
-
-
- |
- 131
- |
-
- R2708E
- |
-
- BXD
- |
-
- BXD9
- |
-
- 60
- |
-
- F
- |
-
- R2708E.CEL
- |
-
- 0.024
- |
-
- 0.045
- |
-
- 1.966
- |
-
- 126.46
- |
-
- 57.70%
- |
-
- 40.70%
- |
-
- 1.50%
- |
-
- 1.4
- |
-
- 0.84
- |
-
- GU
- |
-
-
- |
- 132
- |
-
- R2547E1
- |
-
- GDP
- |
-
- WSB/Ei
- |
-
- 67
- |
-
- M
- |
-
- R2547E.CEL
- |
-
- 0.041
- |
-
- 0.039
- |
-
- 2.14
- |
-
- 90
- |
-
- 58.20%
- |
-
- 40.10%
- |
-
- 1.60%
- |
-
- 1.32
- |
-
- 0.77
- |
-
- UTM RW
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R/acknowledgment.rtf b/general/datasets/Eye_M2_0908_R/acknowledgment.rtf
deleted file mode 100644
index 5098d32..0000000
--- a/general/datasets/Eye_M2_0908_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant and from funds from NEI grant to Dr. Eldon Geisert (R01EY017841), an NEI Vision Core grant (EY14080) and an Unrestricted Grant from Research To Prevent Blindness.
-
-We thank Dr. Ted Choi, Chief Scientific Director of Predictive Biology, Inc. (past director of molecular genetics at Deltagen Inc.) for providing us with eye samples from several interesting DeltaGen knockouts.
diff --git a/general/datasets/Eye_M2_0908_R/cases.rtf b/general/datasets/Eye_M2_0908_R/cases.rtf
deleted file mode 100644
index 552d4a5..0000000
--- a/general/datasets/Eye_M2_0908_R/cases.rtf
+++ /dev/null
@@ -1,57 +0,0 @@
-This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:
-
-
- - 68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.
- - 35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common Mus musculus domesticus inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (Mus musculus domesticus, e.g, WSB/EiJ; M. musculus musculus, e.g., CZECHII/EiJ; M. musculus molossinus, e.g., MOLF/EiJ; M. musculus castaneus, e.g., CAST/EiJ); and even one different species of mouse (Mus spicilegus, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the Nyx-nob mutant:
- - 6 knockouts (KO), including a KO of Rpe65, and 5 DeltaGen Inc. knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: Gabra1, Gabbr1, Gnb1, Gpr19, and Clcn3. We also included one spontaneous mutant of the nyctalopin (Nyx no b wave "nob") gene (Pardue et al., 1998) that is on a BALB/cByJ background.
-
-
-Rod photoreceptor degeneration in inbred mice: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the retinal degeneration 1 (rd1) mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (Pde6b). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.
-
-As expected (Dickerson LW et al., 2002) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, Clcn3) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of Gnat2, a gene associated with cones and achromatopsia in mice and humans.
-
-Lines of mice were selected using the following criteria:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - representation of a fairly wide variety of different subspecies of Mus
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - interesting mutations or knockouts affecting genes with high expression in the eye
- - general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.
-
-
-We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see Perlegen's excellent data resources and browser).
-
-
- - 129S1/SvImJ : Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a cone photoreceptor function loss 3 mutant (Cpfl3 allele) of the Gnat2 gene that is a model for achromatopsia (JAX Stock Number: 002448)
- - A/J: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (Tyr c allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: 000646)
- - BALB/cByJ: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Small brain, not aggressive (JAX Stock Number: 001026)
- - BALB/cJ: Phenome Project A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Large brain and aggressive (JAX Stock Number: 000651)
- - BXSB/MpJ: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the Yaa gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: 000740)
- - C3H/HeJ: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a Pdeb6 rd1 mutant with near total photoreceptor loss at as early as postnatal day 30. Also a Tlr4 mutant that is endotoxin resistant. (JAX Stock Number: 000659)
- - C57BL/6J: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: 000664)
- - C57BLKS/J: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: 000662)
- - CAST/EiJ: A wild-derived inbred Mus musculus castaneus strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: 000928)
- - CBA/CaJ: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: 000654)
- - CZECHII/EiJ: Czech 2 is a wild-derived inbred strain M. musculus musculus strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: 001144).
- - DBA/2J: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. A myosin 5a (Myo5a d) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: 000671)
- - FVB/NJ: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. Tyr c locus albino and a Pdeb6 rd1 mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: 001800).
- - KK/HlJ: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: 002106)
- - LG/J: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A Tyr c locus albino strain. (JAX Stock Number: 000675)
- - LP/J: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B Ednrb gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: 000676)
- - MOLF/EiJ: A wild-derived inbred strain derived from M. musculus molossinus samples camputered in Fukuoka, Japan. This strain has the retinal degeneration rd1 allele in Pde6b. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: 000550)
- - NOD/LtJ: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. (JAX Stock Number: 001976)
- - NZO/HlLtJ: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: 002105)
- - NZB/BlNJ: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: 000648)
- - NZW/LacJ: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the Tyr c locus albino mutation, the pink-eye dilution mutation in the Oca2 or p locus, and the brown allele at Tyrp1. (JAX Stock Number: 001058)
- - PANCEVO/EiJ: PANCEVO/EiJ is a wild-derived inbred strain from the Mus spicilegus samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier 10103). M. spicilegus is a colonial mound-building species. No known ocular or retina mutations, but the expression level of Gnat2 is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: 001384)
- - PWD/PhJ: A wild-derived Mus musculus musculus agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: 004660)
- - PWK/PhJ: A wild-derived Mus musculus musculus inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: 003715)
- - SJL/J: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration rd1 allele in Pde6b. It also carries both the Tyr c albino mutation and the pink-eye dilution mutation in the Oca2 or p locus. Highly aggressive males. (JAX Stock Number: 000686)
- - WSB/EiJ: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived Mus musculus domesticus inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: 001145)
- - B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J 100006)
-
-
-Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, 2008 and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (Tyr, or human OCA1), the brown allele of the tyrosinase related protein 1 (Tyrp1), the pink-eye dilution allele of Oca2 (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein Asip, the steel allele of Kitlg, the dilute allele of Myo5a (probe set 1419754), and the piebald allele of Ednrb. In some of these cases, effects of the mutation are easily detected at the transcript level (Tyrp1, Oca2, and Myo5a), but in the other cases (Tyr, Asip, Ednrb, and Kitlg), mutations do not leave a strong imprint on expression.
diff --git a/general/datasets/Eye_M2_0908_R/experiment-design.rtf b/general/datasets/Eye_M2_0908_R/experiment-design.rtf
deleted file mode 100644
index 1ebe0ad..0000000
--- a/general/datasets/Eye_M2_0908_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression profiling by array
diff --git a/general/datasets/Eye_M2_0908_R/notes.rtf b/general/datasets/Eye_M2_0908_R/notes.rtf
deleted file mode 100644
index 7a26eb5..0000000
--- a/general/datasets/Eye_M2_0908_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Eye_M2_0908_R/platform.rtf b/general/datasets/Eye_M2_0908_R/platform.rtf
deleted file mode 100644
index 9024a99..0000000
--- a/general/datasets/Eye_M2_0908_R/platform.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many probes overlap and target the same transcript). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
-As part of the development of HEIMED, we have manually annotated individual probe sets by sequence alignment to the mouse genome and transcriptome. Approximately 13,000 probe sets that have comparatively high expression in eye and CNS were curated by one of the authors (RWW) and now have specific information on the part of the transcript targeted by each probe set. The other 33,000 transcripts have corresponding data that was generated by Xusheng Wang using computational methods (BLAT analysis combined with annotated genome sequence).
-
-One example may help explain how to exploit this annotation. The four probe sets for rhodopsin include information on the target location. Only the first probe set targets the last two coding exons. The other three probe sets target different parts of the 3’ UTR (mid, distal, and far distal regions). The probe sets can be reordered by from high to low expression using the Sort By function in Search Results pages. In the case of rhodopsin, the probe set that targets that last two coding exons and proximal parts of the 3’ UTR also has the highest expression . Finally, the HEIMED gene descriptions have been customized to help vision researchers. In the case of rhodopsin, the description appended after the gene name reads “rod photoreceptor pigment, retinitis pigmentosa-associated”. For less well known genes this kind of annotation can be extremely useful. For example, the more verbose annotation for Cerkl reads “neuronal survival and apoptosis-related, retinal ganglion cell expressed, retinitis pigmentosa 26); alternative 3' UTR of short form message, intron 2”.
-
-
-
-
-
-Legend: Distribution of expression values for all probe sets in HEIMED.
diff --git a/general/datasets/Eye_M2_0908_R/processing.rtf b/general/datasets/Eye_M2_0908_R/processing.rtf
deleted file mode 100644
index 4349e60..0000000
--- a/general/datasets/Eye_M2_0908_R/processing.rtf
+++ /dev/null
@@ -1,3381 +0,0 @@
-Range of Gene Expression in the Eye. Expression of transcripts in the HEIMED and most other GN data sets is measured on a log2 scale. Each unit corresponding approximately to a 2-fold difference in hybridization signal intensity. To simplify comparisons among different data sets and cases, log2 RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units (variance stabilized). Values of all 45,101 probe sets in this data set range from a low of 4.8 (Tcf15, probe set 1420281_at) to a high of 15.5 (crystallin gamma C, Crygc, probe set 1422674_s_at). This corresponds to 10.7 units or a 1 to 1700 dynamic range of expression (2^10.73).
-
-We used pooled RNA samples of whole eyes, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-We calibrated this log intensity scale using Affymetrix spike-in control probe sets. These 18 control probe sets target exogenous bacterial mRNAs that are added to each sample (a graded dose spike cocktail) during preparation at concentrations of 1.5, 5, 25, and 100 pM. (To find these probe sets, search GN’s ALL search field using the string “AFFX pM”.) A value of 6 or less is equivalent to an mRNA concentration of under 0.4 pM, a value of 8 is equivalent to ~1.5 pM, 9.5 is equivalent to ~5 pM, 11.5 is equivalent to ~25 pM, 13.5 is equivalent to ~100 pM, and a value of 15.5 is equivalent to an mRNA concentration of 400 pM or greater.
-
-This range can be converted to the mRNA molecules per cell in the eye assuming that a value of 8 is equivalent to about 1 mRNA copy per cell (Kanno et al. 2006, see http://www.biomedcentral.com/1471-2164/7/64). Since the expression of rhodopsin mRNA is normally 15 units, we predict that there are 27 or ~128 Rho mRNAs per cell in the whole eye and ~256 in rods themselves (assuming that rods make up about half of all cells in the eye). For this purpose it may be useful to know that a normal mouse eye contains between 6 and 8 million rod photoreceptors (Guo, Lu, and Williams; GN BXD Phenotype ID 11024).
-
-Note that some probe sets with very low expression still provide reliable data. For example, probe set 1440397_at (Cacna2d1) has expression of only 5.5 units (a value that would be declared as "absent" using conventional Affymetrix procedures), but the values for this calcium channel transcript are associated with a very strong cis QTL with an LRS of 79 (LOD = 17). This strong linkage is definitely not due to chance since the probability of the expression data mapping precisely to the location of the parent gene itself is about 10e-16. This indicates a high signal to noise ratio and the detection of significant strain variation of the correct transcript.
-
-The standard error of the mean for the HEIMED data set is computed for 2 to 6 biological replicates. The standard error of such small samples tends to systematically underestimate the population standard error. With n = 2 the underestimate is about 25%, whereas for n = 6 the underestimate is 5%. Gurland and Tripathi (1971) provide a correction and equation for this effect (see Sokal and Rohlf, Biometry, 2nd ed., 1981, p 53 for an equation of the correction factor for small samples of n < 20.) Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the first three batches together. The last batch was processed separately and merged as described below.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing using Biobase affy10 build running under R version 2.7.1, all array data sets were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (FVB/NJ, NOD/LtJ, MOLF/EiJ, C3H/HeJ and BXD24), samples from wild subspecies such as WSB/EiJ, CAST/EiJ, PWD/PhJ, and PWK/PhJ, and knockouts. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. The assumption is that anomolous data are much more likely due to experimental and technical errors than to informative biological variation. Approximately 10% of arrays were discarded.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We reviewed the data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g., 1800) represented the QTL harvest for the full data set. We then dropped a single array from the data set, recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 1750 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs. Values ranged from approximately -90 (good arrays) to +40 (bad arrays). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a method to polish a data set.
-
-During this process we discovered that nearly 20 arrays in the batch 2 had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of high quality.
-
-A third batch of approximately 40 arrays were processed by Yan Jiao and Weikuan Gu in August 2006. These complete data set assembled by Hongqiang Li. This process again included a correction for a batch effect.
-
-For the June 2006 data set Hongqiang Li used a new batch correction method that stabilizes the range of expression in each batch. For each of the three large batches, we extracted the minumum and maximum raw probe expression (CEL file level) value. We then adjusted raw probe values in each batch to have the same range as the first and largest batch (batch 1) using a simple linear interpolation. These procedures generated new correct CEL files which were then used with RMA to generate final probe set estimates.
-
-For the final fourth batch of arrays (Sept 2008) Arthur Centeno and Rob Williams corrected for a systematic difference in probe set expression values between original arrays run in 2005 and 2006 and the new arrays added in 2008 (n = 45 acceptable arrays). This difference is due to unknown technical batch effects that are probably associated with labeling, hybridization, and scanning. We performed a simple correction to normalize values of the new set of arrays to those of the old set (batches 1 through 3). No changes were made to any values of the previous three batches. We corrected only the probe set level (RMA) values and not the CEL files. For this final batch, we corrected for the difference (offset) in probe set expression between the first three batches arrays run in 2005 and 2006 (a total of 174 acceptable arrays) and the new batch (n = 47 acceptable arrays). This difference is due to unknown technical effects that are probably related to various steps in labeling, hybridization, and scanning. The correction was applied as follows: (1) RWW selected 51 high quality arrays with similar expression characteristics (r = 0.97 or better between pairs of arrays) in the old data set (from batches 1, 2, and 3) and 34 high quality arrays in the final batch. RWW used scatterplots of full RMA transcriptome data sets to review many pairs of arrays within these new and old array batches. Strains with retinal degeneration or unusual eye gene expression characteristics were excluded from these selected subsets. The average expression values for each probe set were then computed for both the old and new array subsets. The offset value (old minus new) was added to each probe set across all 47 new arrays. This processes forces the average probe set in the new arrays to be very close to that of the previous arrays.
-
-Table 2: Sample tube ID, strain, original CEL filename, and Affymetrix quality control values. Columns labeled Scale factor, Background Average, Present, Absent, Marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Strain |
- Original CEL |
- Scale factor |
- Background Average |
- Present |
- Absent |
- Marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- Batch Id |
- Used for batch control |
-
-
- | 1 |
- R2595E.1 |
- 129S1/SvImJ |
- R2595E.1.CEL |
- 1.79 |
- 115 |
- 61.00% |
- 37.50% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 2 |
- R2533E.1 |
- 129S1/SvImJ |
- R2533E.1.CEL |
- 2.11 |
- 94 |
- 57.90% |
- 40.50% |
- 1.60% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 3 |
- R0754E.1 |
- A/J |
- R0754E.1.CEL |
- 2.72 |
- 86 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.36 |
- 0.76 |
- 1 |
- Y |
-
-
- | 4 |
- R4521E |
- B6129P2F2N1-Clcn3 |
- R4521E.CEL |
- 4.83 |
- 38.7 |
- 63.30% |
- 35.30% |
- 1.40% |
- 1.25 |
- 0.77 |
- 4 |
- |
-
-
- | 5 |
- R4522E |
- B6129P2F2N1-Clcn3 |
- R4522E.CEL |
- 5.76 |
- 37.36 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.37 |
- 0.83 |
- 4 |
- |
-
-
- | 6 |
- R4523E |
- B6129P2F2N1-Clcn3 |
- R4523E.CEL |
- 4.88 |
- 40.42 |
- 63.90% |
- 34.70% |
- 1.40% |
- 1.27 |
- 0.77 |
- 4 |
- |
-
-
- | 7 |
- R4526E |
- B6129P2F2N1-Gabbr1 |
- R4526E.CEL |
- 3.84 |
- 44.18 |
- 65.00% |
- 33.70% |
- 1.30% |
- 1.34 |
- 0.78 |
- 4 |
- Y |
-
-
- | 8 |
- R4509E |
- B6129P2F2N1-Gabbr1 |
- R4509E.CEL |
- 7.45 |
- 34.76 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.45 |
- 0.83 |
- 4 |
- |
-
-
- | 9 |
- R4510E |
- B6129P2F2N1-Gabbr1 |
- R4510E.CEL |
- 8.44 |
- 37.44 |
- 57.40% |
- 41.10% |
- 1.50% |
- 1.35 |
- 0.83 |
- 4 |
- |
-
-
- | 10 |
- R4511E |
- B6129P2F2N1-Gabbr1 |
- R4511E.CEL |
- 5.91 |
- 42.02 |
- 61.40% |
- 37.20% |
- 1.40% |
- 1.41 |
- 0.83 |
- 4 |
- |
-
-
- | 11 |
- R4524E |
- B6129P2F2N1-Gabbr1 |
- R4524E.CEL |
- 5.49 |
- 42.34 |
- 62.40% |
- 36.20% |
- 1.40% |
- 1.29 |
- 0.78 |
- 4 |
- Y |
-
-
- | 12 |
- R4525E |
- B6129P2F2N1-Gabbr1 |
- R4525E.CEL |
- 4.69 |
- 41.3 |
- 63.10% |
- 35.50% |
- 1.40% |
- 1.27 |
- 0.8 |
- 4 |
- Y |
-
-
- | 13 |
- R4515E |
- B6129P2F2N1-Gabra1 |
- R4515E.CEL |
- 5.75 |
- 41.76 |
- 62.80% |
- 35.80% |
- 1.40% |
- 1.41 |
- 0.81 |
- 4 |
- Y |
-
-
- | 14 |
- R4516E |
- B6129P2F2N1-Gabra1 |
- R4516E.CEL |
- 7.07 |
- 40.73 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.32 |
- 0.87 |
- 4 |
- Y |
-
-
- | 15 |
- R4517E |
- B6129P2F2N1-Gabra1 |
- R4517E.CEL |
- 5.45 |
- 38.09 |
- 62.70% |
- 35.80% |
- 1.40% |
- 1.34 |
- 0.82 |
- 4 |
- Y |
-
-
- | 16 |
- R4512E |
- B6129P2F2N1-Gnb5 |
- R4512E.CEL |
- 6.56 |
- 38.02 |
- 59.90% |
- 38.70% |
- 1.50% |
- 1.33 |
- 0.83 |
- 4 |
- |
-
-
- | 17 |
- R4513E |
- B6129P2F2N1-Gnb5 |
- R4513E.CEL |
- 4.15 |
- 41.6 |
- 63.40% |
- 35.10% |
- 1.50% |
- 1.34 |
- 0.82 |
- 4 |
- |
-
-
- | 18 |
- R4514E |
- B6129P2F2N1-Gnb5 |
- R4514E.CEL |
- 5.86 |
- 39.2 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.34 |
- 0.81 |
- 4 |
- |
-
-
- | 19 |
- R4518E |
- B6129P2F2N1-Gpr19 |
- R4518E.CEL |
- 5.58 |
- 38.9 |
- 62.60% |
- 36.00% |
- 1.30% |
- 1.39 |
- 0.79 |
- 4 |
- Y |
-
-
- | 20 |
- R4519E |
- B6129P2F2N1-Gpr19 |
- R4519E.CEL |
- 5.95 |
- 41.91 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.35 |
- 0.84 |
- 4 |
- Y |
-
-
- | 21 |
- R2601E.1 |
- B6D2F1 |
- R2601E.1.CEL |
- 2.55 |
- 92 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.44 |
- 0.78 |
- 1 |
- Y |
-
-
- | 22 |
- R2602E.1 |
- B6D2F1 |
- R2602E.1.CEL |
- 2.6 |
- 84 |
- 59.70% |
- 38.80% |
- 1.50% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 23 |
- R1676E.1 |
- BALB/cByJ |
- R1676E.1.CEL |
- 2.69 |
- 98 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.46 |
- 0.74 |
- 1 |
- |
-
-
- | 24 |
- R1672E.1 |
- BALB/cByJ |
- R1672E.1.CEL |
- 2.22 |
- 111 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 25 |
- R4530E |
- BALB/cJ |
- R4530E.CEL |
- 6.37 |
- 37.53 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.3 |
- 0.84 |
- 4 |
- Y |
-
-
- | 26 |
- R4529E |
- BALB/cJ |
- R4529E.CEL |
- 5.71 |
- 41.33 |
- 60.50% |
- 38.00% |
- 1.50% |
- 1.48 |
- 0.8 |
- 4 |
- Y |
-
-
- | 27 |
- R2704E.2 |
- BXD1 |
- R2704E.2.CEL |
- 2.066 |
- 139.61 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 28 |
- R2707E.3 |
- BXD1 |
- R2707E.3.CEL |
- 1 |
- 80 |
- 56.40% |
- 42.10% |
- 1.50% |
- 1.43 |
- 0.79 |
- 3 |
- |
-
-
- | 29 |
- R1231E.2 |
- BXD2 |
- R1231E.2.CEL |
- 2.197 |
- 138.73 |
- 57.30% |
- 41.30% |
- 1.40% |
- 1.41 |
- 0.77 |
- 2 |
- |
-
-
- | 30 |
- R2598E.1 |
- BXD2 |
- R2598E.1.CEL |
- 1.99 |
- 106 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 31 |
- R2591E.1 |
- BXD5 |
- R2591E.1.CEL |
- 1.7 |
- 136 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.33 |
- 0.78 |
- 1 |
- Y |
-
-
- | 32 |
- R2714E.2 |
- BXD5 |
- R2714E.2.CEL |
- 1.404 |
- 144.35 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 33 |
- R2570E.1 |
- BXD6 |
- R2570E.1.CEL |
- 1.99 |
- 87 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.46 |
- 0.76 |
- 1 |
- Y |
-
-
- | 34 |
- R2694E.2 |
- BXD6 |
- R2694E.2.CEL |
- 1.983 |
- 97.23 |
- 61.60% |
- 37.10% |
- 1.30% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 35 |
- R2538E.1 |
- BXD8 |
- R2538E.1.CEL |
- 1.91 |
- 102 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.52 |
- 0.79 |
- 1 |
- Y |
-
-
- | 36 |
- R2709E.2 |
- BXD8 |
- R2709E.2.CEL |
- 1.99 |
- 99.79 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.42 |
- 0.76 |
- 2 |
- |
-
-
- | 37 |
- R2708E.2 |
- BXD9 |
- R2708E.2.CEL |
- 1.966 |
- 126.46 |
- 57.70% |
- 40.70% |
- 1.50% |
- 1.4 |
- 0.84 |
- 2 |
- |
-
-
- | 38 |
- R2569E.1 |
- BXD9 |
- R2569E.1.CEL |
- 1.75 |
- 87 |
- 55.10% |
- 43.40% |
- 1.50% |
- 2.82 |
- 3.14 |
- 1 |
- |
-
-
- | 39 |
- R2581E.1 |
- BXD11 |
- R2581E.1.CEL |
- 1.94 |
- 89 |
- 62.10% |
- 36.40% |
- 1.60% |
- 1.55 |
- 0.81 |
- 1 |
- Y |
-
-
- | 40 |
- R2612E.2 |
- BXD11 |
- R2612E.2.CEL |
- 1.83 |
- 142.03 |
- 58.20% |
- 40.50% |
- 1.40% |
- 1.78 |
- 0.81 |
- 2 |
- |
-
-
- | 41 |
- R2742E.2 |
- BXD12 |
- R2742E.2.CEL |
- 2.127 |
- 134.14 |
- 57.00% |
- 41.60% |
- 1.40% |
- 1.64 |
- 0.78 |
- 2 |
- |
-
-
- | 42 |
- R2543E.1 |
- BXD12 |
- R2543E.1.CEL |
- 1.61 |
- 118 |
- 58.60% |
- 39.90% |
- 1.60% |
- 1.43 |
- 0.77 |
- 1 |
- Y |
-
-
- | 43 |
- R2586E.1 |
- BXD13 |
- R2586E.1.CEL |
- 2.01 |
- 74 |
- 56.40% |
- 42.00% |
- 1.60% |
- 2.85 |
- 3.81 |
- 1 |
- |
-
-
- | 44 |
- R877E.2 |
- BXD13 |
- R877E.2.CEL |
- 1.558 |
- 125.63 |
- 61.20% |
- 37.50% |
- 1.20% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 45 |
- R2557E.1 |
- BXD14 |
- R2557E.1.CEL |
- 1.83 |
- 99 |
- 62.50% |
- 36.10% |
- 1.40% |
- 1.31 |
- 0.78 |
- 1 |
- Y |
-
-
- | 46 |
- R1128E.2 |
- BXD14 |
- R1128E.2.CEL |
- 1.91 |
- 115 |
- 59.90% |
- 38.80% |
- 1.40% |
- 1.2 |
- 0.82 |
- 1 |
- Y |
-
-
- | 47 |
- R2701E.3 |
- BXD15 |
- R2701E.3.CEL |
- 1 |
- 88 |
- 60.60% |
- 37.90% |
- 1.40% |
- 1.5 |
- 0.77 |
- 3 |
- |
-
-
- | 48 |
- R2716E.2 |
- BXD15 |
- R2716E.2.CEL |
- 2.015 |
- 150.83 |
- 56.40% |
- 42.10% |
- 1.60% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 49 |
- R2711E.2 |
- BXD16 |
- R2711E.2.CEL |
- 1.953 |
- 118.53 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 50 |
- R2567E.1 |
- BXD16 |
- R2567E.1.CEL |
- 2.24 |
- 82 |
- 56.70% |
- 41.60% |
- 1.70% |
- 1.37 |
- 0.75 |
- 1 |
- |
-
-
- | 51 |
- R2720E.2 |
- BXD18 |
- R2720E.2.CEL |
- 2.32 |
- 99.93 |
- 59.50% |
- 39.00% |
- 1.50% |
- 1.33 |
- 0.77 |
- 2 |
- |
-
-
- | 52 |
- R2559E.1 |
- BXD18 |
- R2559E.1.CEL |
- 1.65 |
- 104 |
- 60.80% |
- 37.70% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 53 |
- R2560E.1 |
- BXD19 |
- R2560E.1.CEL |
- 1.79 |
- 98 |
- 60.90% |
- 37.50% |
- 1.60% |
- 1.35 |
- 0.8 |
- 1 |
- Y |
-
-
- | 54 |
- R2713E.2 |
- BXD19 |
- R2713E.2.CEL |
- 1.67 |
- 120.82 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 55 |
- R2584E.1 |
- BXD20 |
- R2584E.1.CEL |
- 2.07 |
- 84 |
- 59.30% |
- 39.10% |
- 1.60% |
- 1.4 |
- 0.76 |
- 1 |
- Y |
-
-
- | 56 |
- R2731E.2 |
- BXD20 |
- R2731E.2.CEL |
- 1.825 |
- 147 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.4 |
- 0.8 |
- 2 |
- |
-
-
- | 57 |
- R2702E.2 |
- BXD21 |
- R2702E.2.CEL |
- 1.811 |
- 128.65 |
- 59.40% |
- 39.10% |
- 1.40% |
- 1.26 |
- 0.8 |
- 2 |
- |
-
-
- | 58 |
- R2541E2.1 |
- BXD21 |
- R2541E2.1.CEL |
- 2.63 |
- 125 |
- 56.00% |
- 42.40% |
- 1.50% |
- 1.29 |
- 0.78 |
- 1 |
- |
-
-
- | 59 |
- R2553E.1 |
- BXD22 |
- R2553E.1.CEL |
- 1.95 |
- 111 |
- 59.90% |
- 38.50% |
- 1.50% |
- 1.28 |
- 0.76 |
- 1 |
- Y |
-
-
- | 60 |
- R2700E.2 |
- BXD22 |
- R2700E.2.CEL |
- 1.858 |
- 102.96 |
- 61.50% |
- 37.10% |
- 1.30% |
- 1.48 |
- 0.79 |
- 2 |
- |
-
-
- | 61 |
- R2558E-2.1 |
- BXD23 |
- R2558E-2.1.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 62 |
- R1086E.2 |
- BXD23 |
- R1086E.2.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 63 |
- R2719E.2 |
- BXD24 |
- R2719E.2.CEL |
- 1.47 |
- 140.38 |
- 61.50% |
- 37.20% |
- 1.30% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 64 |
- R2589E2.1 |
- BXD24 |
- R2589E2.1.CEL |
- 2.61 |
- 112 |
- 57.50% |
- 40.90% |
- 1.60% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 65 |
- R2573E-2.1 |
- BXD25 |
- R2573E-2.1.CEL |
- 3.15 |
- 72 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.77 |
- 0.97 |
- 1 |
- |
-
-
- | 66 |
- R2683E.2 |
- BXD25 |
- R2683E.2.CEL |
- 1.777 |
- 115.64 |
- 58.30% |
- 40.30% |
- 1.40% |
- 2.01 |
- 0.79 |
- 2 |
- |
-
-
- | 67 |
- R2703E.2 |
- BXD27 |
- R2703E.2.CEL |
- 1.263 |
- 134.78 |
- 62.60% |
- 36.10% |
- 1.40% |
- 1.44 |
- 0.78 |
- 2 |
- |
-
-
- | 68 |
- R2729E.3 |
- BXD27 |
- R2729E.3.CEL |
- 1 |
- 87 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.56 |
- 0.84 |
- 3 |
- Y |
-
-
- | 69 |
- R2562E.3 |
- BXD28 |
- R2562E.3.CEL |
- 1.65 |
- 116 |
- 59.90% |
- 38.40% |
- 1.70% |
- 1.37 |
- 0.79 |
- 3 |
- Y |
-
-
- | 70 |
- R2721E.2 |
- BXD28 |
- R2721E.2.CEL |
- 2.065 |
- 157.39 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 71 |
- R2561E.3 |
- BXD29 |
- R2561E.3.CEL |
- 1 |
- 77 |
- 53.30% |
- 45.40% |
- 1.40% |
- 3.36 |
- 19.66 |
- 3 |
- |
-
-
- | 72 |
- R1258E.2 |
- BXD31 |
- R1258E.2.CEL |
- 2.063 |
- 117.09 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.54 |
- 0.78 |
- 2 |
- |
-
-
- | 73 |
- R2597E.1 |
- BXD31 |
- R2597E.1.CEL |
- 2.37 |
- 94 |
- 60.30% |
- 38.30% |
- 1.50% |
- 1.34 |
- 0.77 |
- 1 |
- Y |
-
-
- | 74 |
- R2563E.1 |
- BXD32 |
- R2563E.1.CEL |
- 1.55 |
- 102 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.5 |
- 0.8 |
- 1 |
- |
-
-
- | 75 |
- R1216E.2 |
- BXD32 |
- R1216E.2.CEL |
- 2.23 |
- 111.99 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.35 |
- 0.79 |
- 2 |
- |
-
-
- | 76 |
- R2542E.1 |
- BXD33 |
- R2542E.1.CEL |
- 2.13 |
- 97 |
- 56.50% |
- 41.80% |
- 1.60% |
- 1.91 |
- 0.93 |
- 1 |
- |
-
-
- | 77 |
- R857E.2 |
- BXD33 |
- R857E.2.CEL |
- 1.737 |
- 113.98 |
- 61.90% |
- 36.70% |
- 1.30% |
- 1.6 |
- 0.77 |
- 2 |
- |
-
-
- | 78 |
- R1451E.2 |
- BXD34 |
- R1451E.2.CEL |
- 1.843 |
- 140.05 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.42 |
- 0.81 |
- 2 |
- Y |
-
-
- | 79 |
- R2585E.1 |
- BXD34 |
- R2585E.1.CEL |
- 2.64 |
- 75 |
- 58.30% |
- 40.00% |
- 1.70% |
- 1.25 |
- 0.77 |
- 1 |
- |
-
-
- | 80 |
- R2698E.3 |
- BXD36 |
- R2698E.3.CEL |
- 1 |
- 86 |
- 59.70% |
- 39.00% |
- 1.30% |
- 1.46 |
- 0.78 |
- 3 |
- |
-
-
- | 81 |
- R2705E.3 |
- BXD36 |
- R2705E.3.CEL |
- 1 |
- 86 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.46 |
- 0.77 |
- 3 |
- |
-
-
- | 82 |
- R2710E.2 |
- BXD38 |
- R2710E.2.CEL |
- 2.112 |
- 122.1 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.37 |
- 0.78 |
- 2 |
- |
-
-
- | 83 |
- R2532E.1 |
- BXD38 |
- R2532E.1.CEL |
- 2.04 |
- 94 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.37 |
- 0.8 |
- 1 |
- Y |
-
-
- | 84 |
- R2574E.1 |
- BXD39 |
- R2574E.1.CEL |
- 1.98 |
- 91 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.39 |
- 0.78 |
- 1 |
- |
-
-
- | 85 |
- R2695E.2 |
- BXD39 |
- R2695E.2.CEL |
- 1.638 |
- 122.7 |
- 60.80% |
- 37.80% |
- 1.50% |
- 1.42 |
- 0.8 |
- 2 |
- |
-
-
- | 86 |
- R2699E.2 |
- BXD40 |
- R2699E.2.CEL |
- 1.827 |
- 105.23 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 87 |
- R2590E.1 |
- BXD40 |
- R2590E.1.CEL |
- 2.71 |
- 77 |
- 59.10% |
- 39.30% |
- 1.50% |
- 1.4 |
- 0.77 |
- 1 |
- Y |
-
-
- | 88 |
- R2696E.2 |
- BXD42 |
- R2696E.2.CEL |
- 1.622 |
- 118.95 |
- 62.00% |
- 36.60% |
- 1.50% |
- 1.53 |
- 0.79 |
- 2 |
- |
-
-
- | 89 |
- R2596E.1 |
- BXD42 |
- R2596E.1.CEL |
- 2.63 |
- 108 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 90 |
- R994E.2 |
- BXD43 |
- R994E.2.CEL |
- 1.966 |
- 113.12 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.66 |
- 0.8 |
- 2 |
- |
-
-
- | 91 |
- R2607E.1 |
- BXD43 |
- R2607E.1.CEL |
- 2.43 |
- 115 |
- 58.60% |
- 40.00% |
- 1.40% |
- 1.31 |
- 0.76 |
- 1 |
- Y |
-
-
- | 92 |
- R2594E.1 |
- BXD44 |
- R2594E.1.CEL |
- 1.77 |
- 117 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.35 |
- 0.85 |
- 1 |
- |
-
-
- | 93 |
- R2610E.2 |
- BXD44 |
- R2610E.2.CEL |
- 1.814 |
- 142.91 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.35 |
- 0.8 |
- 2 |
- |
-
-
- | 94 |
- R2732E.2 |
- BXD45 |
- R2732E.2.CEL |
- 2.154 |
- 122.45 |
- 56.50% |
- 42.10% |
- 1.40% |
- 1.8 |
- 0.83 |
- 2 |
- |
-
-
- | 95 |
- R2592E.1 |
- BXD45 |
- R2592E.1.CEL |
- 1.85 |
- 106 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.43 |
- 0.85 |
- 1 |
- Y |
-
-
- | 96 |
- R967E.2 |
- BXD48 |
- R967E.2.CEL |
- 1.948 |
- 130.95 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.63 |
- 0.81 |
- 2 |
- |
-
-
- | 97 |
- R2606E.1 |
- BXD48 |
- R2606E.1.CEL |
- 2.56 |
- 106 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.35 |
- 0.83 |
- 1 |
- Y |
-
-
- | 98 |
- R2933E.3 |
- BXD50 |
- R2933E.3.CEL |
- 1 |
- 72 |
- 52.90% |
- 45.60% |
- 1.50% |
- 2.45 |
- 0.98 |
- 3 |
- |
-
-
- | 99 |
- R2937E.3 |
- BXD50 |
- R2937E.3.CEL |
- 1 |
- 89 |
- 56.90% |
- 41.60% |
- 1.40% |
- 1.81 |
- 0.82 |
- 3 |
- |
-
-
- | 100 |
- R2603E.1 |
- BXD51 |
- R2603E.1.CEL |
- 2.49 |
- 115 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.24 |
- 0.79 |
- 1 |
- |
-
-
- | 101 |
- R1042E.2 |
- BXD51 |
- R1042E.2.CEL |
- 2.352 |
- 104.12 |
- 58.70% |
- 39.90% |
- 1.40% |
- 1.53 |
- 0.82 |
- 2 |
- |
-
-
- | 102 |
- R2980E.3 |
- BXD55 |
- R2980E.3.CEL |
- 1 |
- 82 |
- 56.90% |
- 41.70% |
- 1.50% |
- 1.77 |
- 0.84 |
- 3 |
- |
-
-
- | 103 |
- R2690E.2 |
- BXD55 |
- R2690E.2.CEL |
- 1.887 |
- 164.01 |
- 56.10% |
- 42.30% |
- 1.60% |
- 1.43 |
- 0.8 |
- 2 |
- |
-
-
- | 104 |
- R4176E |
- BXD56 |
- R4176E.CEL |
- 4.75 |
- 43.08 |
- 63.00% |
- 35.60% |
- 1.30% |
- 1.39 |
- 0.81 |
- 4 |
- Y |
-
-
- | 105 |
- R4175E |
- BXD56 |
- R4175E.CEL |
- 6 |
- 38.49 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.47 |
- 0.81 |
- 4 |
- Y |
-
-
- | 106 |
- R1006E.3 |
- BXD60 |
- R1006E.3.CEL |
- 1 |
- 98 |
- 54.90% |
- 43.70% |
- 1.50% |
- 2.7 |
- 0.86 |
- 3 |
- |
-
-
- | 107 |
- R2725E.2 |
- BXD60 |
- R2725E.2.CEL |
- 1.551 |
- 148.01 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 108 |
- R1074E.3 |
- BXD60 |
- R1074E.3.CEL |
- 1 |
- 118 |
- 55.50% |
- 43.10% |
- 1.40% |
- 1.96 |
- 0.81 |
- 3 |
- |
-
-
- | 109 |
- R2534E2.1 |
- BXD61 |
- R2534E2.1.CEL |
- 2.47 |
- 118 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.42 |
- 0.79 |
- 1 |
- |
-
-
- | 110 |
- R2684E.2 |
- BXD61 |
- R2684E.2.CEL |
- 2.01 |
- 131.03 |
- 57.00% |
- 41.50% |
- 1.50% |
- 1.34 |
- 0.78 |
- 2 |
- |
-
-
- | 111 |
- R1107E.3 |
- BXD62 |
- R1107E.3.CEL |
- 1 |
- 83 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.43 |
- 0.93 |
- 3 |
- |
-
-
- | 112 |
- R2681E.2 |
- BXD62 |
- R2681E.2.CEL |
- 2.086 |
- 148.24 |
- 57.20% |
- 41.30% |
- 1.50% |
- 1.29 |
- 0.81 |
- 2 |
- |
-
-
- | 113 |
- R965E.3 |
- BXD62 |
- R965E.3.CEL |
- 1 |
- 93.55 |
- 53.30% |
- 45.20% |
- 1.50% |
- 3.11 |
- 0.94 |
- 3 |
- |
-
-
- | 114 |
- R1425E.2 |
- BXD63 |
- R1425E.2.CEL |
- 1.7 |
- 136 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.43 |
- 0.82 |
- 2 |
- |
-
-
- | 115 |
- R2576E.3 |
- BXD63 |
- R2576E.3.CEL |
- 1 |
- 84 |
- 61.30% |
- 37.40% |
- 1.40% |
- 1.48 |
- 0.76 |
- 3 |
- |
-
-
- | 116 |
- R943E-2.2 |
- BXD64 |
- R943E-2.2.CEL |
- 1.591 |
- 141.34 |
- 60.10% |
- 38.40% |
- 1.50% |
- 1.32 |
- 0.76 |
- 2 |
- |
-
-
- | 117 |
- R2611E.1 |
- BXD64 |
- R2611E.1.CEL |
- 2.29 |
- 92 |
- 58.00% |
- 40.50% |
- 1.50% |
- 1.57 |
- 1.06 |
- 1 |
- |
-
-
- | 118 |
- R2689E.2 |
- BXD65 |
- R2689E.2.CEL |
- 1.721 |
- 142.44 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.38 |
- 0.76 |
- 2 |
- |
-
-
- | 119 |
- R2583E.1 |
- BXD65 |
- R2583E.1.CEL |
- 2.49 |
- 70 |
- 56.90% |
- 41.50% |
- 1.60% |
- 1.67 |
- 1.01 |
- 1 |
- |
-
-
- | 120 |
- R2728E.2 |
- BXD66 |
- R2728E.2.CEL |
- 1.714 |
- 137.45 |
- 59.40% |
- 39.00% |
- 1.60% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 121 |
- R2536E2.1 |
- BXD66 |
- R2536E2.1.CEL |
- 2.74 |
- 109 |
- 56.10% |
- 42.30% |
- 1.70% |
- 1.28 |
- 0.79 |
- 1 |
- |
-
-
- | 122 |
- R1207E.2 |
- BXD66 |
- R1207E.2.CEL |
- 1.681 |
- 136.86 |
- 60.40% |
- 38.10% |
- 1.50% |
- 1.45 |
- 0.77 |
- 2 |
- |
-
-
- | 123 |
- R1192E.2 |
- BXD67 |
- R1192E.2.CEL |
- 2.126 |
- 123.37 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 124 |
- R2727E.3 |
- BXD67 |
- R2727E.3.CEL |
- 1 |
- 82.55 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.97 |
- 0.87 |
- 2 |
- |
-
-
- | 125 |
- R2691E.3 |
- BXD67 |
- R2691E.3.CEL |
- 1 |
- 90 |
- 54.80% |
- 43.80% |
- 1.50% |
- 2.61 |
- 0.81 |
- 3 |
- |
-
-
- | 126 |
- R2551E.1 |
- BXD68 |
- R2551E.1.CEL |
- 2.49 |
- 92 |
- 54.30% |
- 44.10% |
- 1.60% |
- 2.91 |
- 1.55 |
- 1 |
- |
-
-
- | 127 |
- R2726E.2 |
- BXD68 |
- R2726E.2.CEL |
- 1.811 |
- 153.09 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.39 |
- 0.78 |
- 2 |
- |
-
-
- | 128 |
- R2593E.1 |
- BXD69 |
- R2593E.1.CEL |
- 1.67 |
- 128 |
- 59.20% |
- 39.50% |
- 1.30% |
- 1.47 |
- 0.92 |
- 1 |
- Y |
-
-
- | 129 |
- R975E.2 |
- BXD70 |
- R975E.2.CEL |
- 1.841 |
- 137.97 |
- 58.00% |
- 40.50% |
- 1.40% |
- 1.36 |
- 0.79 |
- 2 |
- |
-
-
- | 130 |
- R2537E2.1 |
- BXD70 |
- R2537E2.1.CEL |
- 2.93 |
- 99 |
- 58.00% |
- 40.50% |
- 1.60% |
- 1.29 |
- 0.75 |
- 1 |
- |
-
-
- | 131 |
- R4531E |
- BXD71 |
- R4531E.CEL |
- 4.77 |
- 43.48 |
- 62.40% |
- 36.30% |
- 1.40% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 132 |
- R4532E |
- BXD71 |
- R4532E.CEL |
- 5.89 |
- 40.68 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.24 |
- 0.79 |
- 4 |
- Y |
-
-
- | 133 |
- R2779E.2 |
- BXD73 |
- R2779E.2.CEL |
- 1.746 |
- 121.11 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 134 |
- R3024E.3 |
- BXD73 |
- R3024E.3.CEL |
- 1 |
- 78.05 |
- 51.70% |
- 46.60% |
- 1.70% |
- 2.3 |
- 0.94 |
- 3 |
- |
-
-
- | 135 |
- R2565E.1 |
- BXD75 |
- R2565E.1.CEL |
- 1.79 |
- 102 |
- 58.00% |
- 40.50% |
- 1.50% |
- 2.31 |
- 3.47 |
- 1 |
- |
-
-
- | 136 |
- R1397E-re.2 |
- BXD75 |
- R1397E-re.2.CEL |
- 1.449 |
- 189.71 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 137 |
- R2687E.3 |
- BXD77 |
- R2687E.3.CEL |
- 1 |
- 80 |
- 58.00% |
- 40.60% |
- 1.40% |
- 1.57 |
- 0.8 |
- 3 |
- Y |
-
-
- | 138 |
- R2717E.2 |
- BXD77 |
- R2717E.2.CEL |
- 1.797 |
- 84.43 |
- 61.60% |
- 36.90% |
- 1.40% |
- 1.49 |
- 0.76 |
- 2 |
- |
-
-
- | 139 |
- R1421E.3 |
- BXD77 |
- R1421E.3.CEL |
- 1 |
- 94 |
- 52.40% |
- 46.20% |
- 1.40% |
- 2.29 |
- 0.82 |
- 3 |
- |
-
-
- | 140 |
- R2579E.1 |
- BXD80 |
- R2579E.1.CEL |
- 2.42 |
- 72 |
- 59.20% |
- 39.40% |
- 1.50% |
- 1.73 |
- 0.82 |
- 1 |
- |
-
-
- | 141 |
- R2686E.2 |
- BXD80 |
- R2686E.2.CEL |
- 2.342 |
- 119.63 |
- 56.00% |
- 42.60% |
- 1.50% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 142 |
- R2956E.3 |
- BXD83 |
- R2956E.3.CEL |
- 1 |
- 84 |
- 55.40% |
- 43.20% |
- 1.40% |
- 1.39 |
- 0.84 |
- 3 |
- |
-
-
- | 143 |
- R2960E.3 |
- BXD83 |
- R2960E.3.CEL |
- 1 |
- 80 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.5 |
- 0.82 |
- 3 |
- Y |
-
-
- | 144 |
- R2922E.3 |
- BXD84 |
- R2922E.3.CEL |
- 1 |
- 91 |
- 57.80% |
- 40.80% |
- 1.50% |
- 1.47 |
- 0.83 |
- 3 |
- Y |
-
-
- | 145 |
- R2895E.3 |
- BXD84 |
- R2895E.3.CEL |
- 1 |
- 75 |
- 58.30% |
- 40.20% |
- 1.50% |
- 1.56 |
- 0.77 |
- 3 |
- Y |
-
-
- | 146 |
- R2692E.2 |
- BXD85 |
- R2692E.2.CEL |
- 1.423 |
- 160.87 |
- 60.20% |
- 38.30% |
- 1.40% |
- 1.46 |
- 0.79 |
- 2 |
- |
-
-
- | 147 |
- R2715E.2 |
- BXD85 |
- R2715E.2.CEL |
- 1.488 |
- 142.6 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.5 |
- 0.78 |
- 2 |
- |
-
-
- | 148 |
- R1405E.2 |
- BXD86 |
- R1405E.2.CEL |
- 2.351 |
- 119.34 |
- 56.40% |
- 42.20% |
- 1.40% |
- 1.64 |
- 0.81 |
- 2 |
- |
-
-
- | 149 |
- R1225E.3 |
- BXD86 |
- R1225E.3.CEL |
- 1 |
- 71 |
- 53.90% |
- 44.60% |
- 1.40% |
- 3.2 |
- 1.61 |
- 3 |
- |
-
-
- | 150 |
- R2724E.2 |
- BXD87 |
- R2724E.2.CEL |
- 1.906 |
- 113.71 |
- 60.70% |
- 37.90% |
- 1.40% |
- 1.45 |
- 0.79 |
- 2 |
- |
-
-
- | 151 |
- R2540E.1 |
- BXD87 |
- R2540E.1.CEL |
- 2.33 |
- 93 |
- 61.10% |
- 37.40% |
- 1.40% |
- 1.22 |
- 0.81 |
- 1 |
- Y |
-
-
- | 152 |
- R1433E.2 |
- BXD89 |
- R1433E.2.CEL |
- 1 |
- 2.241 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.41 |
- 0.78 |
- 2 |
- |
-
-
- | 153 |
- R2546E.1 |
- BXD89 |
- R2546E.1.CEL |
- 1.99 |
- 96 |
- 58.60% |
- 39.70% |
- 1.70% |
- 1.47 |
- 0.78 |
- 1 |
- |
-
-
- | 154 |
- R2578E2.1 |
- BXD90 |
- R2578E2.1.CEL |
- 2.79 |
- 92 |
- 58.60% |
- 39.80% |
- 1.60% |
- 1.52 |
- 0.77 |
- 1 |
- Y |
-
-
- | 155 |
- R859E.2 |
- BXD90 |
- R859E.2.CEL |
- 1.847 |
- 152.22 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.36 |
- 0.77 |
- 2 |
- |
-
-
- | 156 |
- R2682E.2 |
- BXD92 |
- R2682E.2.CEL |
- 1.547 |
- 156.31 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.37 |
- 0.77 |
- 2 |
- |
-
-
- | 157 |
- R1388E.3 |
- BXD92 |
- R1388E.3.CEL |
- 1 |
- 63 |
- 60.00% |
- 38.60% |
- 1.40% |
- 1.85 |
- 1.03 |
- 3 |
- |
-
-
- | 158 |
- R1322E.3 |
- BXD92 |
- R1322E.3.CEL |
- 1 |
- 80 |
- 55.90% |
- 42.60% |
- 1.50% |
- 1.75 |
- 0.74 |
- 3 |
- |
-
-
- | 159 |
- R2733E.2 |
- BXD96 |
- R2733E.2.CEL |
- 1.7 |
- 113.99 |
- 62.10% |
- 36.60% |
- 1.30% |
- 1.4 |
- 0.78 |
- 2 |
- |
-
-
- | 160 |
- R2554E.1 |
- BXD96 |
- R2554E.1.CEL |
- 2.18 |
- 93 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 161 |
- R2649E.2 |
- BXD97 |
- R2649E.2.CEL |
- 2.343 |
- 119.04 |
- 57.50% |
- 41.20% |
- 1.40% |
- 1.53 |
- 0.8 |
- 2 |
- |
-
-
- | 162 |
- R2577E.1 |
- BXD97 |
- R2577E.1.CEL |
- 2.07 |
- 77 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.87 |
- 1.29 |
- 1 |
- |
-
-
- | 163 |
- R2645E.3 |
- BXD98 |
- R2645E.3.CEL |
- 1 |
- 88 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.59 |
- 0.81 |
- 3 |
- Y |
-
-
- | 164 |
- R2688E.2 |
- BXD98 |
- R2688E.2.CEL |
- 1.772 |
- 145.24 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.48 |
- 0.81 |
- 2 |
- |
-
-
- | 165 |
- R4533E |
- BXD99 |
- R4533E.CEL |
- 1 |
- 37.69 |
- 60.30% |
- 38.20% |
- 1.40% |
- 1.33 |
- 0.89 |
- 4 |
- Y |
-
-
- | 166 |
- R4534E |
- BXD99 |
- R4534E.CEL |
- 5.69 |
- 36.62 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.16 |
- 0.8 |
- 4 |
- Y |
-
-
- | 167 |
- R2885E.3 |
- BXSB/MpJ |
- R2885E.3.CEL |
- 1 |
- 76 |
- 58.10% |
- 40.60% |
- 1.30% |
- 1.88 |
- 1.06 |
- 3 |
- |
-
-
- | 168 |
- R2883E.3 |
- BXSB/MpJ |
- R2883E.3.CEL |
- 1 |
- 71 |
- 56.40% |
- 42.00% |
- 1.50% |
- 1.59 |
- 0.84 |
- 3 |
- Y |
-
-
- | 169 |
- R1700E.1 |
- C3H/HeJ |
- R1700E.1.CEL |
- 2.98 |
- 69 |
- 60.80% |
- 37.90% |
- 1.40% |
- 1.48 |
- 0.78 |
- 1 |
- |
-
-
- | 170 |
- R1704E.1 |
- C3H/HeJ |
- R1704E.1.CEL |
- 2.58 |
- 88 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.38 |
- 0.84 |
- 1 |
- |
-
-
- | 171 |
- R2605E.1 |
- C57BL/6J |
- R2605E.1.CEL |
- 1.82 |
- 131 |
- 60.50% |
- 38.20% |
- 1.30% |
- 1.32 |
- 0.8 |
- 1 |
- Y |
-
-
- | 172 |
- R0871E |
- C57BL/6J |
- R0871E.CEL |
- 6.24 |
- 37.38 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.41 |
- 0.8 |
- 4 |
- Y |
-
-
- | 173 |
- R0872E.1 |
- C57BL/6J |
- R0872E.1.CEL |
- 3.13 |
- 89 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 174 |
- R0872E |
- C57BL/6J |
- R0872E.CEL |
- 3.128 |
- 88.58 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- |
-
-
- | 175 |
- R4507E |
- C57BL/6J-Nyx |
- R4507E.CEL |
- 8.13 |
- 37.5 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.32 |
- 0.8 |
- 4 |
- Y |
-
-
- | 176 |
- R4508E |
- C57BL/6J-Nyx |
- R4508E.CEL |
- 6.33 |
- 37.26 |
- 60.90% |
- 37.80% |
- 1.30% |
- 1.24 |
- 0.82 |
- 4 |
- Y |
-
-
- | 177 |
- R4505E |
- C57BL/6J-Rpe65 |
- R4505E.CEL |
- 5.98 |
- 37.48 |
- 61.80% |
- 36.80% |
- 1.40% |
- 1.45 |
- 0.85 |
- 4 |
- Y |
-
-
- | 178 |
- R4506E |
- C57BL/6J-Rpe65 |
- R4506E.CEL |
- 6.94 |
- 37.9 |
- 61.10% |
- 37.50% |
- 1.30% |
- 1.5 |
- 0.83 |
- 4 |
- Y |
-
-
- | 179 |
- R4535E |
- C57BLKS/J |
- R4535E.CEL |
- 6.59 |
- 37.28 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.26 |
- 0.83 |
- 4 |
- Y |
-
-
- | 180 |
- R4536E |
- C57BLKS/J |
- R4536E.CEL |
- 1 |
- 40.71 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.25 |
- 0.77 |
- 4 |
- Y |
-
-
- | 181 |
- R2564E.1 |
- CAST/EiJ |
- R2564E.1.CEL |
- 1.94 |
- 89 |
- 58.50% |
- 39.90% |
- 1.60% |
- 1.6 |
- 0.77 |
- 1 |
- |
-
-
- | 182 |
- R2580E.1 |
- CAST/EiJ |
- R2580E.1.CEL |
- 2.09 |
- 95 |
- 58.20% |
- 40.10% |
- 1.70% |
- 1.4 |
- 0.76 |
- 1 |
- |
-
-
- | 183 |
- R4537E |
- CBA/CaJ |
- R4537E.CEL |
- 1 |
- 38.45 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.63 |
- 0.82 |
- 4 |
- Y |
-
-
- | 184 |
- R4538E |
- CBA/CaJ |
- R4538E.CEL |
- 5.89 |
- 39.18 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.45 |
- 0.8 |
- 4 |
- Y |
-
-
- | 185 |
- R4539E |
- CZECHII/EiJ |
- R4539E.CEL |
- 7.73 |
- 37.1 |
- 58.30% |
- 40.10% |
- 1.50% |
- 1.7 |
- 0.95 |
- 4 |
- Y |
-
-
- | 186 |
- R4540E |
- CZECHII/EiJ |
- R4540E.CEL |
- 11.04 |
- 36.69 |
- 53.00% |
- 45.30% |
- 1.70% |
- 1.83 |
- 1.32 |
- 4 |
- |
-
-
- | 187 |
- R2600E.1 |
- D2B6F1 |
- R2600E.1.CEL |
- 2.47 |
- 95 |
- 58.10% |
- 40.20% |
- 1.70% |
- 1.41 |
- 0.78 |
- 1 |
- Y |
-
-
- | 188 |
- R2604E.1 |
- D2B6F1 |
- R2604E.1.CEL |
- 2.66 |
- 90 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.28 |
- 0.79 |
- 1 |
- Y |
-
-
- | 189 |
- R1002E.3 |
- DBA/2J |
- R1002E.3.CEL |
- 1 |
- 102 |
- 54.80% |
- 43.70% |
- 1.50% |
- 2.84 |
- 0.83 |
- 3 |
- |
-
-
- | 190 |
- R4541E |
- DBA/2J |
- R4541E.CEL |
- 1 |
- 43.4 |
- 61.40% |
- 37.00% |
- 1.50% |
- 1.37 |
- 0.73 |
- 4 |
- Y |
-
-
- | 191 |
- R959E.3 |
- DBA/2J |
- R959E.3.CEL |
- 1 |
- 89.97 |
- 53.20% |
- 45.30% |
- 1.50% |
- 3.66 |
- 1.09 |
- 4 |
- |
-
-
- | 192 |
- R2572E.1 |
- DBA/2J |
- R2572E.1.CEL |
- 2.41 |
- 79 |
- 55.50% |
- 42.90% |
- 1.60% |
- 1.37 |
- 0.79 |
- 1 |
- |
-
-
- | 193 |
- R4542E |
- DBA/2J |
- R4542E.CEL |
- 5.7 |
- 39.95 |
- 61.00% |
- 37.40% |
- 1.50% |
- 1.23 |
- 0.81 |
- 4 |
- Y |
-
-
- | 194 |
- R2771E.3 |
- FVB/NJ |
- R2771E.3.CEL |
- 1 |
- 70 |
- 55.30% |
- 43.20% |
- 1.50% |
- 1.69 |
- 0.83 |
- 3 |
- |
-
-
- | 195 |
- R2772E.3 |
- FVB/NJ |
- R2772E.3.CEL |
- 1 |
- 76 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.13 |
- 1.02 |
- 3 |
- |
-
-
- | 196 |
- R2636E.1 |
- KK/HlJ |
- R2636E.1.CEL |
- 2.61 |
- 93 |
- 58.90% |
- 39.50% |
- 1.50% |
- 1.39 |
- 0.76 |
- 1 |
- Y |
-
-
- | 197 |
- R2637E.1 |
- KK/HlJ |
- R2637E.1.CEL |
- 2.19 |
- 103 |
- 59.40% |
- 39.00% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 198 |
- R0999E.1 |
- LG/J |
- R0999E.1.CEL |
- 2.45 |
- 82 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 199 |
- R1004E.1 |
- LG/J |
- R1004E.1.CEL |
- 2.44 |
- 92 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 200 |
- R4543E |
- LP/J |
- R4543E.CEL |
- 6.57 |
- 41.99 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.28 |
- 0.75 |
- 4 |
- Y |
-
-
- | 201 |
- R4544E |
- LP/J |
- R4544E.CEL |
- 4.56 |
- 39.9 |
- 62.40% |
- 36.10% |
- 1.50% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 202 |
- R2858E.3 |
- MOLF/EiJ |
- R2858E.3.CEL |
- 1 |
- 64 |
- 53.80% |
- 44.70% |
- 1.50% |
- 1.59 |
- 0.95 |
- 3 |
- |
-
-
- | 203 |
- R2919.3 |
- MOLF/EiJ |
- R2919.3.CEL |
- 1 |
- 64 |
- 52.40% |
- 46.00% |
- 1.60% |
- 2.15 |
- 1.07 |
- 3 |
- |
-
-
- | 204 |
- R1688E.1 |
- NOD/LtJ |
- R1688E.1.CEL |
- 2.66 |
- 98 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 205 |
- R2566E-2.1 |
- NOD/LtJ |
- R2566E-2.1.CEL |
- 3.03 |
- 69 |
- 59.80% |
- 38.80% |
- 1.50% |
- 1.38 |
- 0.75 |
- 1 |
- Y |
-
-
- | 206 |
- R4545E |
- NZB/BlNJ |
- R4545E.CEL |
- 4.23 |
- 43.48 |
- 62.10% |
- 36.40% |
- 1.50% |
- 1.33 |
- 0.76 |
- 4 |
- Y |
-
-
- | 207 |
- R4546E |
- NZB/BlNJ |
- R4546E.CEL |
- 6.27 |
- 44.22 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.17 |
- 0.82 |
- 4 |
- Y |
-
-
- | 208 |
- R2535E.1 |
- NZO/HlLtJ |
- R2535E.1.CEL |
- 1.89 |
- 86 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.41 |
- 0.85 |
- 1 |
- |
-
-
- | 209 |
- R2550E.1 |
- NZO/HlLtJ |
- R2550E.1.CEL |
- 1.79 |
- 87 |
- 60.70% |
- 37.80% |
- 1.50% |
- 1.52 |
- 0.82 |
- 1 |
- |
-
-
- | 210 |
- R2817E.3 |
- NZW/LacJ |
- R2817E.3.CEL |
- 1 |
- 59 |
- 50.90% |
- 47.60% |
- 1.50% |
- 3.59 |
- 1.48 |
- 3 |
- |
-
-
- | 211 |
- R2810E |
- NZW/LacJ |
- R2810E.CEL |
- |
- |
- |
- |
- |
- |
- |
- 3 |
- |
-
-
- | 212 |
- R2810E.3 |
- NZW/LacJ |
- R2810E.3.CEL |
- 1 |
- 74 |
- 57.00% |
- 41.70% |
- 1.40% |
- 2.15 |
- 1.03 |
- 4 |
- Y |
-
-
- | 213 |
- R4547E |
- PANCEVO/EiJ |
- R4547E.CEL |
- 5.27 |
- 51.34 |
- 57.20% |
- 41.10% |
- 1.70% |
- 1.7 |
- 0.83 |
- 4 |
- |
-
-
- | 214 |
- R4548E |
- PANCEVO/EiJ |
- R4548E.CEL |
- 10.54 |
- 37.39 |
- 50.30% |
- 48.00% |
- 1.70% |
- 1.68 |
- 1.09 |
- 4 |
- |
-
-
- | 215 |
- R2635E.1 |
- PWD/PhJ |
- R2635E.1.CEL |
- 3.72 |
- 80 |
- 54.20% |
- 44.10% |
- 1.70% |
- 1.53 |
- 0.85 |
- 1 |
- |
-
-
- | 216 |
- R2634E.1 |
- PWD/PhJ |
- R2634E.1.CEL |
- 3.29 |
- 90 |
- 55.90% |
- 42.50% |
- 1.60% |
- 1.57 |
- 0.81 |
- 1 |
- |
-
-
- | 217 |
- R2544E.1 |
- PWK/PhJ |
- R2544E.1.CEL |
- 2.2 |
- 108 |
- 54.90% |
- 43.50% |
- 1.70% |
- 1.36 |
- 0.82 |
- 1 |
- |
-
-
- | 218 |
- R2549E.1 |
- PWK/PhJ |
- R2549E.1.CEL |
- 2.28 |
- 84 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.57 |
- 0.83 |
- 1 |
- |
-
-
- | 219 |
- R4550E |
- SJL/J |
- R4550E.CEL |
- 5.35 |
- 40.44 |
- 62.30% |
- 36.20% |
- 1.40% |
- 1.24 |
- 0.79 |
- 4 |
- |
-
-
- | 220 |
- R2368E.1 |
- WSB/EiJ |
- R2368E.1.CEL |
- 2.57 |
- 86 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.29 |
- 0.74 |
- 1 |
- Y |
-
-
- | 221 |
- R2547E.1 |
- WSB/EiJ |
- R2547E.1.CEL |
- 2.14 |
- 90 |
- 58.20% |
- 40.10% |
- 1.60% |
- 1.32 |
- 0.77 |
- 1 |
- Y |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R/summary.rtf b/general/datasets/Eye_M2_0908_R/summary.rtf
deleted file mode 100644
index 44b7e23..0000000
--- a/general/datasets/Eye_M2_0908_R/summary.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-FINAL RECOMMENDED EYE DATA SET. The HEIMED September 2008 RMA data release provides estimates of gene expression in whole eyes of 103 lines of young adult mice generated using 221 Affymetrix M430 2.0 arrays. This data set is intended for exploration of the genetics and genomics of the mouse eye, retina, lens, retinal pigment epithelium, cornea, iris and choroid. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
diff --git a/general/datasets/Eye_M2_0908_R/tissue.rtf b/general/datasets/Eye_M2_0908_R/tissue.rtf
deleted file mode 100644
index 9b6ee0f..0000000
--- a/general/datasets/Eye_M2_0908_R/tissue.rtf
+++ /dev/null
@@ -1,2058 +0,0 @@
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.
-
-Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well balanced sample of males and females, in general without within-strain-by-sex replication. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.
-
-Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.
-
-Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.
-
-
- - Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
- - Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
- - Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
- - Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
-
-
-Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Group |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- R2595E.1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- UTHSC RW |
-
-
- | 2 |
- R2533E.1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- UTHSC RW |
-
-
- | 3 |
- R0754E.1 |
- GDP |
- A/J |
- 60 |
- M |
- JAX |
-
-
- | 4 |
- R4521E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 5 |
- R4522E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 6 |
- R4523E |
- KO |
- B6129P2F2N1-Clcn3 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 7 |
- R4526E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- F |
- TChoi_Deltagen |
-
-
- | 8 |
- R4509E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- M |
- TChoi_Deltagen |
-
-
- | 9 |
- R4510E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 10 |
- R4511E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 20 |
- M |
- TChoi_Deltagen |
-
-
- | 11 |
- R4524E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 12 |
- R4525E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 13 |
- R4515E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 14 |
- R4516E |
- KO |
- B6129P2F2N1-Gabra1 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 15 |
- R4517E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 16 |
- R4512E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- F |
- TChoi_Deltagen |
-
-
- | 17 |
- R4513E |
- KO |
- B6129P2F2N1-Gnb5 |
- 25 |
- M |
- TChoi_Deltagen |
-
-
- | 18 |
- R4514E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 19 |
- R4518E |
- KO |
- B6129P2F2N1-Gpr19 |
- 70 |
- M |
- TChoi_Deltagen |
-
-
- | 20 |
- R4519E |
- KO |
- B6129P2F2N1-Gpr19 |
- 68 |
- M |
- TChoi_Deltagen |
-
-
- | 21 |
- R2601E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 22 |
- R2602E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 23 |
- R1676E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- JAX |
-
-
- | 24 |
- R1672E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- JAX |
-
-
- | 25 |
- R4530E |
- GDP |
- BALB/cJ |
- 66 |
- F |
- JAX |
-
-
- | 26 |
- R4529E |
- GDP |
- BALB/cJ |
- 66 |
- M |
- JAX |
-
-
- | 27 |
- R2704E.2 |
- BXD |
- BXD1 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 28 |
- R2707E.3 |
- BXD |
- BXD1 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 29 |
- R1231E.2 |
- BXD |
- BXD2 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 30 |
- R2598E.1 |
- BXD |
- BXD2 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 31 |
- R2591E.1 |
- BXD |
- BXD5 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 32 |
- R2714E.2 |
- BXD |
- BXD5 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 33 |
- R2570E.1 |
- BXD |
- BXD6 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 34 |
- R2694E.2 |
- BXD |
- BXD6 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 35 |
- R2538E.1 |
- BXD |
- BXD8 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 36 |
- R2709E.2 |
- BXD |
- BXD8 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 37 |
- R2708E.2 |
- BXD |
- BXD9 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 38 |
- R2569E.1 |
- BXD |
- BXD9 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 39 |
- R2581E.1 |
- BXD |
- BXD11 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 40 |
- R2612E.2 |
- BXD |
- BXD11 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 41 |
- R2742E.2 |
- BXD |
- BXD12 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 42 |
- R2543E.1 |
- BXD |
- BXD12 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 43 |
- R2586E.1 |
- BXD |
- BXD13 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 44 |
- R877E.2 |
- BXD |
- BXD13 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 45 |
- R2557E.1 |
- BXD |
- BXD14 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 46 |
- R1128E.2 |
- BXD |
- BXD14 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 47 |
- R2701E.3 |
- BXD |
- BXD15 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 48 |
- R2716E.2 |
- BXD |
- BXD15 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 49 |
- R2711E.2 |
- BXD |
- BXD16 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 50 |
- R2567E.1 |
- BXD |
- BXD16 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 51 |
- R2720E.2 |
- BXD |
- BXD18 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 52 |
- R2559E.1 |
- BXD |
- BXD18 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 53 |
- R2560E.1 |
- BXD |
- BXD19 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 54 |
- R2713E.2 |
- BXD |
- BXD19 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 55 |
- R2584E.1 |
- BXD |
- BXD20 |
- 59 |
- F |
- BIDMC GR |
-
-
- | 56 |
- R2731E.2 |
- BXD |
- BXD20 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 57 |
- R2702E.2 |
- BXD |
- BXD21 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 58 |
- R2541E2.1 |
- BXD |
- BXD21 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 59 |
- R2553E.1 |
- BXD |
- BXD22 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 60 |
- R2700E.2 |
- BXD |
- BXD22 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 61 |
- R2558E-2.1 |
- BXD |
- BXD23 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 62 |
- R1086E.2 |
- BXD |
- BXD23 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 63 |
- R2719E.2 |
- BXD |
- BXD24 |
- 123 |
- F |
- UTHSC RW |
-
-
- | 64 |
- R2589E2.1 |
- BXD |
- BXD24 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 65 |
- R2573E-2.1 |
- BXD |
- BXD25 |
- 67 |
- F |
- UAB |
-
-
- | 66 |
- R2683E.2 |
- BXD |
- BXD25 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 67 |
- R2703E.2 |
- BXD |
- BXD27 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 68 |
- R2729E.3 |
- BXD |
- BXD27 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 69 |
- R2562E.3 |
- BXD |
- BXD28 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 70 |
- R2721E.2 |
- BXD |
- BXD28 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 71 |
- R2561E.3 |
- BXD |
- BXD29 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 72 |
- R1258E.2 |
- BXD |
- BXD31 |
- 57 |
- F |
- UTHSC RW |
-
-
- | 73 |
- R2597E.1 |
- BXD |
- BXD31 |
- 61 |
- M |
- BIDMC GR |
-
-
- | 74 |
- R2563E.1 |
- BXD |
- BXD32 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 75 |
- R1216E.2 |
- BXD |
- BXD32 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 76 |
- R2542E.1 |
- BXD |
- BXD33 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- R857E.2 |
- BXD |
- BXD33 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 78 |
- R1451E.2 |
- BXD |
- BXD34 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 79 |
- R2585E.1 |
- BXD |
- BXD34 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 80 |
- R2698E.3 |
- BXD |
- BXD36 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 81 |
- R2705E.3 |
- BXD |
- BXD36 |
- 57 |
- M |
- BIDMC GR |
-
-
- | 82 |
- R2710E.2 |
- BXD |
- BXD38 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 83 |
- R2532E.1 |
- BXD |
- BXD38 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 84 |
- R2574E.1 |
- BXD |
- BXD39 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 85 |
- R2695E.2 |
- BXD |
- BXD39 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 86 |
- R2699E.2 |
- BXD |
- BXD40 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 87 |
- R2590E.1 |
- BXD |
- BXD40 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 88 |
- R2696E.2 |
- BXD |
- BXD42 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 89 |
- R2596E.1 |
- BXD |
- BXD42 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 90 |
- R994E.2 |
- BXD |
- BXD43 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 91 |
- R2607E.1 |
- BXD |
- BXD43 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 92 |
- R2594E.1 |
- BXD |
- BXD44 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 93 |
- R2610E.2 |
- BXD |
- BXD44 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 94 |
- R2732E.2 |
- BXD |
- BXD45 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 95 |
- R2592E.1 |
- BXD |
- BXD45 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- R967E.2 |
- BXD |
- BXD48 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 97 |
- R2606E.1 |
- BXD |
- BXD48 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 98 |
- R2933E.3 |
- BXD |
- BXD50 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 99 |
- R2937E.3 |
- BXD |
- BXD50 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 100 |
- R2603E.1 |
- BXD |
- BXD51 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 101 |
- R1042E.2 |
- BXD |
- BXD51 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 102 |
- R2980E.3 |
- BXD |
- BXD55 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 103 |
- R2690E.2 |
- BXD |
- BXD55 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 104 |
- R4176E |
- BXD |
- BXD56 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 105 |
- R4175E |
- BXD |
- BXD56 |
- 53 |
- M |
- UTHSC RW |
-
-
- | 106 |
- R1006E.3 |
- BXD |
- BXD60 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 107 |
- R2725E.2 |
- BXD |
- BXD60 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 108 |
- R1074E.3 |
- BXD |
- BXD60 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 109 |
- R2534E2.1 |
- BXD |
- BXD61 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 110 |
- R2684E.2 |
- BXD |
- BXD61 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 111 |
- R1107E.3 |
- BXD |
- BXD62 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 112 |
- R2681E.2 |
- BXD |
- BXD62 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 113 |
- R965E.3 |
- BXD |
- BXD62 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 114 |
- R1425E.2 |
- BXD |
- BXD63 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 115 |
- R2576E.3 |
- BXD |
- BXD63 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 116 |
- R943E-2.2 |
- BXD |
- BXD64 |
- 56 |
- F |
- UTHSC RW |
-
-
- | 117 |
- R2611E.1 |
- BXD |
- BXD64 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 118 |
- R2689E.2 |
- BXD |
- BXD65 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 119 |
- R2583E.1 |
- BXD |
- BXD65 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 120 |
- R2728E.2 |
- BXD |
- BXD66 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 121 |
- R2536E2.1 |
- BXD |
- BXD66 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 122 |
- R1207E.2 |
- BXD |
- BXD66 |
- 83 |
- M |
- UTHSC RW |
-
-
- | 123 |
- R1192E.2 |
- BXD |
- BXD67 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 124 |
- R2727E.3 |
- BXD |
- BXD67 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 125 |
- R2691E.3 |
- BXD |
- BXD67 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 126 |
- R2551E.1 |
- BXD |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 127 |
- R2726E.2 |
- BXD |
- BXD68 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 128 |
- R2593E.1 |
- BXD |
- BXD69 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 129 |
- R975E.2 |
- BXD |
- BXD70 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 130 |
- R2537E2.1 |
- BXD |
- BXD70 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 131 |
- R4531E |
- BXD |
- BXD71 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 132 |
- R4532E |
- BXD |
- BXD71 |
- 86 |
- M |
- UTHSC RW |
-
-
- | 133 |
- R2779E.2 |
- BXD |
- BXD73 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 134 |
- R3024E.3 |
- BXD |
- BXD73 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 135 |
- R2565E.1 |
- BXD |
- BXD75 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 136 |
- R1397E-re.2 |
- BXD |
- BXD75 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 137 |
- R2687E.3 |
- BXD |
- BXD77 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 138 |
- R2717E.2 |
- BXD |
- BXD77 |
- 107 |
- M |
- UTHSC RW |
-
-
- | 139 |
- R1421E.3 |
- BXD |
- BXD77 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 140 |
- R2579E.1 |
- BXD |
- BXD80 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 141 |
- R2686E.2 |
- BXD |
- BXD80 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 142 |
- R2956E.3 |
- BXD |
- BXD83 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 143 |
- R2960E.3 |
- BXD |
- BXD83 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 144 |
- R2922E.3 |
- BXD |
- BXD84 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 145 |
- R2895E.3 |
- BXD |
- BXD84 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- R2692E.2 |
- BXD |
- BXD85 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 147 |
- R2715E.2 |
- BXD |
- BXD85 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 148 |
- R1405E.2 |
- BXD |
- BXD86 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 149 |
- R1225E.3 |
- BXD |
- BXD86 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 150 |
- R2724E.2 |
- BXD |
- BXD87 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 151 |
- R2540E.1 |
- BXD |
- BXD87 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 152 |
- R1433E.2 |
- BXD |
- BXD89 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 153 |
- R2546E.1 |
- BXD |
- BXD89 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 154 |
- R2578E2.1 |
- BXD |
- BXD90 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 155 |
- R859E.2 |
- BXD |
- BXD90 |
- 72 |
- M |
- UTHSC RW |
-
-
- | 156 |
- R2682E.2 |
- BXD |
- BXD92 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 157 |
- R1388E.3 |
- BXD |
- BXD92 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 158 |
- R1322E.3 |
- BXD |
- BXD92 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 159 |
- R2733E.2 |
- BXD |
- BXD96 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 160 |
- R2554E.1 |
- BXD |
- BXD96 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 161 |
- R2649E.2 |
- BXD |
- BXD97 |
- 74 |
- F |
- UTHSC RW |
-
-
- | 162 |
- R2577E.1 |
- BXD |
- BXD97 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 163 |
- R2645E.3 |
- BXD |
- BXD98 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 164 |
- R2688E.2 |
- BXD |
- BXD98 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 165 |
- R4533E |
- BXD |
- BXD99 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 166 |
- R4534E |
- BXD |
- BXD99 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 167 |
- R2885E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 168 |
- R2883E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- M |
- BIDMC GR |
-
-
- | 169 |
- R1700E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- UTHSC RW |
-
-
- | 170 |
- R1704E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- UTHSC RW |
-
-
- | 171 |
- R2605E.1 |
- GDP BXD |
- C57BL/6J |
- 79 |
- F |
- UTHSC RW |
-
-
- | 172 |
- R0871E |
- GDP BXD |
- C57BL/6J |
- 65 |
- F |
- UTHSC RW |
-
-
- | 173 |
- R0872E.1 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 174 |
- R0872E |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 175 |
- R4507E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 176 |
- R4508E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 177 |
- R4505E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 178 |
- R4506E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 179 |
- R4535E |
- GDP |
- C57BLKS/J |
- 66 |
- F |
- JAX |
-
-
- | 180 |
- R4536E |
- GDP |
- C57BLKS/J |
- 66 |
- M |
- JAX |
-
-
- | 181 |
- R2564E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- F |
- JAX |
-
-
- | 182 |
- R2580E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- M |
- JAX |
-
-
- | 183 |
- R4537E |
- GDP |
- CBA/CaJ |
- 66 |
- F |
- JAX |
-
-
- | 184 |
- R4538E |
- GDP |
- CBA/CaJ |
- 66 |
- M |
- JAX |
-
-
- | 185 |
- R4539E |
- GDP |
- CZECHII/EiJ |
- 66 |
- F |
- JAX |
-
-
- | 186 |
- R4540E |
- GDP |
- CZECHII/EiJ |
- 66 |
- M |
- JAX |
-
-
- | 187 |
- R2600E.1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- UTHSC RW |
-
-
- | 188 |
- R2604E.1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- UTHSC RW |
-
-
- | 189 |
- R1002E.3 |
- GDP BXD |
- DBA/2J |
- 72 |
- F |
- UTHSC RW |
-
-
- | 190 |
- R4541E |
- GDP BXD |
- DBA/2J |
- 65 |
- F |
- JAX |
-
-
- | 191 |
- R959E.3 |
- GDP BXD |
- DBA/2J |
- 60 |
- M |
- UTHSC RW |
-
-
- | 192 |
- R2572E.1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 193 |
- R4542E |
- GDP BXD |
- DBA/2J |
- 59 |
- M |
- JAX |
-
-
- | 194 |
- R2771E.3 |
- GDP |
- FVB/NJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 195 |
- R2772E.3 |
- GDP |
- FVB/NJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 196 |
- R2636E.1 |
- GDP |
- KK/HlJ |
- 64 |
- F |
- UTHSC RW |
-
-
- | 197 |
- R2637E.1 |
- GDP |
- KK/HlJ |
- 64 |
- M |
- UTHSC RW |
-
-
- | 198 |
- R0999E.1 |
- GDP |
- LG/J |
- 57 |
- F |
- UTHSC RW |
-
-
- | 199 |
- R1004E.1 |
- GDP |
- LG/J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 200 |
- R4543E |
- GDP |
- LP/J |
- 65 |
- F |
- JAX |
-
-
- | 201 |
- R4544E |
- GDP |
- LP/J |
- 65 |
- M |
- JAX |
-
-
- | 202 |
- R2858E.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 203 |
- R2919.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 204 |
- R1688E.1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- JAX |
-
-
- | 205 |
- R2566E-2.1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- UTHSC RW |
-
-
- | 206 |
- R4545E |
- GDP |
- NZB/BlNJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 207 |
- R4546E |
- GDP |
- NZB/BlNJ |
- 58 |
- M |
- BIDMC GR |
-
-
- | 208 |
- R2535E.1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- JAX |
-
-
- | 209 |
- R2550E.1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- JAX |
-
-
- | 210 |
- R2817E.3 |
- GDP |
- NZW/LacJ |
- 65 |
- F |
- BIDMC GR |
-
-
- | 211 |
- R2810E |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 212 |
- R2810E.3 |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 213 |
- R4547E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- F |
- JAX |
-
-
- | 214 |
- R4548E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- M |
- JAX |
-
-
- | 215 |
- R2635E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- JAX |
-
-
- | 216 |
- R2634E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- JAX |
-
-
- | 217 |
- R2544E.1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- JAX |
-
-
- | 218 |
- R2549E.1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- JAX |
-
-
- | 219 |
- R4550E |
- GDP |
- SJL/J |
- 65 |
- M+F |
- JAX |
-
-
- | 220 |
- R2368E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- UTHSC RW |
-
-
- | 221 |
- R2547E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- UTHSC RW |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_MT/acknowledgment.rtf b/general/datasets/Eye_M2_0908_R_MT/acknowledgment.rtf
deleted file mode 100644
index 5098d32..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant and from funds from NEI grant to Dr. Eldon Geisert (R01EY017841), an NEI Vision Core grant (EY14080) and an Unrestricted Grant from Research To Prevent Blindness.
-
-We thank Dr. Ted Choi, Chief Scientific Director of Predictive Biology, Inc. (past director of molecular genetics at Deltagen Inc.) for providing us with eye samples from several interesting DeltaGen knockouts.
diff --git a/general/datasets/Eye_M2_0908_R_MT/cases.rtf b/general/datasets/Eye_M2_0908_R_MT/cases.rtf
deleted file mode 100644
index 552d4a5..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/cases.rtf
+++ /dev/null
@@ -1,57 +0,0 @@
-This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:
-
-
- - 68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.
- - 35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common Mus musculus domesticus inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (Mus musculus domesticus, e.g, WSB/EiJ; M. musculus musculus, e.g., CZECHII/EiJ; M. musculus molossinus, e.g., MOLF/EiJ; M. musculus castaneus, e.g., CAST/EiJ); and even one different species of mouse (Mus spicilegus, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the Nyx-nob mutant:
- - 6 knockouts (KO), including a KO of Rpe65, and 5 DeltaGen Inc. knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: Gabra1, Gabbr1, Gnb1, Gpr19, and Clcn3. We also included one spontaneous mutant of the nyctalopin (Nyx no b wave "nob") gene (Pardue et al., 1998) that is on a BALB/cByJ background.
-
-
-Rod photoreceptor degeneration in inbred mice: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the retinal degeneration 1 (rd1) mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (Pde6b). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.
-
-As expected (Dickerson LW et al., 2002) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, Clcn3) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of Gnat2, a gene associated with cones and achromatopsia in mice and humans.
-
-Lines of mice were selected using the following criteria:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - representation of a fairly wide variety of different subspecies of Mus
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - interesting mutations or knockouts affecting genes with high expression in the eye
- - general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.
-
-
-We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see Perlegen's excellent data resources and browser).
-
-
- - 129S1/SvImJ : Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a cone photoreceptor function loss 3 mutant (Cpfl3 allele) of the Gnat2 gene that is a model for achromatopsia (JAX Stock Number: 002448)
- - A/J: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (Tyr c allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: 000646)
- - BALB/cByJ: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Small brain, not aggressive (JAX Stock Number: 001026)
- - BALB/cJ: Phenome Project A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Large brain and aggressive (JAX Stock Number: 000651)
- - BXSB/MpJ: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the Yaa gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: 000740)
- - C3H/HeJ: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a Pdeb6 rd1 mutant with near total photoreceptor loss at as early as postnatal day 30. Also a Tlr4 mutant that is endotoxin resistant. (JAX Stock Number: 000659)
- - C57BL/6J: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: 000664)
- - C57BLKS/J: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: 000662)
- - CAST/EiJ: A wild-derived inbred Mus musculus castaneus strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: 000928)
- - CBA/CaJ: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: 000654)
- - CZECHII/EiJ: Czech 2 is a wild-derived inbred strain M. musculus musculus strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: 001144).
- - DBA/2J: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. A myosin 5a (Myo5a d) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: 000671)
- - FVB/NJ: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. Tyr c locus albino and a Pdeb6 rd1 mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: 001800).
- - KK/HlJ: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: 002106)
- - LG/J: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A Tyr c locus albino strain. (JAX Stock Number: 000675)
- - LP/J: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B Ednrb gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: 000676)
- - MOLF/EiJ: A wild-derived inbred strain derived from M. musculus molossinus samples camputered in Fukuoka, Japan. This strain has the retinal degeneration rd1 allele in Pde6b. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: 000550)
- - NOD/LtJ: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. (JAX Stock Number: 001976)
- - NZO/HlLtJ: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: 002105)
- - NZB/BlNJ: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: 000648)
- - NZW/LacJ: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the Tyr c locus albino mutation, the pink-eye dilution mutation in the Oca2 or p locus, and the brown allele at Tyrp1. (JAX Stock Number: 001058)
- - PANCEVO/EiJ: PANCEVO/EiJ is a wild-derived inbred strain from the Mus spicilegus samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier 10103). M. spicilegus is a colonial mound-building species. No known ocular or retina mutations, but the expression level of Gnat2 is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: 001384)
- - PWD/PhJ: A wild-derived Mus musculus musculus agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: 004660)
- - PWK/PhJ: A wild-derived Mus musculus musculus inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: 003715)
- - SJL/J: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration rd1 allele in Pde6b. It also carries both the Tyr c albino mutation and the pink-eye dilution mutation in the Oca2 or p locus. Highly aggressive males. (JAX Stock Number: 000686)
- - WSB/EiJ: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived Mus musculus domesticus inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: 001145)
- - B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J 100006)
-
-
-Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, 2008 and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (Tyr, or human OCA1), the brown allele of the tyrosinase related protein 1 (Tyrp1), the pink-eye dilution allele of Oca2 (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein Asip, the steel allele of Kitlg, the dilute allele of Myo5a (probe set 1419754), and the piebald allele of Ednrb. In some of these cases, effects of the mutation are easily detected at the transcript level (Tyrp1, Oca2, and Myo5a), but in the other cases (Tyr, Asip, Ednrb, and Kitlg), mutations do not leave a strong imprint on expression.
diff --git a/general/datasets/Eye_M2_0908_R_MT/experiment-design.rtf b/general/datasets/Eye_M2_0908_R_MT/experiment-design.rtf
deleted file mode 100644
index 1ebe0ad..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression profiling by array
diff --git a/general/datasets/Eye_M2_0908_R_MT/notes.rtf b/general/datasets/Eye_M2_0908_R_MT/notes.rtf
deleted file mode 100644
index 7a26eb5..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Eye_M2_0908_R_MT/platform.rtf b/general/datasets/Eye_M2_0908_R_MT/platform.rtf
deleted file mode 100644
index 9024a99..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/platform.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many probes overlap and target the same transcript). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
-As part of the development of HEIMED, we have manually annotated individual probe sets by sequence alignment to the mouse genome and transcriptome. Approximately 13,000 probe sets that have comparatively high expression in eye and CNS were curated by one of the authors (RWW) and now have specific information on the part of the transcript targeted by each probe set. The other 33,000 transcripts have corresponding data that was generated by Xusheng Wang using computational methods (BLAT analysis combined with annotated genome sequence).
-
-One example may help explain how to exploit this annotation. The four probe sets for rhodopsin include information on the target location. Only the first probe set targets the last two coding exons. The other three probe sets target different parts of the 3’ UTR (mid, distal, and far distal regions). The probe sets can be reordered by from high to low expression using the Sort By function in Search Results pages. In the case of rhodopsin, the probe set that targets that last two coding exons and proximal parts of the 3’ UTR also has the highest expression . Finally, the HEIMED gene descriptions have been customized to help vision researchers. In the case of rhodopsin, the description appended after the gene name reads “rod photoreceptor pigment, retinitis pigmentosa-associated”. For less well known genes this kind of annotation can be extremely useful. For example, the more verbose annotation for Cerkl reads “neuronal survival and apoptosis-related, retinal ganglion cell expressed, retinitis pigmentosa 26); alternative 3' UTR of short form message, intron 2”.
-
-
-
-
-
-Legend: Distribution of expression values for all probe sets in HEIMED.
diff --git a/general/datasets/Eye_M2_0908_R_MT/processing.rtf b/general/datasets/Eye_M2_0908_R_MT/processing.rtf
deleted file mode 100644
index 4349e60..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/processing.rtf
+++ /dev/null
@@ -1,3381 +0,0 @@
-Range of Gene Expression in the Eye. Expression of transcripts in the HEIMED and most other GN data sets is measured on a log2 scale. Each unit corresponding approximately to a 2-fold difference in hybridization signal intensity. To simplify comparisons among different data sets and cases, log2 RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units (variance stabilized). Values of all 45,101 probe sets in this data set range from a low of 4.8 (Tcf15, probe set 1420281_at) to a high of 15.5 (crystallin gamma C, Crygc, probe set 1422674_s_at). This corresponds to 10.7 units or a 1 to 1700 dynamic range of expression (2^10.73).
-
-We used pooled RNA samples of whole eyes, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-We calibrated this log intensity scale using Affymetrix spike-in control probe sets. These 18 control probe sets target exogenous bacterial mRNAs that are added to each sample (a graded dose spike cocktail) during preparation at concentrations of 1.5, 5, 25, and 100 pM. (To find these probe sets, search GN’s ALL search field using the string “AFFX pM”.) A value of 6 or less is equivalent to an mRNA concentration of under 0.4 pM, a value of 8 is equivalent to ~1.5 pM, 9.5 is equivalent to ~5 pM, 11.5 is equivalent to ~25 pM, 13.5 is equivalent to ~100 pM, and a value of 15.5 is equivalent to an mRNA concentration of 400 pM or greater.
-
-This range can be converted to the mRNA molecules per cell in the eye assuming that a value of 8 is equivalent to about 1 mRNA copy per cell (Kanno et al. 2006, see http://www.biomedcentral.com/1471-2164/7/64). Since the expression of rhodopsin mRNA is normally 15 units, we predict that there are 27 or ~128 Rho mRNAs per cell in the whole eye and ~256 in rods themselves (assuming that rods make up about half of all cells in the eye). For this purpose it may be useful to know that a normal mouse eye contains between 6 and 8 million rod photoreceptors (Guo, Lu, and Williams; GN BXD Phenotype ID 11024).
-
-Note that some probe sets with very low expression still provide reliable data. For example, probe set 1440397_at (Cacna2d1) has expression of only 5.5 units (a value that would be declared as "absent" using conventional Affymetrix procedures), but the values for this calcium channel transcript are associated with a very strong cis QTL with an LRS of 79 (LOD = 17). This strong linkage is definitely not due to chance since the probability of the expression data mapping precisely to the location of the parent gene itself is about 10e-16. This indicates a high signal to noise ratio and the detection of significant strain variation of the correct transcript.
-
-The standard error of the mean for the HEIMED data set is computed for 2 to 6 biological replicates. The standard error of such small samples tends to systematically underestimate the population standard error. With n = 2 the underestimate is about 25%, whereas for n = 6 the underestimate is 5%. Gurland and Tripathi (1971) provide a correction and equation for this effect (see Sokal and Rohlf, Biometry, 2nd ed., 1981, p 53 for an equation of the correction factor for small samples of n < 20.) Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the first three batches together. The last batch was processed separately and merged as described below.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing using Biobase affy10 build running under R version 2.7.1, all array data sets were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (FVB/NJ, NOD/LtJ, MOLF/EiJ, C3H/HeJ and BXD24), samples from wild subspecies such as WSB/EiJ, CAST/EiJ, PWD/PhJ, and PWK/PhJ, and knockouts. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. The assumption is that anomolous data are much more likely due to experimental and technical errors than to informative biological variation. Approximately 10% of arrays were discarded.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We reviewed the data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g., 1800) represented the QTL harvest for the full data set. We then dropped a single array from the data set, recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 1750 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs. Values ranged from approximately -90 (good arrays) to +40 (bad arrays). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a method to polish a data set.
-
-During this process we discovered that nearly 20 arrays in the batch 2 had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of high quality.
-
-A third batch of approximately 40 arrays were processed by Yan Jiao and Weikuan Gu in August 2006. These complete data set assembled by Hongqiang Li. This process again included a correction for a batch effect.
-
-For the June 2006 data set Hongqiang Li used a new batch correction method that stabilizes the range of expression in each batch. For each of the three large batches, we extracted the minumum and maximum raw probe expression (CEL file level) value. We then adjusted raw probe values in each batch to have the same range as the first and largest batch (batch 1) using a simple linear interpolation. These procedures generated new correct CEL files which were then used with RMA to generate final probe set estimates.
-
-For the final fourth batch of arrays (Sept 2008) Arthur Centeno and Rob Williams corrected for a systematic difference in probe set expression values between original arrays run in 2005 and 2006 and the new arrays added in 2008 (n = 45 acceptable arrays). This difference is due to unknown technical batch effects that are probably associated with labeling, hybridization, and scanning. We performed a simple correction to normalize values of the new set of arrays to those of the old set (batches 1 through 3). No changes were made to any values of the previous three batches. We corrected only the probe set level (RMA) values and not the CEL files. For this final batch, we corrected for the difference (offset) in probe set expression between the first three batches arrays run in 2005 and 2006 (a total of 174 acceptable arrays) and the new batch (n = 47 acceptable arrays). This difference is due to unknown technical effects that are probably related to various steps in labeling, hybridization, and scanning. The correction was applied as follows: (1) RWW selected 51 high quality arrays with similar expression characteristics (r = 0.97 or better between pairs of arrays) in the old data set (from batches 1, 2, and 3) and 34 high quality arrays in the final batch. RWW used scatterplots of full RMA transcriptome data sets to review many pairs of arrays within these new and old array batches. Strains with retinal degeneration or unusual eye gene expression characteristics were excluded from these selected subsets. The average expression values for each probe set were then computed for both the old and new array subsets. The offset value (old minus new) was added to each probe set across all 47 new arrays. This processes forces the average probe set in the new arrays to be very close to that of the previous arrays.
-
-Table 2: Sample tube ID, strain, original CEL filename, and Affymetrix quality control values. Columns labeled Scale factor, Background Average, Present, Absent, Marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Strain |
- Original CEL |
- Scale factor |
- Background Average |
- Present |
- Absent |
- Marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- Batch Id |
- Used for batch control |
-
-
- | 1 |
- R2595E.1 |
- 129S1/SvImJ |
- R2595E.1.CEL |
- 1.79 |
- 115 |
- 61.00% |
- 37.50% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 2 |
- R2533E.1 |
- 129S1/SvImJ |
- R2533E.1.CEL |
- 2.11 |
- 94 |
- 57.90% |
- 40.50% |
- 1.60% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 3 |
- R0754E.1 |
- A/J |
- R0754E.1.CEL |
- 2.72 |
- 86 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.36 |
- 0.76 |
- 1 |
- Y |
-
-
- | 4 |
- R4521E |
- B6129P2F2N1-Clcn3 |
- R4521E.CEL |
- 4.83 |
- 38.7 |
- 63.30% |
- 35.30% |
- 1.40% |
- 1.25 |
- 0.77 |
- 4 |
- |
-
-
- | 5 |
- R4522E |
- B6129P2F2N1-Clcn3 |
- R4522E.CEL |
- 5.76 |
- 37.36 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.37 |
- 0.83 |
- 4 |
- |
-
-
- | 6 |
- R4523E |
- B6129P2F2N1-Clcn3 |
- R4523E.CEL |
- 4.88 |
- 40.42 |
- 63.90% |
- 34.70% |
- 1.40% |
- 1.27 |
- 0.77 |
- 4 |
- |
-
-
- | 7 |
- R4526E |
- B6129P2F2N1-Gabbr1 |
- R4526E.CEL |
- 3.84 |
- 44.18 |
- 65.00% |
- 33.70% |
- 1.30% |
- 1.34 |
- 0.78 |
- 4 |
- Y |
-
-
- | 8 |
- R4509E |
- B6129P2F2N1-Gabbr1 |
- R4509E.CEL |
- 7.45 |
- 34.76 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.45 |
- 0.83 |
- 4 |
- |
-
-
- | 9 |
- R4510E |
- B6129P2F2N1-Gabbr1 |
- R4510E.CEL |
- 8.44 |
- 37.44 |
- 57.40% |
- 41.10% |
- 1.50% |
- 1.35 |
- 0.83 |
- 4 |
- |
-
-
- | 10 |
- R4511E |
- B6129P2F2N1-Gabbr1 |
- R4511E.CEL |
- 5.91 |
- 42.02 |
- 61.40% |
- 37.20% |
- 1.40% |
- 1.41 |
- 0.83 |
- 4 |
- |
-
-
- | 11 |
- R4524E |
- B6129P2F2N1-Gabbr1 |
- R4524E.CEL |
- 5.49 |
- 42.34 |
- 62.40% |
- 36.20% |
- 1.40% |
- 1.29 |
- 0.78 |
- 4 |
- Y |
-
-
- | 12 |
- R4525E |
- B6129P2F2N1-Gabbr1 |
- R4525E.CEL |
- 4.69 |
- 41.3 |
- 63.10% |
- 35.50% |
- 1.40% |
- 1.27 |
- 0.8 |
- 4 |
- Y |
-
-
- | 13 |
- R4515E |
- B6129P2F2N1-Gabra1 |
- R4515E.CEL |
- 5.75 |
- 41.76 |
- 62.80% |
- 35.80% |
- 1.40% |
- 1.41 |
- 0.81 |
- 4 |
- Y |
-
-
- | 14 |
- R4516E |
- B6129P2F2N1-Gabra1 |
- R4516E.CEL |
- 7.07 |
- 40.73 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.32 |
- 0.87 |
- 4 |
- Y |
-
-
- | 15 |
- R4517E |
- B6129P2F2N1-Gabra1 |
- R4517E.CEL |
- 5.45 |
- 38.09 |
- 62.70% |
- 35.80% |
- 1.40% |
- 1.34 |
- 0.82 |
- 4 |
- Y |
-
-
- | 16 |
- R4512E |
- B6129P2F2N1-Gnb5 |
- R4512E.CEL |
- 6.56 |
- 38.02 |
- 59.90% |
- 38.70% |
- 1.50% |
- 1.33 |
- 0.83 |
- 4 |
- |
-
-
- | 17 |
- R4513E |
- B6129P2F2N1-Gnb5 |
- R4513E.CEL |
- 4.15 |
- 41.6 |
- 63.40% |
- 35.10% |
- 1.50% |
- 1.34 |
- 0.82 |
- 4 |
- |
-
-
- | 18 |
- R4514E |
- B6129P2F2N1-Gnb5 |
- R4514E.CEL |
- 5.86 |
- 39.2 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.34 |
- 0.81 |
- 4 |
- |
-
-
- | 19 |
- R4518E |
- B6129P2F2N1-Gpr19 |
- R4518E.CEL |
- 5.58 |
- 38.9 |
- 62.60% |
- 36.00% |
- 1.30% |
- 1.39 |
- 0.79 |
- 4 |
- Y |
-
-
- | 20 |
- R4519E |
- B6129P2F2N1-Gpr19 |
- R4519E.CEL |
- 5.95 |
- 41.91 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.35 |
- 0.84 |
- 4 |
- Y |
-
-
- | 21 |
- R2601E.1 |
- B6D2F1 |
- R2601E.1.CEL |
- 2.55 |
- 92 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.44 |
- 0.78 |
- 1 |
- Y |
-
-
- | 22 |
- R2602E.1 |
- B6D2F1 |
- R2602E.1.CEL |
- 2.6 |
- 84 |
- 59.70% |
- 38.80% |
- 1.50% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 23 |
- R1676E.1 |
- BALB/cByJ |
- R1676E.1.CEL |
- 2.69 |
- 98 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.46 |
- 0.74 |
- 1 |
- |
-
-
- | 24 |
- R1672E.1 |
- BALB/cByJ |
- R1672E.1.CEL |
- 2.22 |
- 111 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 25 |
- R4530E |
- BALB/cJ |
- R4530E.CEL |
- 6.37 |
- 37.53 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.3 |
- 0.84 |
- 4 |
- Y |
-
-
- | 26 |
- R4529E |
- BALB/cJ |
- R4529E.CEL |
- 5.71 |
- 41.33 |
- 60.50% |
- 38.00% |
- 1.50% |
- 1.48 |
- 0.8 |
- 4 |
- Y |
-
-
- | 27 |
- R2704E.2 |
- BXD1 |
- R2704E.2.CEL |
- 2.066 |
- 139.61 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 28 |
- R2707E.3 |
- BXD1 |
- R2707E.3.CEL |
- 1 |
- 80 |
- 56.40% |
- 42.10% |
- 1.50% |
- 1.43 |
- 0.79 |
- 3 |
- |
-
-
- | 29 |
- R1231E.2 |
- BXD2 |
- R1231E.2.CEL |
- 2.197 |
- 138.73 |
- 57.30% |
- 41.30% |
- 1.40% |
- 1.41 |
- 0.77 |
- 2 |
- |
-
-
- | 30 |
- R2598E.1 |
- BXD2 |
- R2598E.1.CEL |
- 1.99 |
- 106 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 31 |
- R2591E.1 |
- BXD5 |
- R2591E.1.CEL |
- 1.7 |
- 136 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.33 |
- 0.78 |
- 1 |
- Y |
-
-
- | 32 |
- R2714E.2 |
- BXD5 |
- R2714E.2.CEL |
- 1.404 |
- 144.35 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 33 |
- R2570E.1 |
- BXD6 |
- R2570E.1.CEL |
- 1.99 |
- 87 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.46 |
- 0.76 |
- 1 |
- Y |
-
-
- | 34 |
- R2694E.2 |
- BXD6 |
- R2694E.2.CEL |
- 1.983 |
- 97.23 |
- 61.60% |
- 37.10% |
- 1.30% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 35 |
- R2538E.1 |
- BXD8 |
- R2538E.1.CEL |
- 1.91 |
- 102 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.52 |
- 0.79 |
- 1 |
- Y |
-
-
- | 36 |
- R2709E.2 |
- BXD8 |
- R2709E.2.CEL |
- 1.99 |
- 99.79 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.42 |
- 0.76 |
- 2 |
- |
-
-
- | 37 |
- R2708E.2 |
- BXD9 |
- R2708E.2.CEL |
- 1.966 |
- 126.46 |
- 57.70% |
- 40.70% |
- 1.50% |
- 1.4 |
- 0.84 |
- 2 |
- |
-
-
- | 38 |
- R2569E.1 |
- BXD9 |
- R2569E.1.CEL |
- 1.75 |
- 87 |
- 55.10% |
- 43.40% |
- 1.50% |
- 2.82 |
- 3.14 |
- 1 |
- |
-
-
- | 39 |
- R2581E.1 |
- BXD11 |
- R2581E.1.CEL |
- 1.94 |
- 89 |
- 62.10% |
- 36.40% |
- 1.60% |
- 1.55 |
- 0.81 |
- 1 |
- Y |
-
-
- | 40 |
- R2612E.2 |
- BXD11 |
- R2612E.2.CEL |
- 1.83 |
- 142.03 |
- 58.20% |
- 40.50% |
- 1.40% |
- 1.78 |
- 0.81 |
- 2 |
- |
-
-
- | 41 |
- R2742E.2 |
- BXD12 |
- R2742E.2.CEL |
- 2.127 |
- 134.14 |
- 57.00% |
- 41.60% |
- 1.40% |
- 1.64 |
- 0.78 |
- 2 |
- |
-
-
- | 42 |
- R2543E.1 |
- BXD12 |
- R2543E.1.CEL |
- 1.61 |
- 118 |
- 58.60% |
- 39.90% |
- 1.60% |
- 1.43 |
- 0.77 |
- 1 |
- Y |
-
-
- | 43 |
- R2586E.1 |
- BXD13 |
- R2586E.1.CEL |
- 2.01 |
- 74 |
- 56.40% |
- 42.00% |
- 1.60% |
- 2.85 |
- 3.81 |
- 1 |
- |
-
-
- | 44 |
- R877E.2 |
- BXD13 |
- R877E.2.CEL |
- 1.558 |
- 125.63 |
- 61.20% |
- 37.50% |
- 1.20% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 45 |
- R2557E.1 |
- BXD14 |
- R2557E.1.CEL |
- 1.83 |
- 99 |
- 62.50% |
- 36.10% |
- 1.40% |
- 1.31 |
- 0.78 |
- 1 |
- Y |
-
-
- | 46 |
- R1128E.2 |
- BXD14 |
- R1128E.2.CEL |
- 1.91 |
- 115 |
- 59.90% |
- 38.80% |
- 1.40% |
- 1.2 |
- 0.82 |
- 1 |
- Y |
-
-
- | 47 |
- R2701E.3 |
- BXD15 |
- R2701E.3.CEL |
- 1 |
- 88 |
- 60.60% |
- 37.90% |
- 1.40% |
- 1.5 |
- 0.77 |
- 3 |
- |
-
-
- | 48 |
- R2716E.2 |
- BXD15 |
- R2716E.2.CEL |
- 2.015 |
- 150.83 |
- 56.40% |
- 42.10% |
- 1.60% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 49 |
- R2711E.2 |
- BXD16 |
- R2711E.2.CEL |
- 1.953 |
- 118.53 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 50 |
- R2567E.1 |
- BXD16 |
- R2567E.1.CEL |
- 2.24 |
- 82 |
- 56.70% |
- 41.60% |
- 1.70% |
- 1.37 |
- 0.75 |
- 1 |
- |
-
-
- | 51 |
- R2720E.2 |
- BXD18 |
- R2720E.2.CEL |
- 2.32 |
- 99.93 |
- 59.50% |
- 39.00% |
- 1.50% |
- 1.33 |
- 0.77 |
- 2 |
- |
-
-
- | 52 |
- R2559E.1 |
- BXD18 |
- R2559E.1.CEL |
- 1.65 |
- 104 |
- 60.80% |
- 37.70% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 53 |
- R2560E.1 |
- BXD19 |
- R2560E.1.CEL |
- 1.79 |
- 98 |
- 60.90% |
- 37.50% |
- 1.60% |
- 1.35 |
- 0.8 |
- 1 |
- Y |
-
-
- | 54 |
- R2713E.2 |
- BXD19 |
- R2713E.2.CEL |
- 1.67 |
- 120.82 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 55 |
- R2584E.1 |
- BXD20 |
- R2584E.1.CEL |
- 2.07 |
- 84 |
- 59.30% |
- 39.10% |
- 1.60% |
- 1.4 |
- 0.76 |
- 1 |
- Y |
-
-
- | 56 |
- R2731E.2 |
- BXD20 |
- R2731E.2.CEL |
- 1.825 |
- 147 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.4 |
- 0.8 |
- 2 |
- |
-
-
- | 57 |
- R2702E.2 |
- BXD21 |
- R2702E.2.CEL |
- 1.811 |
- 128.65 |
- 59.40% |
- 39.10% |
- 1.40% |
- 1.26 |
- 0.8 |
- 2 |
- |
-
-
- | 58 |
- R2541E2.1 |
- BXD21 |
- R2541E2.1.CEL |
- 2.63 |
- 125 |
- 56.00% |
- 42.40% |
- 1.50% |
- 1.29 |
- 0.78 |
- 1 |
- |
-
-
- | 59 |
- R2553E.1 |
- BXD22 |
- R2553E.1.CEL |
- 1.95 |
- 111 |
- 59.90% |
- 38.50% |
- 1.50% |
- 1.28 |
- 0.76 |
- 1 |
- Y |
-
-
- | 60 |
- R2700E.2 |
- BXD22 |
- R2700E.2.CEL |
- 1.858 |
- 102.96 |
- 61.50% |
- 37.10% |
- 1.30% |
- 1.48 |
- 0.79 |
- 2 |
- |
-
-
- | 61 |
- R2558E-2.1 |
- BXD23 |
- R2558E-2.1.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 62 |
- R1086E.2 |
- BXD23 |
- R1086E.2.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 63 |
- R2719E.2 |
- BXD24 |
- R2719E.2.CEL |
- 1.47 |
- 140.38 |
- 61.50% |
- 37.20% |
- 1.30% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 64 |
- R2589E2.1 |
- BXD24 |
- R2589E2.1.CEL |
- 2.61 |
- 112 |
- 57.50% |
- 40.90% |
- 1.60% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 65 |
- R2573E-2.1 |
- BXD25 |
- R2573E-2.1.CEL |
- 3.15 |
- 72 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.77 |
- 0.97 |
- 1 |
- |
-
-
- | 66 |
- R2683E.2 |
- BXD25 |
- R2683E.2.CEL |
- 1.777 |
- 115.64 |
- 58.30% |
- 40.30% |
- 1.40% |
- 2.01 |
- 0.79 |
- 2 |
- |
-
-
- | 67 |
- R2703E.2 |
- BXD27 |
- R2703E.2.CEL |
- 1.263 |
- 134.78 |
- 62.60% |
- 36.10% |
- 1.40% |
- 1.44 |
- 0.78 |
- 2 |
- |
-
-
- | 68 |
- R2729E.3 |
- BXD27 |
- R2729E.3.CEL |
- 1 |
- 87 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.56 |
- 0.84 |
- 3 |
- Y |
-
-
- | 69 |
- R2562E.3 |
- BXD28 |
- R2562E.3.CEL |
- 1.65 |
- 116 |
- 59.90% |
- 38.40% |
- 1.70% |
- 1.37 |
- 0.79 |
- 3 |
- Y |
-
-
- | 70 |
- R2721E.2 |
- BXD28 |
- R2721E.2.CEL |
- 2.065 |
- 157.39 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 71 |
- R2561E.3 |
- BXD29 |
- R2561E.3.CEL |
- 1 |
- 77 |
- 53.30% |
- 45.40% |
- 1.40% |
- 3.36 |
- 19.66 |
- 3 |
- |
-
-
- | 72 |
- R1258E.2 |
- BXD31 |
- R1258E.2.CEL |
- 2.063 |
- 117.09 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.54 |
- 0.78 |
- 2 |
- |
-
-
- | 73 |
- R2597E.1 |
- BXD31 |
- R2597E.1.CEL |
- 2.37 |
- 94 |
- 60.30% |
- 38.30% |
- 1.50% |
- 1.34 |
- 0.77 |
- 1 |
- Y |
-
-
- | 74 |
- R2563E.1 |
- BXD32 |
- R2563E.1.CEL |
- 1.55 |
- 102 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.5 |
- 0.8 |
- 1 |
- |
-
-
- | 75 |
- R1216E.2 |
- BXD32 |
- R1216E.2.CEL |
- 2.23 |
- 111.99 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.35 |
- 0.79 |
- 2 |
- |
-
-
- | 76 |
- R2542E.1 |
- BXD33 |
- R2542E.1.CEL |
- 2.13 |
- 97 |
- 56.50% |
- 41.80% |
- 1.60% |
- 1.91 |
- 0.93 |
- 1 |
- |
-
-
- | 77 |
- R857E.2 |
- BXD33 |
- R857E.2.CEL |
- 1.737 |
- 113.98 |
- 61.90% |
- 36.70% |
- 1.30% |
- 1.6 |
- 0.77 |
- 2 |
- |
-
-
- | 78 |
- R1451E.2 |
- BXD34 |
- R1451E.2.CEL |
- 1.843 |
- 140.05 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.42 |
- 0.81 |
- 2 |
- Y |
-
-
- | 79 |
- R2585E.1 |
- BXD34 |
- R2585E.1.CEL |
- 2.64 |
- 75 |
- 58.30% |
- 40.00% |
- 1.70% |
- 1.25 |
- 0.77 |
- 1 |
- |
-
-
- | 80 |
- R2698E.3 |
- BXD36 |
- R2698E.3.CEL |
- 1 |
- 86 |
- 59.70% |
- 39.00% |
- 1.30% |
- 1.46 |
- 0.78 |
- 3 |
- |
-
-
- | 81 |
- R2705E.3 |
- BXD36 |
- R2705E.3.CEL |
- 1 |
- 86 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.46 |
- 0.77 |
- 3 |
- |
-
-
- | 82 |
- R2710E.2 |
- BXD38 |
- R2710E.2.CEL |
- 2.112 |
- 122.1 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.37 |
- 0.78 |
- 2 |
- |
-
-
- | 83 |
- R2532E.1 |
- BXD38 |
- R2532E.1.CEL |
- 2.04 |
- 94 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.37 |
- 0.8 |
- 1 |
- Y |
-
-
- | 84 |
- R2574E.1 |
- BXD39 |
- R2574E.1.CEL |
- 1.98 |
- 91 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.39 |
- 0.78 |
- 1 |
- |
-
-
- | 85 |
- R2695E.2 |
- BXD39 |
- R2695E.2.CEL |
- 1.638 |
- 122.7 |
- 60.80% |
- 37.80% |
- 1.50% |
- 1.42 |
- 0.8 |
- 2 |
- |
-
-
- | 86 |
- R2699E.2 |
- BXD40 |
- R2699E.2.CEL |
- 1.827 |
- 105.23 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 87 |
- R2590E.1 |
- BXD40 |
- R2590E.1.CEL |
- 2.71 |
- 77 |
- 59.10% |
- 39.30% |
- 1.50% |
- 1.4 |
- 0.77 |
- 1 |
- Y |
-
-
- | 88 |
- R2696E.2 |
- BXD42 |
- R2696E.2.CEL |
- 1.622 |
- 118.95 |
- 62.00% |
- 36.60% |
- 1.50% |
- 1.53 |
- 0.79 |
- 2 |
- |
-
-
- | 89 |
- R2596E.1 |
- BXD42 |
- R2596E.1.CEL |
- 2.63 |
- 108 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 90 |
- R994E.2 |
- BXD43 |
- R994E.2.CEL |
- 1.966 |
- 113.12 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.66 |
- 0.8 |
- 2 |
- |
-
-
- | 91 |
- R2607E.1 |
- BXD43 |
- R2607E.1.CEL |
- 2.43 |
- 115 |
- 58.60% |
- 40.00% |
- 1.40% |
- 1.31 |
- 0.76 |
- 1 |
- Y |
-
-
- | 92 |
- R2594E.1 |
- BXD44 |
- R2594E.1.CEL |
- 1.77 |
- 117 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.35 |
- 0.85 |
- 1 |
- |
-
-
- | 93 |
- R2610E.2 |
- BXD44 |
- R2610E.2.CEL |
- 1.814 |
- 142.91 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.35 |
- 0.8 |
- 2 |
- |
-
-
- | 94 |
- R2732E.2 |
- BXD45 |
- R2732E.2.CEL |
- 2.154 |
- 122.45 |
- 56.50% |
- 42.10% |
- 1.40% |
- 1.8 |
- 0.83 |
- 2 |
- |
-
-
- | 95 |
- R2592E.1 |
- BXD45 |
- R2592E.1.CEL |
- 1.85 |
- 106 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.43 |
- 0.85 |
- 1 |
- Y |
-
-
- | 96 |
- R967E.2 |
- BXD48 |
- R967E.2.CEL |
- 1.948 |
- 130.95 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.63 |
- 0.81 |
- 2 |
- |
-
-
- | 97 |
- R2606E.1 |
- BXD48 |
- R2606E.1.CEL |
- 2.56 |
- 106 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.35 |
- 0.83 |
- 1 |
- Y |
-
-
- | 98 |
- R2933E.3 |
- BXD50 |
- R2933E.3.CEL |
- 1 |
- 72 |
- 52.90% |
- 45.60% |
- 1.50% |
- 2.45 |
- 0.98 |
- 3 |
- |
-
-
- | 99 |
- R2937E.3 |
- BXD50 |
- R2937E.3.CEL |
- 1 |
- 89 |
- 56.90% |
- 41.60% |
- 1.40% |
- 1.81 |
- 0.82 |
- 3 |
- |
-
-
- | 100 |
- R2603E.1 |
- BXD51 |
- R2603E.1.CEL |
- 2.49 |
- 115 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.24 |
- 0.79 |
- 1 |
- |
-
-
- | 101 |
- R1042E.2 |
- BXD51 |
- R1042E.2.CEL |
- 2.352 |
- 104.12 |
- 58.70% |
- 39.90% |
- 1.40% |
- 1.53 |
- 0.82 |
- 2 |
- |
-
-
- | 102 |
- R2980E.3 |
- BXD55 |
- R2980E.3.CEL |
- 1 |
- 82 |
- 56.90% |
- 41.70% |
- 1.50% |
- 1.77 |
- 0.84 |
- 3 |
- |
-
-
- | 103 |
- R2690E.2 |
- BXD55 |
- R2690E.2.CEL |
- 1.887 |
- 164.01 |
- 56.10% |
- 42.30% |
- 1.60% |
- 1.43 |
- 0.8 |
- 2 |
- |
-
-
- | 104 |
- R4176E |
- BXD56 |
- R4176E.CEL |
- 4.75 |
- 43.08 |
- 63.00% |
- 35.60% |
- 1.30% |
- 1.39 |
- 0.81 |
- 4 |
- Y |
-
-
- | 105 |
- R4175E |
- BXD56 |
- R4175E.CEL |
- 6 |
- 38.49 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.47 |
- 0.81 |
- 4 |
- Y |
-
-
- | 106 |
- R1006E.3 |
- BXD60 |
- R1006E.3.CEL |
- 1 |
- 98 |
- 54.90% |
- 43.70% |
- 1.50% |
- 2.7 |
- 0.86 |
- 3 |
- |
-
-
- | 107 |
- R2725E.2 |
- BXD60 |
- R2725E.2.CEL |
- 1.551 |
- 148.01 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 108 |
- R1074E.3 |
- BXD60 |
- R1074E.3.CEL |
- 1 |
- 118 |
- 55.50% |
- 43.10% |
- 1.40% |
- 1.96 |
- 0.81 |
- 3 |
- |
-
-
- | 109 |
- R2534E2.1 |
- BXD61 |
- R2534E2.1.CEL |
- 2.47 |
- 118 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.42 |
- 0.79 |
- 1 |
- |
-
-
- | 110 |
- R2684E.2 |
- BXD61 |
- R2684E.2.CEL |
- 2.01 |
- 131.03 |
- 57.00% |
- 41.50% |
- 1.50% |
- 1.34 |
- 0.78 |
- 2 |
- |
-
-
- | 111 |
- R1107E.3 |
- BXD62 |
- R1107E.3.CEL |
- 1 |
- 83 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.43 |
- 0.93 |
- 3 |
- |
-
-
- | 112 |
- R2681E.2 |
- BXD62 |
- R2681E.2.CEL |
- 2.086 |
- 148.24 |
- 57.20% |
- 41.30% |
- 1.50% |
- 1.29 |
- 0.81 |
- 2 |
- |
-
-
- | 113 |
- R965E.3 |
- BXD62 |
- R965E.3.CEL |
- 1 |
- 93.55 |
- 53.30% |
- 45.20% |
- 1.50% |
- 3.11 |
- 0.94 |
- 3 |
- |
-
-
- | 114 |
- R1425E.2 |
- BXD63 |
- R1425E.2.CEL |
- 1.7 |
- 136 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.43 |
- 0.82 |
- 2 |
- |
-
-
- | 115 |
- R2576E.3 |
- BXD63 |
- R2576E.3.CEL |
- 1 |
- 84 |
- 61.30% |
- 37.40% |
- 1.40% |
- 1.48 |
- 0.76 |
- 3 |
- |
-
-
- | 116 |
- R943E-2.2 |
- BXD64 |
- R943E-2.2.CEL |
- 1.591 |
- 141.34 |
- 60.10% |
- 38.40% |
- 1.50% |
- 1.32 |
- 0.76 |
- 2 |
- |
-
-
- | 117 |
- R2611E.1 |
- BXD64 |
- R2611E.1.CEL |
- 2.29 |
- 92 |
- 58.00% |
- 40.50% |
- 1.50% |
- 1.57 |
- 1.06 |
- 1 |
- |
-
-
- | 118 |
- R2689E.2 |
- BXD65 |
- R2689E.2.CEL |
- 1.721 |
- 142.44 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.38 |
- 0.76 |
- 2 |
- |
-
-
- | 119 |
- R2583E.1 |
- BXD65 |
- R2583E.1.CEL |
- 2.49 |
- 70 |
- 56.90% |
- 41.50% |
- 1.60% |
- 1.67 |
- 1.01 |
- 1 |
- |
-
-
- | 120 |
- R2728E.2 |
- BXD66 |
- R2728E.2.CEL |
- 1.714 |
- 137.45 |
- 59.40% |
- 39.00% |
- 1.60% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 121 |
- R2536E2.1 |
- BXD66 |
- R2536E2.1.CEL |
- 2.74 |
- 109 |
- 56.10% |
- 42.30% |
- 1.70% |
- 1.28 |
- 0.79 |
- 1 |
- |
-
-
- | 122 |
- R1207E.2 |
- BXD66 |
- R1207E.2.CEL |
- 1.681 |
- 136.86 |
- 60.40% |
- 38.10% |
- 1.50% |
- 1.45 |
- 0.77 |
- 2 |
- |
-
-
- | 123 |
- R1192E.2 |
- BXD67 |
- R1192E.2.CEL |
- 2.126 |
- 123.37 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 124 |
- R2727E.3 |
- BXD67 |
- R2727E.3.CEL |
- 1 |
- 82.55 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.97 |
- 0.87 |
- 2 |
- |
-
-
- | 125 |
- R2691E.3 |
- BXD67 |
- R2691E.3.CEL |
- 1 |
- 90 |
- 54.80% |
- 43.80% |
- 1.50% |
- 2.61 |
- 0.81 |
- 3 |
- |
-
-
- | 126 |
- R2551E.1 |
- BXD68 |
- R2551E.1.CEL |
- 2.49 |
- 92 |
- 54.30% |
- 44.10% |
- 1.60% |
- 2.91 |
- 1.55 |
- 1 |
- |
-
-
- | 127 |
- R2726E.2 |
- BXD68 |
- R2726E.2.CEL |
- 1.811 |
- 153.09 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.39 |
- 0.78 |
- 2 |
- |
-
-
- | 128 |
- R2593E.1 |
- BXD69 |
- R2593E.1.CEL |
- 1.67 |
- 128 |
- 59.20% |
- 39.50% |
- 1.30% |
- 1.47 |
- 0.92 |
- 1 |
- Y |
-
-
- | 129 |
- R975E.2 |
- BXD70 |
- R975E.2.CEL |
- 1.841 |
- 137.97 |
- 58.00% |
- 40.50% |
- 1.40% |
- 1.36 |
- 0.79 |
- 2 |
- |
-
-
- | 130 |
- R2537E2.1 |
- BXD70 |
- R2537E2.1.CEL |
- 2.93 |
- 99 |
- 58.00% |
- 40.50% |
- 1.60% |
- 1.29 |
- 0.75 |
- 1 |
- |
-
-
- | 131 |
- R4531E |
- BXD71 |
- R4531E.CEL |
- 4.77 |
- 43.48 |
- 62.40% |
- 36.30% |
- 1.40% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 132 |
- R4532E |
- BXD71 |
- R4532E.CEL |
- 5.89 |
- 40.68 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.24 |
- 0.79 |
- 4 |
- Y |
-
-
- | 133 |
- R2779E.2 |
- BXD73 |
- R2779E.2.CEL |
- 1.746 |
- 121.11 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 134 |
- R3024E.3 |
- BXD73 |
- R3024E.3.CEL |
- 1 |
- 78.05 |
- 51.70% |
- 46.60% |
- 1.70% |
- 2.3 |
- 0.94 |
- 3 |
- |
-
-
- | 135 |
- R2565E.1 |
- BXD75 |
- R2565E.1.CEL |
- 1.79 |
- 102 |
- 58.00% |
- 40.50% |
- 1.50% |
- 2.31 |
- 3.47 |
- 1 |
- |
-
-
- | 136 |
- R1397E-re.2 |
- BXD75 |
- R1397E-re.2.CEL |
- 1.449 |
- 189.71 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 137 |
- R2687E.3 |
- BXD77 |
- R2687E.3.CEL |
- 1 |
- 80 |
- 58.00% |
- 40.60% |
- 1.40% |
- 1.57 |
- 0.8 |
- 3 |
- Y |
-
-
- | 138 |
- R2717E.2 |
- BXD77 |
- R2717E.2.CEL |
- 1.797 |
- 84.43 |
- 61.60% |
- 36.90% |
- 1.40% |
- 1.49 |
- 0.76 |
- 2 |
- |
-
-
- | 139 |
- R1421E.3 |
- BXD77 |
- R1421E.3.CEL |
- 1 |
- 94 |
- 52.40% |
- 46.20% |
- 1.40% |
- 2.29 |
- 0.82 |
- 3 |
- |
-
-
- | 140 |
- R2579E.1 |
- BXD80 |
- R2579E.1.CEL |
- 2.42 |
- 72 |
- 59.20% |
- 39.40% |
- 1.50% |
- 1.73 |
- 0.82 |
- 1 |
- |
-
-
- | 141 |
- R2686E.2 |
- BXD80 |
- R2686E.2.CEL |
- 2.342 |
- 119.63 |
- 56.00% |
- 42.60% |
- 1.50% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 142 |
- R2956E.3 |
- BXD83 |
- R2956E.3.CEL |
- 1 |
- 84 |
- 55.40% |
- 43.20% |
- 1.40% |
- 1.39 |
- 0.84 |
- 3 |
- |
-
-
- | 143 |
- R2960E.3 |
- BXD83 |
- R2960E.3.CEL |
- 1 |
- 80 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.5 |
- 0.82 |
- 3 |
- Y |
-
-
- | 144 |
- R2922E.3 |
- BXD84 |
- R2922E.3.CEL |
- 1 |
- 91 |
- 57.80% |
- 40.80% |
- 1.50% |
- 1.47 |
- 0.83 |
- 3 |
- Y |
-
-
- | 145 |
- R2895E.3 |
- BXD84 |
- R2895E.3.CEL |
- 1 |
- 75 |
- 58.30% |
- 40.20% |
- 1.50% |
- 1.56 |
- 0.77 |
- 3 |
- Y |
-
-
- | 146 |
- R2692E.2 |
- BXD85 |
- R2692E.2.CEL |
- 1.423 |
- 160.87 |
- 60.20% |
- 38.30% |
- 1.40% |
- 1.46 |
- 0.79 |
- 2 |
- |
-
-
- | 147 |
- R2715E.2 |
- BXD85 |
- R2715E.2.CEL |
- 1.488 |
- 142.6 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.5 |
- 0.78 |
- 2 |
- |
-
-
- | 148 |
- R1405E.2 |
- BXD86 |
- R1405E.2.CEL |
- 2.351 |
- 119.34 |
- 56.40% |
- 42.20% |
- 1.40% |
- 1.64 |
- 0.81 |
- 2 |
- |
-
-
- | 149 |
- R1225E.3 |
- BXD86 |
- R1225E.3.CEL |
- 1 |
- 71 |
- 53.90% |
- 44.60% |
- 1.40% |
- 3.2 |
- 1.61 |
- 3 |
- |
-
-
- | 150 |
- R2724E.2 |
- BXD87 |
- R2724E.2.CEL |
- 1.906 |
- 113.71 |
- 60.70% |
- 37.90% |
- 1.40% |
- 1.45 |
- 0.79 |
- 2 |
- |
-
-
- | 151 |
- R2540E.1 |
- BXD87 |
- R2540E.1.CEL |
- 2.33 |
- 93 |
- 61.10% |
- 37.40% |
- 1.40% |
- 1.22 |
- 0.81 |
- 1 |
- Y |
-
-
- | 152 |
- R1433E.2 |
- BXD89 |
- R1433E.2.CEL |
- 1 |
- 2.241 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.41 |
- 0.78 |
- 2 |
- |
-
-
- | 153 |
- R2546E.1 |
- BXD89 |
- R2546E.1.CEL |
- 1.99 |
- 96 |
- 58.60% |
- 39.70% |
- 1.70% |
- 1.47 |
- 0.78 |
- 1 |
- |
-
-
- | 154 |
- R2578E2.1 |
- BXD90 |
- R2578E2.1.CEL |
- 2.79 |
- 92 |
- 58.60% |
- 39.80% |
- 1.60% |
- 1.52 |
- 0.77 |
- 1 |
- Y |
-
-
- | 155 |
- R859E.2 |
- BXD90 |
- R859E.2.CEL |
- 1.847 |
- 152.22 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.36 |
- 0.77 |
- 2 |
- |
-
-
- | 156 |
- R2682E.2 |
- BXD92 |
- R2682E.2.CEL |
- 1.547 |
- 156.31 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.37 |
- 0.77 |
- 2 |
- |
-
-
- | 157 |
- R1388E.3 |
- BXD92 |
- R1388E.3.CEL |
- 1 |
- 63 |
- 60.00% |
- 38.60% |
- 1.40% |
- 1.85 |
- 1.03 |
- 3 |
- |
-
-
- | 158 |
- R1322E.3 |
- BXD92 |
- R1322E.3.CEL |
- 1 |
- 80 |
- 55.90% |
- 42.60% |
- 1.50% |
- 1.75 |
- 0.74 |
- 3 |
- |
-
-
- | 159 |
- R2733E.2 |
- BXD96 |
- R2733E.2.CEL |
- 1.7 |
- 113.99 |
- 62.10% |
- 36.60% |
- 1.30% |
- 1.4 |
- 0.78 |
- 2 |
- |
-
-
- | 160 |
- R2554E.1 |
- BXD96 |
- R2554E.1.CEL |
- 2.18 |
- 93 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 161 |
- R2649E.2 |
- BXD97 |
- R2649E.2.CEL |
- 2.343 |
- 119.04 |
- 57.50% |
- 41.20% |
- 1.40% |
- 1.53 |
- 0.8 |
- 2 |
- |
-
-
- | 162 |
- R2577E.1 |
- BXD97 |
- R2577E.1.CEL |
- 2.07 |
- 77 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.87 |
- 1.29 |
- 1 |
- |
-
-
- | 163 |
- R2645E.3 |
- BXD98 |
- R2645E.3.CEL |
- 1 |
- 88 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.59 |
- 0.81 |
- 3 |
- Y |
-
-
- | 164 |
- R2688E.2 |
- BXD98 |
- R2688E.2.CEL |
- 1.772 |
- 145.24 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.48 |
- 0.81 |
- 2 |
- |
-
-
- | 165 |
- R4533E |
- BXD99 |
- R4533E.CEL |
- 1 |
- 37.69 |
- 60.30% |
- 38.20% |
- 1.40% |
- 1.33 |
- 0.89 |
- 4 |
- Y |
-
-
- | 166 |
- R4534E |
- BXD99 |
- R4534E.CEL |
- 5.69 |
- 36.62 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.16 |
- 0.8 |
- 4 |
- Y |
-
-
- | 167 |
- R2885E.3 |
- BXSB/MpJ |
- R2885E.3.CEL |
- 1 |
- 76 |
- 58.10% |
- 40.60% |
- 1.30% |
- 1.88 |
- 1.06 |
- 3 |
- |
-
-
- | 168 |
- R2883E.3 |
- BXSB/MpJ |
- R2883E.3.CEL |
- 1 |
- 71 |
- 56.40% |
- 42.00% |
- 1.50% |
- 1.59 |
- 0.84 |
- 3 |
- Y |
-
-
- | 169 |
- R1700E.1 |
- C3H/HeJ |
- R1700E.1.CEL |
- 2.98 |
- 69 |
- 60.80% |
- 37.90% |
- 1.40% |
- 1.48 |
- 0.78 |
- 1 |
- |
-
-
- | 170 |
- R1704E.1 |
- C3H/HeJ |
- R1704E.1.CEL |
- 2.58 |
- 88 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.38 |
- 0.84 |
- 1 |
- |
-
-
- | 171 |
- R2605E.1 |
- C57BL/6J |
- R2605E.1.CEL |
- 1.82 |
- 131 |
- 60.50% |
- 38.20% |
- 1.30% |
- 1.32 |
- 0.8 |
- 1 |
- Y |
-
-
- | 172 |
- R0871E |
- C57BL/6J |
- R0871E.CEL |
- 6.24 |
- 37.38 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.41 |
- 0.8 |
- 4 |
- Y |
-
-
- | 173 |
- R0872E.1 |
- C57BL/6J |
- R0872E.1.CEL |
- 3.13 |
- 89 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 174 |
- R0872E |
- C57BL/6J |
- R0872E.CEL |
- 3.128 |
- 88.58 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- |
-
-
- | 175 |
- R4507E |
- C57BL/6J-Nyx |
- R4507E.CEL |
- 8.13 |
- 37.5 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.32 |
- 0.8 |
- 4 |
- Y |
-
-
- | 176 |
- R4508E |
- C57BL/6J-Nyx |
- R4508E.CEL |
- 6.33 |
- 37.26 |
- 60.90% |
- 37.80% |
- 1.30% |
- 1.24 |
- 0.82 |
- 4 |
- Y |
-
-
- | 177 |
- R4505E |
- C57BL/6J-Rpe65 |
- R4505E.CEL |
- 5.98 |
- 37.48 |
- 61.80% |
- 36.80% |
- 1.40% |
- 1.45 |
- 0.85 |
- 4 |
- Y |
-
-
- | 178 |
- R4506E |
- C57BL/6J-Rpe65 |
- R4506E.CEL |
- 6.94 |
- 37.9 |
- 61.10% |
- 37.50% |
- 1.30% |
- 1.5 |
- 0.83 |
- 4 |
- Y |
-
-
- | 179 |
- R4535E |
- C57BLKS/J |
- R4535E.CEL |
- 6.59 |
- 37.28 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.26 |
- 0.83 |
- 4 |
- Y |
-
-
- | 180 |
- R4536E |
- C57BLKS/J |
- R4536E.CEL |
- 1 |
- 40.71 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.25 |
- 0.77 |
- 4 |
- Y |
-
-
- | 181 |
- R2564E.1 |
- CAST/EiJ |
- R2564E.1.CEL |
- 1.94 |
- 89 |
- 58.50% |
- 39.90% |
- 1.60% |
- 1.6 |
- 0.77 |
- 1 |
- |
-
-
- | 182 |
- R2580E.1 |
- CAST/EiJ |
- R2580E.1.CEL |
- 2.09 |
- 95 |
- 58.20% |
- 40.10% |
- 1.70% |
- 1.4 |
- 0.76 |
- 1 |
- |
-
-
- | 183 |
- R4537E |
- CBA/CaJ |
- R4537E.CEL |
- 1 |
- 38.45 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.63 |
- 0.82 |
- 4 |
- Y |
-
-
- | 184 |
- R4538E |
- CBA/CaJ |
- R4538E.CEL |
- 5.89 |
- 39.18 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.45 |
- 0.8 |
- 4 |
- Y |
-
-
- | 185 |
- R4539E |
- CZECHII/EiJ |
- R4539E.CEL |
- 7.73 |
- 37.1 |
- 58.30% |
- 40.10% |
- 1.50% |
- 1.7 |
- 0.95 |
- 4 |
- Y |
-
-
- | 186 |
- R4540E |
- CZECHII/EiJ |
- R4540E.CEL |
- 11.04 |
- 36.69 |
- 53.00% |
- 45.30% |
- 1.70% |
- 1.83 |
- 1.32 |
- 4 |
- |
-
-
- | 187 |
- R2600E.1 |
- D2B6F1 |
- R2600E.1.CEL |
- 2.47 |
- 95 |
- 58.10% |
- 40.20% |
- 1.70% |
- 1.41 |
- 0.78 |
- 1 |
- Y |
-
-
- | 188 |
- R2604E.1 |
- D2B6F1 |
- R2604E.1.CEL |
- 2.66 |
- 90 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.28 |
- 0.79 |
- 1 |
- Y |
-
-
- | 189 |
- R1002E.3 |
- DBA/2J |
- R1002E.3.CEL |
- 1 |
- 102 |
- 54.80% |
- 43.70% |
- 1.50% |
- 2.84 |
- 0.83 |
- 3 |
- |
-
-
- | 190 |
- R4541E |
- DBA/2J |
- R4541E.CEL |
- 1 |
- 43.4 |
- 61.40% |
- 37.00% |
- 1.50% |
- 1.37 |
- 0.73 |
- 4 |
- Y |
-
-
- | 191 |
- R959E.3 |
- DBA/2J |
- R959E.3.CEL |
- 1 |
- 89.97 |
- 53.20% |
- 45.30% |
- 1.50% |
- 3.66 |
- 1.09 |
- 4 |
- |
-
-
- | 192 |
- R2572E.1 |
- DBA/2J |
- R2572E.1.CEL |
- 2.41 |
- 79 |
- 55.50% |
- 42.90% |
- 1.60% |
- 1.37 |
- 0.79 |
- 1 |
- |
-
-
- | 193 |
- R4542E |
- DBA/2J |
- R4542E.CEL |
- 5.7 |
- 39.95 |
- 61.00% |
- 37.40% |
- 1.50% |
- 1.23 |
- 0.81 |
- 4 |
- Y |
-
-
- | 194 |
- R2771E.3 |
- FVB/NJ |
- R2771E.3.CEL |
- 1 |
- 70 |
- 55.30% |
- 43.20% |
- 1.50% |
- 1.69 |
- 0.83 |
- 3 |
- |
-
-
- | 195 |
- R2772E.3 |
- FVB/NJ |
- R2772E.3.CEL |
- 1 |
- 76 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.13 |
- 1.02 |
- 3 |
- |
-
-
- | 196 |
- R2636E.1 |
- KK/HlJ |
- R2636E.1.CEL |
- 2.61 |
- 93 |
- 58.90% |
- 39.50% |
- 1.50% |
- 1.39 |
- 0.76 |
- 1 |
- Y |
-
-
- | 197 |
- R2637E.1 |
- KK/HlJ |
- R2637E.1.CEL |
- 2.19 |
- 103 |
- 59.40% |
- 39.00% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 198 |
- R0999E.1 |
- LG/J |
- R0999E.1.CEL |
- 2.45 |
- 82 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 199 |
- R1004E.1 |
- LG/J |
- R1004E.1.CEL |
- 2.44 |
- 92 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 200 |
- R4543E |
- LP/J |
- R4543E.CEL |
- 6.57 |
- 41.99 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.28 |
- 0.75 |
- 4 |
- Y |
-
-
- | 201 |
- R4544E |
- LP/J |
- R4544E.CEL |
- 4.56 |
- 39.9 |
- 62.40% |
- 36.10% |
- 1.50% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 202 |
- R2858E.3 |
- MOLF/EiJ |
- R2858E.3.CEL |
- 1 |
- 64 |
- 53.80% |
- 44.70% |
- 1.50% |
- 1.59 |
- 0.95 |
- 3 |
- |
-
-
- | 203 |
- R2919.3 |
- MOLF/EiJ |
- R2919.3.CEL |
- 1 |
- 64 |
- 52.40% |
- 46.00% |
- 1.60% |
- 2.15 |
- 1.07 |
- 3 |
- |
-
-
- | 204 |
- R1688E.1 |
- NOD/LtJ |
- R1688E.1.CEL |
- 2.66 |
- 98 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 205 |
- R2566E-2.1 |
- NOD/LtJ |
- R2566E-2.1.CEL |
- 3.03 |
- 69 |
- 59.80% |
- 38.80% |
- 1.50% |
- 1.38 |
- 0.75 |
- 1 |
- Y |
-
-
- | 206 |
- R4545E |
- NZB/BlNJ |
- R4545E.CEL |
- 4.23 |
- 43.48 |
- 62.10% |
- 36.40% |
- 1.50% |
- 1.33 |
- 0.76 |
- 4 |
- Y |
-
-
- | 207 |
- R4546E |
- NZB/BlNJ |
- R4546E.CEL |
- 6.27 |
- 44.22 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.17 |
- 0.82 |
- 4 |
- Y |
-
-
- | 208 |
- R2535E.1 |
- NZO/HlLtJ |
- R2535E.1.CEL |
- 1.89 |
- 86 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.41 |
- 0.85 |
- 1 |
- |
-
-
- | 209 |
- R2550E.1 |
- NZO/HlLtJ |
- R2550E.1.CEL |
- 1.79 |
- 87 |
- 60.70% |
- 37.80% |
- 1.50% |
- 1.52 |
- 0.82 |
- 1 |
- |
-
-
- | 210 |
- R2817E.3 |
- NZW/LacJ |
- R2817E.3.CEL |
- 1 |
- 59 |
- 50.90% |
- 47.60% |
- 1.50% |
- 3.59 |
- 1.48 |
- 3 |
- |
-
-
- | 211 |
- R2810E |
- NZW/LacJ |
- R2810E.CEL |
- |
- |
- |
- |
- |
- |
- |
- 3 |
- |
-
-
- | 212 |
- R2810E.3 |
- NZW/LacJ |
- R2810E.3.CEL |
- 1 |
- 74 |
- 57.00% |
- 41.70% |
- 1.40% |
- 2.15 |
- 1.03 |
- 4 |
- Y |
-
-
- | 213 |
- R4547E |
- PANCEVO/EiJ |
- R4547E.CEL |
- 5.27 |
- 51.34 |
- 57.20% |
- 41.10% |
- 1.70% |
- 1.7 |
- 0.83 |
- 4 |
- |
-
-
- | 214 |
- R4548E |
- PANCEVO/EiJ |
- R4548E.CEL |
- 10.54 |
- 37.39 |
- 50.30% |
- 48.00% |
- 1.70% |
- 1.68 |
- 1.09 |
- 4 |
- |
-
-
- | 215 |
- R2635E.1 |
- PWD/PhJ |
- R2635E.1.CEL |
- 3.72 |
- 80 |
- 54.20% |
- 44.10% |
- 1.70% |
- 1.53 |
- 0.85 |
- 1 |
- |
-
-
- | 216 |
- R2634E.1 |
- PWD/PhJ |
- R2634E.1.CEL |
- 3.29 |
- 90 |
- 55.90% |
- 42.50% |
- 1.60% |
- 1.57 |
- 0.81 |
- 1 |
- |
-
-
- | 217 |
- R2544E.1 |
- PWK/PhJ |
- R2544E.1.CEL |
- 2.2 |
- 108 |
- 54.90% |
- 43.50% |
- 1.70% |
- 1.36 |
- 0.82 |
- 1 |
- |
-
-
- | 218 |
- R2549E.1 |
- PWK/PhJ |
- R2549E.1.CEL |
- 2.28 |
- 84 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.57 |
- 0.83 |
- 1 |
- |
-
-
- | 219 |
- R4550E |
- SJL/J |
- R4550E.CEL |
- 5.35 |
- 40.44 |
- 62.30% |
- 36.20% |
- 1.40% |
- 1.24 |
- 0.79 |
- 4 |
- |
-
-
- | 220 |
- R2368E.1 |
- WSB/EiJ |
- R2368E.1.CEL |
- 2.57 |
- 86 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.29 |
- 0.74 |
- 1 |
- Y |
-
-
- | 221 |
- R2547E.1 |
- WSB/EiJ |
- R2547E.1.CEL |
- 2.14 |
- 90 |
- 58.20% |
- 40.10% |
- 1.60% |
- 1.32 |
- 0.77 |
- 1 |
- Y |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_MT/summary.rtf b/general/datasets/Eye_M2_0908_R_MT/summary.rtf
deleted file mode 100644
index 44b7e23..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/summary.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-FINAL RECOMMENDED EYE DATA SET. The HEIMED September 2008 RMA data release provides estimates of gene expression in whole eyes of 103 lines of young adult mice generated using 221 Affymetrix M430 2.0 arrays. This data set is intended for exploration of the genetics and genomics of the mouse eye, retina, lens, retinal pigment epithelium, cornea, iris and choroid. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
diff --git a/general/datasets/Eye_M2_0908_R_MT/tissue.rtf b/general/datasets/Eye_M2_0908_R_MT/tissue.rtf
deleted file mode 100644
index 9b6ee0f..0000000
--- a/general/datasets/Eye_M2_0908_R_MT/tissue.rtf
+++ /dev/null
@@ -1,2058 +0,0 @@
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.
-
-Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well balanced sample of males and females, in general without within-strain-by-sex replication. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.
-
-Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.
-
-Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.
-
-
- - Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
- - Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
- - Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
- - Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
-
-
-Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Group |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- R2595E.1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- UTHSC RW |
-
-
- | 2 |
- R2533E.1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- UTHSC RW |
-
-
- | 3 |
- R0754E.1 |
- GDP |
- A/J |
- 60 |
- M |
- JAX |
-
-
- | 4 |
- R4521E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 5 |
- R4522E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 6 |
- R4523E |
- KO |
- B6129P2F2N1-Clcn3 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 7 |
- R4526E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- F |
- TChoi_Deltagen |
-
-
- | 8 |
- R4509E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- M |
- TChoi_Deltagen |
-
-
- | 9 |
- R4510E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 10 |
- R4511E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 20 |
- M |
- TChoi_Deltagen |
-
-
- | 11 |
- R4524E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 12 |
- R4525E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 13 |
- R4515E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 14 |
- R4516E |
- KO |
- B6129P2F2N1-Gabra1 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 15 |
- R4517E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 16 |
- R4512E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- F |
- TChoi_Deltagen |
-
-
- | 17 |
- R4513E |
- KO |
- B6129P2F2N1-Gnb5 |
- 25 |
- M |
- TChoi_Deltagen |
-
-
- | 18 |
- R4514E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 19 |
- R4518E |
- KO |
- B6129P2F2N1-Gpr19 |
- 70 |
- M |
- TChoi_Deltagen |
-
-
- | 20 |
- R4519E |
- KO |
- B6129P2F2N1-Gpr19 |
- 68 |
- M |
- TChoi_Deltagen |
-
-
- | 21 |
- R2601E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 22 |
- R2602E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 23 |
- R1676E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- JAX |
-
-
- | 24 |
- R1672E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- JAX |
-
-
- | 25 |
- R4530E |
- GDP |
- BALB/cJ |
- 66 |
- F |
- JAX |
-
-
- | 26 |
- R4529E |
- GDP |
- BALB/cJ |
- 66 |
- M |
- JAX |
-
-
- | 27 |
- R2704E.2 |
- BXD |
- BXD1 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 28 |
- R2707E.3 |
- BXD |
- BXD1 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 29 |
- R1231E.2 |
- BXD |
- BXD2 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 30 |
- R2598E.1 |
- BXD |
- BXD2 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 31 |
- R2591E.1 |
- BXD |
- BXD5 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 32 |
- R2714E.2 |
- BXD |
- BXD5 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 33 |
- R2570E.1 |
- BXD |
- BXD6 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 34 |
- R2694E.2 |
- BXD |
- BXD6 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 35 |
- R2538E.1 |
- BXD |
- BXD8 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 36 |
- R2709E.2 |
- BXD |
- BXD8 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 37 |
- R2708E.2 |
- BXD |
- BXD9 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 38 |
- R2569E.1 |
- BXD |
- BXD9 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 39 |
- R2581E.1 |
- BXD |
- BXD11 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 40 |
- R2612E.2 |
- BXD |
- BXD11 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 41 |
- R2742E.2 |
- BXD |
- BXD12 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 42 |
- R2543E.1 |
- BXD |
- BXD12 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 43 |
- R2586E.1 |
- BXD |
- BXD13 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 44 |
- R877E.2 |
- BXD |
- BXD13 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 45 |
- R2557E.1 |
- BXD |
- BXD14 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 46 |
- R1128E.2 |
- BXD |
- BXD14 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 47 |
- R2701E.3 |
- BXD |
- BXD15 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 48 |
- R2716E.2 |
- BXD |
- BXD15 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 49 |
- R2711E.2 |
- BXD |
- BXD16 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 50 |
- R2567E.1 |
- BXD |
- BXD16 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 51 |
- R2720E.2 |
- BXD |
- BXD18 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 52 |
- R2559E.1 |
- BXD |
- BXD18 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 53 |
- R2560E.1 |
- BXD |
- BXD19 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 54 |
- R2713E.2 |
- BXD |
- BXD19 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 55 |
- R2584E.1 |
- BXD |
- BXD20 |
- 59 |
- F |
- BIDMC GR |
-
-
- | 56 |
- R2731E.2 |
- BXD |
- BXD20 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 57 |
- R2702E.2 |
- BXD |
- BXD21 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 58 |
- R2541E2.1 |
- BXD |
- BXD21 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 59 |
- R2553E.1 |
- BXD |
- BXD22 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 60 |
- R2700E.2 |
- BXD |
- BXD22 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 61 |
- R2558E-2.1 |
- BXD |
- BXD23 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 62 |
- R1086E.2 |
- BXD |
- BXD23 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 63 |
- R2719E.2 |
- BXD |
- BXD24 |
- 123 |
- F |
- UTHSC RW |
-
-
- | 64 |
- R2589E2.1 |
- BXD |
- BXD24 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 65 |
- R2573E-2.1 |
- BXD |
- BXD25 |
- 67 |
- F |
- UAB |
-
-
- | 66 |
- R2683E.2 |
- BXD |
- BXD25 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 67 |
- R2703E.2 |
- BXD |
- BXD27 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 68 |
- R2729E.3 |
- BXD |
- BXD27 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 69 |
- R2562E.3 |
- BXD |
- BXD28 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 70 |
- R2721E.2 |
- BXD |
- BXD28 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 71 |
- R2561E.3 |
- BXD |
- BXD29 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 72 |
- R1258E.2 |
- BXD |
- BXD31 |
- 57 |
- F |
- UTHSC RW |
-
-
- | 73 |
- R2597E.1 |
- BXD |
- BXD31 |
- 61 |
- M |
- BIDMC GR |
-
-
- | 74 |
- R2563E.1 |
- BXD |
- BXD32 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 75 |
- R1216E.2 |
- BXD |
- BXD32 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 76 |
- R2542E.1 |
- BXD |
- BXD33 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- R857E.2 |
- BXD |
- BXD33 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 78 |
- R1451E.2 |
- BXD |
- BXD34 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 79 |
- R2585E.1 |
- BXD |
- BXD34 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 80 |
- R2698E.3 |
- BXD |
- BXD36 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 81 |
- R2705E.3 |
- BXD |
- BXD36 |
- 57 |
- M |
- BIDMC GR |
-
-
- | 82 |
- R2710E.2 |
- BXD |
- BXD38 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 83 |
- R2532E.1 |
- BXD |
- BXD38 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 84 |
- R2574E.1 |
- BXD |
- BXD39 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 85 |
- R2695E.2 |
- BXD |
- BXD39 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 86 |
- R2699E.2 |
- BXD |
- BXD40 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 87 |
- R2590E.1 |
- BXD |
- BXD40 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 88 |
- R2696E.2 |
- BXD |
- BXD42 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 89 |
- R2596E.1 |
- BXD |
- BXD42 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 90 |
- R994E.2 |
- BXD |
- BXD43 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 91 |
- R2607E.1 |
- BXD |
- BXD43 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 92 |
- R2594E.1 |
- BXD |
- BXD44 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 93 |
- R2610E.2 |
- BXD |
- BXD44 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 94 |
- R2732E.2 |
- BXD |
- BXD45 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 95 |
- R2592E.1 |
- BXD |
- BXD45 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- R967E.2 |
- BXD |
- BXD48 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 97 |
- R2606E.1 |
- BXD |
- BXD48 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 98 |
- R2933E.3 |
- BXD |
- BXD50 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 99 |
- R2937E.3 |
- BXD |
- BXD50 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 100 |
- R2603E.1 |
- BXD |
- BXD51 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 101 |
- R1042E.2 |
- BXD |
- BXD51 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 102 |
- R2980E.3 |
- BXD |
- BXD55 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 103 |
- R2690E.2 |
- BXD |
- BXD55 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 104 |
- R4176E |
- BXD |
- BXD56 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 105 |
- R4175E |
- BXD |
- BXD56 |
- 53 |
- M |
- UTHSC RW |
-
-
- | 106 |
- R1006E.3 |
- BXD |
- BXD60 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 107 |
- R2725E.2 |
- BXD |
- BXD60 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 108 |
- R1074E.3 |
- BXD |
- BXD60 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 109 |
- R2534E2.1 |
- BXD |
- BXD61 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 110 |
- R2684E.2 |
- BXD |
- BXD61 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 111 |
- R1107E.3 |
- BXD |
- BXD62 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 112 |
- R2681E.2 |
- BXD |
- BXD62 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 113 |
- R965E.3 |
- BXD |
- BXD62 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 114 |
- R1425E.2 |
- BXD |
- BXD63 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 115 |
- R2576E.3 |
- BXD |
- BXD63 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 116 |
- R943E-2.2 |
- BXD |
- BXD64 |
- 56 |
- F |
- UTHSC RW |
-
-
- | 117 |
- R2611E.1 |
- BXD |
- BXD64 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 118 |
- R2689E.2 |
- BXD |
- BXD65 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 119 |
- R2583E.1 |
- BXD |
- BXD65 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 120 |
- R2728E.2 |
- BXD |
- BXD66 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 121 |
- R2536E2.1 |
- BXD |
- BXD66 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 122 |
- R1207E.2 |
- BXD |
- BXD66 |
- 83 |
- M |
- UTHSC RW |
-
-
- | 123 |
- R1192E.2 |
- BXD |
- BXD67 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 124 |
- R2727E.3 |
- BXD |
- BXD67 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 125 |
- R2691E.3 |
- BXD |
- BXD67 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 126 |
- R2551E.1 |
- BXD |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 127 |
- R2726E.2 |
- BXD |
- BXD68 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 128 |
- R2593E.1 |
- BXD |
- BXD69 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 129 |
- R975E.2 |
- BXD |
- BXD70 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 130 |
- R2537E2.1 |
- BXD |
- BXD70 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 131 |
- R4531E |
- BXD |
- BXD71 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 132 |
- R4532E |
- BXD |
- BXD71 |
- 86 |
- M |
- UTHSC RW |
-
-
- | 133 |
- R2779E.2 |
- BXD |
- BXD73 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 134 |
- R3024E.3 |
- BXD |
- BXD73 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 135 |
- R2565E.1 |
- BXD |
- BXD75 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 136 |
- R1397E-re.2 |
- BXD |
- BXD75 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 137 |
- R2687E.3 |
- BXD |
- BXD77 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 138 |
- R2717E.2 |
- BXD |
- BXD77 |
- 107 |
- M |
- UTHSC RW |
-
-
- | 139 |
- R1421E.3 |
- BXD |
- BXD77 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 140 |
- R2579E.1 |
- BXD |
- BXD80 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 141 |
- R2686E.2 |
- BXD |
- BXD80 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 142 |
- R2956E.3 |
- BXD |
- BXD83 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 143 |
- R2960E.3 |
- BXD |
- BXD83 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 144 |
- R2922E.3 |
- BXD |
- BXD84 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 145 |
- R2895E.3 |
- BXD |
- BXD84 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- R2692E.2 |
- BXD |
- BXD85 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 147 |
- R2715E.2 |
- BXD |
- BXD85 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 148 |
- R1405E.2 |
- BXD |
- BXD86 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 149 |
- R1225E.3 |
- BXD |
- BXD86 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 150 |
- R2724E.2 |
- BXD |
- BXD87 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 151 |
- R2540E.1 |
- BXD |
- BXD87 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 152 |
- R1433E.2 |
- BXD |
- BXD89 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 153 |
- R2546E.1 |
- BXD |
- BXD89 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 154 |
- R2578E2.1 |
- BXD |
- BXD90 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 155 |
- R859E.2 |
- BXD |
- BXD90 |
- 72 |
- M |
- UTHSC RW |
-
-
- | 156 |
- R2682E.2 |
- BXD |
- BXD92 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 157 |
- R1388E.3 |
- BXD |
- BXD92 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 158 |
- R1322E.3 |
- BXD |
- BXD92 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 159 |
- R2733E.2 |
- BXD |
- BXD96 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 160 |
- R2554E.1 |
- BXD |
- BXD96 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 161 |
- R2649E.2 |
- BXD |
- BXD97 |
- 74 |
- F |
- UTHSC RW |
-
-
- | 162 |
- R2577E.1 |
- BXD |
- BXD97 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 163 |
- R2645E.3 |
- BXD |
- BXD98 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 164 |
- R2688E.2 |
- BXD |
- BXD98 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 165 |
- R4533E |
- BXD |
- BXD99 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 166 |
- R4534E |
- BXD |
- BXD99 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 167 |
- R2885E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 168 |
- R2883E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- M |
- BIDMC GR |
-
-
- | 169 |
- R1700E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- UTHSC RW |
-
-
- | 170 |
- R1704E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- UTHSC RW |
-
-
- | 171 |
- R2605E.1 |
- GDP BXD |
- C57BL/6J |
- 79 |
- F |
- UTHSC RW |
-
-
- | 172 |
- R0871E |
- GDP BXD |
- C57BL/6J |
- 65 |
- F |
- UTHSC RW |
-
-
- | 173 |
- R0872E.1 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 174 |
- R0872E |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 175 |
- R4507E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 176 |
- R4508E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 177 |
- R4505E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 178 |
- R4506E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 179 |
- R4535E |
- GDP |
- C57BLKS/J |
- 66 |
- F |
- JAX |
-
-
- | 180 |
- R4536E |
- GDP |
- C57BLKS/J |
- 66 |
- M |
- JAX |
-
-
- | 181 |
- R2564E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- F |
- JAX |
-
-
- | 182 |
- R2580E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- M |
- JAX |
-
-
- | 183 |
- R4537E |
- GDP |
- CBA/CaJ |
- 66 |
- F |
- JAX |
-
-
- | 184 |
- R4538E |
- GDP |
- CBA/CaJ |
- 66 |
- M |
- JAX |
-
-
- | 185 |
- R4539E |
- GDP |
- CZECHII/EiJ |
- 66 |
- F |
- JAX |
-
-
- | 186 |
- R4540E |
- GDP |
- CZECHII/EiJ |
- 66 |
- M |
- JAX |
-
-
- | 187 |
- R2600E.1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- UTHSC RW |
-
-
- | 188 |
- R2604E.1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- UTHSC RW |
-
-
- | 189 |
- R1002E.3 |
- GDP BXD |
- DBA/2J |
- 72 |
- F |
- UTHSC RW |
-
-
- | 190 |
- R4541E |
- GDP BXD |
- DBA/2J |
- 65 |
- F |
- JAX |
-
-
- | 191 |
- R959E.3 |
- GDP BXD |
- DBA/2J |
- 60 |
- M |
- UTHSC RW |
-
-
- | 192 |
- R2572E.1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 193 |
- R4542E |
- GDP BXD |
- DBA/2J |
- 59 |
- M |
- JAX |
-
-
- | 194 |
- R2771E.3 |
- GDP |
- FVB/NJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 195 |
- R2772E.3 |
- GDP |
- FVB/NJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 196 |
- R2636E.1 |
- GDP |
- KK/HlJ |
- 64 |
- F |
- UTHSC RW |
-
-
- | 197 |
- R2637E.1 |
- GDP |
- KK/HlJ |
- 64 |
- M |
- UTHSC RW |
-
-
- | 198 |
- R0999E.1 |
- GDP |
- LG/J |
- 57 |
- F |
- UTHSC RW |
-
-
- | 199 |
- R1004E.1 |
- GDP |
- LG/J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 200 |
- R4543E |
- GDP |
- LP/J |
- 65 |
- F |
- JAX |
-
-
- | 201 |
- R4544E |
- GDP |
- LP/J |
- 65 |
- M |
- JAX |
-
-
- | 202 |
- R2858E.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 203 |
- R2919.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 204 |
- R1688E.1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- JAX |
-
-
- | 205 |
- R2566E-2.1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- UTHSC RW |
-
-
- | 206 |
- R4545E |
- GDP |
- NZB/BlNJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 207 |
- R4546E |
- GDP |
- NZB/BlNJ |
- 58 |
- M |
- BIDMC GR |
-
-
- | 208 |
- R2535E.1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- JAX |
-
-
- | 209 |
- R2550E.1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- JAX |
-
-
- | 210 |
- R2817E.3 |
- GDP |
- NZW/LacJ |
- 65 |
- F |
- BIDMC GR |
-
-
- | 211 |
- R2810E |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 212 |
- R2810E.3 |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 213 |
- R4547E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- F |
- JAX |
-
-
- | 214 |
- R4548E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- M |
- JAX |
-
-
- | 215 |
- R2635E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- JAX |
-
-
- | 216 |
- R2634E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- JAX |
-
-
- | 217 |
- R2544E.1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- JAX |
-
-
- | 218 |
- R2549E.1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- JAX |
-
-
- | 219 |
- R4550E |
- GDP |
- SJL/J |
- 65 |
- M+F |
- JAX |
-
-
- | 220 |
- R2368E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- UTHSC RW |
-
-
- | 221 |
- R2547E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- UTHSC RW |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_NB/acknowledgment.rtf b/general/datasets/Eye_M2_0908_R_NB/acknowledgment.rtf
deleted file mode 100644
index 5098d32..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant and from funds from NEI grant to Dr. Eldon Geisert (R01EY017841), an NEI Vision Core grant (EY14080) and an Unrestricted Grant from Research To Prevent Blindness.
-
-We thank Dr. Ted Choi, Chief Scientific Director of Predictive Biology, Inc. (past director of molecular genetics at Deltagen Inc.) for providing us with eye samples from several interesting DeltaGen knockouts.
diff --git a/general/datasets/Eye_M2_0908_R_NB/cases.rtf b/general/datasets/Eye_M2_0908_R_NB/cases.rtf
deleted file mode 100644
index 552d4a5..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/cases.rtf
+++ /dev/null
@@ -1,57 +0,0 @@
-This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:
-
-
- - 68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.
- - 35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common Mus musculus domesticus inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (Mus musculus domesticus, e.g, WSB/EiJ; M. musculus musculus, e.g., CZECHII/EiJ; M. musculus molossinus, e.g., MOLF/EiJ; M. musculus castaneus, e.g., CAST/EiJ); and even one different species of mouse (Mus spicilegus, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the Nyx-nob mutant:
- - 6 knockouts (KO), including a KO of Rpe65, and 5 DeltaGen Inc. knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: Gabra1, Gabbr1, Gnb1, Gpr19, and Clcn3. We also included one spontaneous mutant of the nyctalopin (Nyx no b wave "nob") gene (Pardue et al., 1998) that is on a BALB/cByJ background.
-
-
-Rod photoreceptor degeneration in inbred mice: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the retinal degeneration 1 (rd1) mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (Pde6b). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.
-
-As expected (Dickerson LW et al., 2002) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, Clcn3) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of Gnat2, a gene associated with cones and achromatopsia in mice and humans.
-
-Lines of mice were selected using the following criteria:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - representation of a fairly wide variety of different subspecies of Mus
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - interesting mutations or knockouts affecting genes with high expression in the eye
- - general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.
-
-
-We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see Perlegen's excellent data resources and browser).
-
-
- - 129S1/SvImJ : Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a cone photoreceptor function loss 3 mutant (Cpfl3 allele) of the Gnat2 gene that is a model for achromatopsia (JAX Stock Number: 002448)
- - A/J: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (Tyr c allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: 000646)
- - BALB/cByJ: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Small brain, not aggressive (JAX Stock Number: 001026)
- - BALB/cJ: Phenome Project A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Large brain and aggressive (JAX Stock Number: 000651)
- - BXSB/MpJ: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the Yaa gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: 000740)
- - C3H/HeJ: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a Pdeb6 rd1 mutant with near total photoreceptor loss at as early as postnatal day 30. Also a Tlr4 mutant that is endotoxin resistant. (JAX Stock Number: 000659)
- - C57BL/6J: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: 000664)
- - C57BLKS/J: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: 000662)
- - CAST/EiJ: A wild-derived inbred Mus musculus castaneus strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: 000928)
- - CBA/CaJ: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: 000654)
- - CZECHII/EiJ: Czech 2 is a wild-derived inbred strain M. musculus musculus strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: 001144).
- - DBA/2J: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. A myosin 5a (Myo5a d) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: 000671)
- - FVB/NJ: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. Tyr c locus albino and a Pdeb6 rd1 mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: 001800).
- - KK/HlJ: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: 002106)
- - LG/J: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A Tyr c locus albino strain. (JAX Stock Number: 000675)
- - LP/J: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B Ednrb gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: 000676)
- - MOLF/EiJ: A wild-derived inbred strain derived from M. musculus molossinus samples camputered in Fukuoka, Japan. This strain has the retinal degeneration rd1 allele in Pde6b. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: 000550)
- - NOD/LtJ: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. (JAX Stock Number: 001976)
- - NZO/HlLtJ: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: 002105)
- - NZB/BlNJ: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: 000648)
- - NZW/LacJ: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the Tyr c locus albino mutation, the pink-eye dilution mutation in the Oca2 or p locus, and the brown allele at Tyrp1. (JAX Stock Number: 001058)
- - PANCEVO/EiJ: PANCEVO/EiJ is a wild-derived inbred strain from the Mus spicilegus samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier 10103). M. spicilegus is a colonial mound-building species. No known ocular or retina mutations, but the expression level of Gnat2 is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: 001384)
- - PWD/PhJ: A wild-derived Mus musculus musculus agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: 004660)
- - PWK/PhJ: A wild-derived Mus musculus musculus inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: 003715)
- - SJL/J: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration rd1 allele in Pde6b. It also carries both the Tyr c albino mutation and the pink-eye dilution mutation in the Oca2 or p locus. Highly aggressive males. (JAX Stock Number: 000686)
- - WSB/EiJ: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived Mus musculus domesticus inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: 001145)
- - B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J 100006)
-
-
-Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, 2008 and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (Tyr, or human OCA1), the brown allele of the tyrosinase related protein 1 (Tyrp1), the pink-eye dilution allele of Oca2 (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein Asip, the steel allele of Kitlg, the dilute allele of Myo5a (probe set 1419754), and the piebald allele of Ednrb. In some of these cases, effects of the mutation are easily detected at the transcript level (Tyrp1, Oca2, and Myo5a), but in the other cases (Tyr, Asip, Ednrb, and Kitlg), mutations do not leave a strong imprint on expression.
diff --git a/general/datasets/Eye_M2_0908_R_NB/experiment-design.rtf b/general/datasets/Eye_M2_0908_R_NB/experiment-design.rtf
deleted file mode 100644
index 1ebe0ad..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression profiling by array
diff --git a/general/datasets/Eye_M2_0908_R_NB/notes.rtf b/general/datasets/Eye_M2_0908_R_NB/notes.rtf
deleted file mode 100644
index 7a26eb5..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Eye_M2_0908_R_NB/platform.rtf b/general/datasets/Eye_M2_0908_R_NB/platform.rtf
deleted file mode 100644
index 9024a99..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/platform.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many probes overlap and target the same transcript). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
-As part of the development of HEIMED, we have manually annotated individual probe sets by sequence alignment to the mouse genome and transcriptome. Approximately 13,000 probe sets that have comparatively high expression in eye and CNS were curated by one of the authors (RWW) and now have specific information on the part of the transcript targeted by each probe set. The other 33,000 transcripts have corresponding data that was generated by Xusheng Wang using computational methods (BLAT analysis combined with annotated genome sequence).
-
-One example may help explain how to exploit this annotation. The four probe sets for rhodopsin include information on the target location. Only the first probe set targets the last two coding exons. The other three probe sets target different parts of the 3’ UTR (mid, distal, and far distal regions). The probe sets can be reordered by from high to low expression using the Sort By function in Search Results pages. In the case of rhodopsin, the probe set that targets that last two coding exons and proximal parts of the 3’ UTR also has the highest expression . Finally, the HEIMED gene descriptions have been customized to help vision researchers. In the case of rhodopsin, the description appended after the gene name reads “rod photoreceptor pigment, retinitis pigmentosa-associated”. For less well known genes this kind of annotation can be extremely useful. For example, the more verbose annotation for Cerkl reads “neuronal survival and apoptosis-related, retinal ganglion cell expressed, retinitis pigmentosa 26); alternative 3' UTR of short form message, intron 2”.
-
-
-
-
-
-Legend: Distribution of expression values for all probe sets in HEIMED.
diff --git a/general/datasets/Eye_M2_0908_R_NB/processing.rtf b/general/datasets/Eye_M2_0908_R_NB/processing.rtf
deleted file mode 100644
index 4349e60..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/processing.rtf
+++ /dev/null
@@ -1,3381 +0,0 @@
-Range of Gene Expression in the Eye. Expression of transcripts in the HEIMED and most other GN data sets is measured on a log2 scale. Each unit corresponding approximately to a 2-fold difference in hybridization signal intensity. To simplify comparisons among different data sets and cases, log2 RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units (variance stabilized). Values of all 45,101 probe sets in this data set range from a low of 4.8 (Tcf15, probe set 1420281_at) to a high of 15.5 (crystallin gamma C, Crygc, probe set 1422674_s_at). This corresponds to 10.7 units or a 1 to 1700 dynamic range of expression (2^10.73).
-
-We used pooled RNA samples of whole eyes, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-We calibrated this log intensity scale using Affymetrix spike-in control probe sets. These 18 control probe sets target exogenous bacterial mRNAs that are added to each sample (a graded dose spike cocktail) during preparation at concentrations of 1.5, 5, 25, and 100 pM. (To find these probe sets, search GN’s ALL search field using the string “AFFX pM”.) A value of 6 or less is equivalent to an mRNA concentration of under 0.4 pM, a value of 8 is equivalent to ~1.5 pM, 9.5 is equivalent to ~5 pM, 11.5 is equivalent to ~25 pM, 13.5 is equivalent to ~100 pM, and a value of 15.5 is equivalent to an mRNA concentration of 400 pM or greater.
-
-This range can be converted to the mRNA molecules per cell in the eye assuming that a value of 8 is equivalent to about 1 mRNA copy per cell (Kanno et al. 2006, see http://www.biomedcentral.com/1471-2164/7/64). Since the expression of rhodopsin mRNA is normally 15 units, we predict that there are 27 or ~128 Rho mRNAs per cell in the whole eye and ~256 in rods themselves (assuming that rods make up about half of all cells in the eye). For this purpose it may be useful to know that a normal mouse eye contains between 6 and 8 million rod photoreceptors (Guo, Lu, and Williams; GN BXD Phenotype ID 11024).
-
-Note that some probe sets with very low expression still provide reliable data. For example, probe set 1440397_at (Cacna2d1) has expression of only 5.5 units (a value that would be declared as "absent" using conventional Affymetrix procedures), but the values for this calcium channel transcript are associated with a very strong cis QTL with an LRS of 79 (LOD = 17). This strong linkage is definitely not due to chance since the probability of the expression data mapping precisely to the location of the parent gene itself is about 10e-16. This indicates a high signal to noise ratio and the detection of significant strain variation of the correct transcript.
-
-The standard error of the mean for the HEIMED data set is computed for 2 to 6 biological replicates. The standard error of such small samples tends to systematically underestimate the population standard error. With n = 2 the underestimate is about 25%, whereas for n = 6 the underestimate is 5%. Gurland and Tripathi (1971) provide a correction and equation for this effect (see Sokal and Rohlf, Biometry, 2nd ed., 1981, p 53 for an equation of the correction factor for small samples of n < 20.) Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the first three batches together. The last batch was processed separately and merged as described below.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing using Biobase affy10 build running under R version 2.7.1, all array data sets were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (FVB/NJ, NOD/LtJ, MOLF/EiJ, C3H/HeJ and BXD24), samples from wild subspecies such as WSB/EiJ, CAST/EiJ, PWD/PhJ, and PWK/PhJ, and knockouts. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. The assumption is that anomolous data are much more likely due to experimental and technical errors than to informative biological variation. Approximately 10% of arrays were discarded.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We reviewed the data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g., 1800) represented the QTL harvest for the full data set. We then dropped a single array from the data set, recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 1750 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs. Values ranged from approximately -90 (good arrays) to +40 (bad arrays). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a method to polish a data set.
-
-During this process we discovered that nearly 20 arrays in the batch 2 had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of high quality.
-
-A third batch of approximately 40 arrays were processed by Yan Jiao and Weikuan Gu in August 2006. These complete data set assembled by Hongqiang Li. This process again included a correction for a batch effect.
-
-For the June 2006 data set Hongqiang Li used a new batch correction method that stabilizes the range of expression in each batch. For each of the three large batches, we extracted the minumum and maximum raw probe expression (CEL file level) value. We then adjusted raw probe values in each batch to have the same range as the first and largest batch (batch 1) using a simple linear interpolation. These procedures generated new correct CEL files which were then used with RMA to generate final probe set estimates.
-
-For the final fourth batch of arrays (Sept 2008) Arthur Centeno and Rob Williams corrected for a systematic difference in probe set expression values between original arrays run in 2005 and 2006 and the new arrays added in 2008 (n = 45 acceptable arrays). This difference is due to unknown technical batch effects that are probably associated with labeling, hybridization, and scanning. We performed a simple correction to normalize values of the new set of arrays to those of the old set (batches 1 through 3). No changes were made to any values of the previous three batches. We corrected only the probe set level (RMA) values and not the CEL files. For this final batch, we corrected for the difference (offset) in probe set expression between the first three batches arrays run in 2005 and 2006 (a total of 174 acceptable arrays) and the new batch (n = 47 acceptable arrays). This difference is due to unknown technical effects that are probably related to various steps in labeling, hybridization, and scanning. The correction was applied as follows: (1) RWW selected 51 high quality arrays with similar expression characteristics (r = 0.97 or better between pairs of arrays) in the old data set (from batches 1, 2, and 3) and 34 high quality arrays in the final batch. RWW used scatterplots of full RMA transcriptome data sets to review many pairs of arrays within these new and old array batches. Strains with retinal degeneration or unusual eye gene expression characteristics were excluded from these selected subsets. The average expression values for each probe set were then computed for both the old and new array subsets. The offset value (old minus new) was added to each probe set across all 47 new arrays. This processes forces the average probe set in the new arrays to be very close to that of the previous arrays.
-
-Table 2: Sample tube ID, strain, original CEL filename, and Affymetrix quality control values. Columns labeled Scale factor, Background Average, Present, Absent, Marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Strain |
- Original CEL |
- Scale factor |
- Background Average |
- Present |
- Absent |
- Marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- Batch Id |
- Used for batch control |
-
-
- | 1 |
- R2595E.1 |
- 129S1/SvImJ |
- R2595E.1.CEL |
- 1.79 |
- 115 |
- 61.00% |
- 37.50% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 2 |
- R2533E.1 |
- 129S1/SvImJ |
- R2533E.1.CEL |
- 2.11 |
- 94 |
- 57.90% |
- 40.50% |
- 1.60% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 3 |
- R0754E.1 |
- A/J |
- R0754E.1.CEL |
- 2.72 |
- 86 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.36 |
- 0.76 |
- 1 |
- Y |
-
-
- | 4 |
- R4521E |
- B6129P2F2N1-Clcn3 |
- R4521E.CEL |
- 4.83 |
- 38.7 |
- 63.30% |
- 35.30% |
- 1.40% |
- 1.25 |
- 0.77 |
- 4 |
- |
-
-
- | 5 |
- R4522E |
- B6129P2F2N1-Clcn3 |
- R4522E.CEL |
- 5.76 |
- 37.36 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.37 |
- 0.83 |
- 4 |
- |
-
-
- | 6 |
- R4523E |
- B6129P2F2N1-Clcn3 |
- R4523E.CEL |
- 4.88 |
- 40.42 |
- 63.90% |
- 34.70% |
- 1.40% |
- 1.27 |
- 0.77 |
- 4 |
- |
-
-
- | 7 |
- R4526E |
- B6129P2F2N1-Gabbr1 |
- R4526E.CEL |
- 3.84 |
- 44.18 |
- 65.00% |
- 33.70% |
- 1.30% |
- 1.34 |
- 0.78 |
- 4 |
- Y |
-
-
- | 8 |
- R4509E |
- B6129P2F2N1-Gabbr1 |
- R4509E.CEL |
- 7.45 |
- 34.76 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.45 |
- 0.83 |
- 4 |
- |
-
-
- | 9 |
- R4510E |
- B6129P2F2N1-Gabbr1 |
- R4510E.CEL |
- 8.44 |
- 37.44 |
- 57.40% |
- 41.10% |
- 1.50% |
- 1.35 |
- 0.83 |
- 4 |
- |
-
-
- | 10 |
- R4511E |
- B6129P2F2N1-Gabbr1 |
- R4511E.CEL |
- 5.91 |
- 42.02 |
- 61.40% |
- 37.20% |
- 1.40% |
- 1.41 |
- 0.83 |
- 4 |
- |
-
-
- | 11 |
- R4524E |
- B6129P2F2N1-Gabbr1 |
- R4524E.CEL |
- 5.49 |
- 42.34 |
- 62.40% |
- 36.20% |
- 1.40% |
- 1.29 |
- 0.78 |
- 4 |
- Y |
-
-
- | 12 |
- R4525E |
- B6129P2F2N1-Gabbr1 |
- R4525E.CEL |
- 4.69 |
- 41.3 |
- 63.10% |
- 35.50% |
- 1.40% |
- 1.27 |
- 0.8 |
- 4 |
- Y |
-
-
- | 13 |
- R4515E |
- B6129P2F2N1-Gabra1 |
- R4515E.CEL |
- 5.75 |
- 41.76 |
- 62.80% |
- 35.80% |
- 1.40% |
- 1.41 |
- 0.81 |
- 4 |
- Y |
-
-
- | 14 |
- R4516E |
- B6129P2F2N1-Gabra1 |
- R4516E.CEL |
- 7.07 |
- 40.73 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.32 |
- 0.87 |
- 4 |
- Y |
-
-
- | 15 |
- R4517E |
- B6129P2F2N1-Gabra1 |
- R4517E.CEL |
- 5.45 |
- 38.09 |
- 62.70% |
- 35.80% |
- 1.40% |
- 1.34 |
- 0.82 |
- 4 |
- Y |
-
-
- | 16 |
- R4512E |
- B6129P2F2N1-Gnb5 |
- R4512E.CEL |
- 6.56 |
- 38.02 |
- 59.90% |
- 38.70% |
- 1.50% |
- 1.33 |
- 0.83 |
- 4 |
- |
-
-
- | 17 |
- R4513E |
- B6129P2F2N1-Gnb5 |
- R4513E.CEL |
- 4.15 |
- 41.6 |
- 63.40% |
- 35.10% |
- 1.50% |
- 1.34 |
- 0.82 |
- 4 |
- |
-
-
- | 18 |
- R4514E |
- B6129P2F2N1-Gnb5 |
- R4514E.CEL |
- 5.86 |
- 39.2 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.34 |
- 0.81 |
- 4 |
- |
-
-
- | 19 |
- R4518E |
- B6129P2F2N1-Gpr19 |
- R4518E.CEL |
- 5.58 |
- 38.9 |
- 62.60% |
- 36.00% |
- 1.30% |
- 1.39 |
- 0.79 |
- 4 |
- Y |
-
-
- | 20 |
- R4519E |
- B6129P2F2N1-Gpr19 |
- R4519E.CEL |
- 5.95 |
- 41.91 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.35 |
- 0.84 |
- 4 |
- Y |
-
-
- | 21 |
- R2601E.1 |
- B6D2F1 |
- R2601E.1.CEL |
- 2.55 |
- 92 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.44 |
- 0.78 |
- 1 |
- Y |
-
-
- | 22 |
- R2602E.1 |
- B6D2F1 |
- R2602E.1.CEL |
- 2.6 |
- 84 |
- 59.70% |
- 38.80% |
- 1.50% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 23 |
- R1676E.1 |
- BALB/cByJ |
- R1676E.1.CEL |
- 2.69 |
- 98 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.46 |
- 0.74 |
- 1 |
- |
-
-
- | 24 |
- R1672E.1 |
- BALB/cByJ |
- R1672E.1.CEL |
- 2.22 |
- 111 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 25 |
- R4530E |
- BALB/cJ |
- R4530E.CEL |
- 6.37 |
- 37.53 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.3 |
- 0.84 |
- 4 |
- Y |
-
-
- | 26 |
- R4529E |
- BALB/cJ |
- R4529E.CEL |
- 5.71 |
- 41.33 |
- 60.50% |
- 38.00% |
- 1.50% |
- 1.48 |
- 0.8 |
- 4 |
- Y |
-
-
- | 27 |
- R2704E.2 |
- BXD1 |
- R2704E.2.CEL |
- 2.066 |
- 139.61 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 28 |
- R2707E.3 |
- BXD1 |
- R2707E.3.CEL |
- 1 |
- 80 |
- 56.40% |
- 42.10% |
- 1.50% |
- 1.43 |
- 0.79 |
- 3 |
- |
-
-
- | 29 |
- R1231E.2 |
- BXD2 |
- R1231E.2.CEL |
- 2.197 |
- 138.73 |
- 57.30% |
- 41.30% |
- 1.40% |
- 1.41 |
- 0.77 |
- 2 |
- |
-
-
- | 30 |
- R2598E.1 |
- BXD2 |
- R2598E.1.CEL |
- 1.99 |
- 106 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 31 |
- R2591E.1 |
- BXD5 |
- R2591E.1.CEL |
- 1.7 |
- 136 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.33 |
- 0.78 |
- 1 |
- Y |
-
-
- | 32 |
- R2714E.2 |
- BXD5 |
- R2714E.2.CEL |
- 1.404 |
- 144.35 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 33 |
- R2570E.1 |
- BXD6 |
- R2570E.1.CEL |
- 1.99 |
- 87 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.46 |
- 0.76 |
- 1 |
- Y |
-
-
- | 34 |
- R2694E.2 |
- BXD6 |
- R2694E.2.CEL |
- 1.983 |
- 97.23 |
- 61.60% |
- 37.10% |
- 1.30% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 35 |
- R2538E.1 |
- BXD8 |
- R2538E.1.CEL |
- 1.91 |
- 102 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.52 |
- 0.79 |
- 1 |
- Y |
-
-
- | 36 |
- R2709E.2 |
- BXD8 |
- R2709E.2.CEL |
- 1.99 |
- 99.79 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.42 |
- 0.76 |
- 2 |
- |
-
-
- | 37 |
- R2708E.2 |
- BXD9 |
- R2708E.2.CEL |
- 1.966 |
- 126.46 |
- 57.70% |
- 40.70% |
- 1.50% |
- 1.4 |
- 0.84 |
- 2 |
- |
-
-
- | 38 |
- R2569E.1 |
- BXD9 |
- R2569E.1.CEL |
- 1.75 |
- 87 |
- 55.10% |
- 43.40% |
- 1.50% |
- 2.82 |
- 3.14 |
- 1 |
- |
-
-
- | 39 |
- R2581E.1 |
- BXD11 |
- R2581E.1.CEL |
- 1.94 |
- 89 |
- 62.10% |
- 36.40% |
- 1.60% |
- 1.55 |
- 0.81 |
- 1 |
- Y |
-
-
- | 40 |
- R2612E.2 |
- BXD11 |
- R2612E.2.CEL |
- 1.83 |
- 142.03 |
- 58.20% |
- 40.50% |
- 1.40% |
- 1.78 |
- 0.81 |
- 2 |
- |
-
-
- | 41 |
- R2742E.2 |
- BXD12 |
- R2742E.2.CEL |
- 2.127 |
- 134.14 |
- 57.00% |
- 41.60% |
- 1.40% |
- 1.64 |
- 0.78 |
- 2 |
- |
-
-
- | 42 |
- R2543E.1 |
- BXD12 |
- R2543E.1.CEL |
- 1.61 |
- 118 |
- 58.60% |
- 39.90% |
- 1.60% |
- 1.43 |
- 0.77 |
- 1 |
- Y |
-
-
- | 43 |
- R2586E.1 |
- BXD13 |
- R2586E.1.CEL |
- 2.01 |
- 74 |
- 56.40% |
- 42.00% |
- 1.60% |
- 2.85 |
- 3.81 |
- 1 |
- |
-
-
- | 44 |
- R877E.2 |
- BXD13 |
- R877E.2.CEL |
- 1.558 |
- 125.63 |
- 61.20% |
- 37.50% |
- 1.20% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 45 |
- R2557E.1 |
- BXD14 |
- R2557E.1.CEL |
- 1.83 |
- 99 |
- 62.50% |
- 36.10% |
- 1.40% |
- 1.31 |
- 0.78 |
- 1 |
- Y |
-
-
- | 46 |
- R1128E.2 |
- BXD14 |
- R1128E.2.CEL |
- 1.91 |
- 115 |
- 59.90% |
- 38.80% |
- 1.40% |
- 1.2 |
- 0.82 |
- 1 |
- Y |
-
-
- | 47 |
- R2701E.3 |
- BXD15 |
- R2701E.3.CEL |
- 1 |
- 88 |
- 60.60% |
- 37.90% |
- 1.40% |
- 1.5 |
- 0.77 |
- 3 |
- |
-
-
- | 48 |
- R2716E.2 |
- BXD15 |
- R2716E.2.CEL |
- 2.015 |
- 150.83 |
- 56.40% |
- 42.10% |
- 1.60% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 49 |
- R2711E.2 |
- BXD16 |
- R2711E.2.CEL |
- 1.953 |
- 118.53 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 50 |
- R2567E.1 |
- BXD16 |
- R2567E.1.CEL |
- 2.24 |
- 82 |
- 56.70% |
- 41.60% |
- 1.70% |
- 1.37 |
- 0.75 |
- 1 |
- |
-
-
- | 51 |
- R2720E.2 |
- BXD18 |
- R2720E.2.CEL |
- 2.32 |
- 99.93 |
- 59.50% |
- 39.00% |
- 1.50% |
- 1.33 |
- 0.77 |
- 2 |
- |
-
-
- | 52 |
- R2559E.1 |
- BXD18 |
- R2559E.1.CEL |
- 1.65 |
- 104 |
- 60.80% |
- 37.70% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 53 |
- R2560E.1 |
- BXD19 |
- R2560E.1.CEL |
- 1.79 |
- 98 |
- 60.90% |
- 37.50% |
- 1.60% |
- 1.35 |
- 0.8 |
- 1 |
- Y |
-
-
- | 54 |
- R2713E.2 |
- BXD19 |
- R2713E.2.CEL |
- 1.67 |
- 120.82 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 55 |
- R2584E.1 |
- BXD20 |
- R2584E.1.CEL |
- 2.07 |
- 84 |
- 59.30% |
- 39.10% |
- 1.60% |
- 1.4 |
- 0.76 |
- 1 |
- Y |
-
-
- | 56 |
- R2731E.2 |
- BXD20 |
- R2731E.2.CEL |
- 1.825 |
- 147 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.4 |
- 0.8 |
- 2 |
- |
-
-
- | 57 |
- R2702E.2 |
- BXD21 |
- R2702E.2.CEL |
- 1.811 |
- 128.65 |
- 59.40% |
- 39.10% |
- 1.40% |
- 1.26 |
- 0.8 |
- 2 |
- |
-
-
- | 58 |
- R2541E2.1 |
- BXD21 |
- R2541E2.1.CEL |
- 2.63 |
- 125 |
- 56.00% |
- 42.40% |
- 1.50% |
- 1.29 |
- 0.78 |
- 1 |
- |
-
-
- | 59 |
- R2553E.1 |
- BXD22 |
- R2553E.1.CEL |
- 1.95 |
- 111 |
- 59.90% |
- 38.50% |
- 1.50% |
- 1.28 |
- 0.76 |
- 1 |
- Y |
-
-
- | 60 |
- R2700E.2 |
- BXD22 |
- R2700E.2.CEL |
- 1.858 |
- 102.96 |
- 61.50% |
- 37.10% |
- 1.30% |
- 1.48 |
- 0.79 |
- 2 |
- |
-
-
- | 61 |
- R2558E-2.1 |
- BXD23 |
- R2558E-2.1.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 62 |
- R1086E.2 |
- BXD23 |
- R1086E.2.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 63 |
- R2719E.2 |
- BXD24 |
- R2719E.2.CEL |
- 1.47 |
- 140.38 |
- 61.50% |
- 37.20% |
- 1.30% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 64 |
- R2589E2.1 |
- BXD24 |
- R2589E2.1.CEL |
- 2.61 |
- 112 |
- 57.50% |
- 40.90% |
- 1.60% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 65 |
- R2573E-2.1 |
- BXD25 |
- R2573E-2.1.CEL |
- 3.15 |
- 72 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.77 |
- 0.97 |
- 1 |
- |
-
-
- | 66 |
- R2683E.2 |
- BXD25 |
- R2683E.2.CEL |
- 1.777 |
- 115.64 |
- 58.30% |
- 40.30% |
- 1.40% |
- 2.01 |
- 0.79 |
- 2 |
- |
-
-
- | 67 |
- R2703E.2 |
- BXD27 |
- R2703E.2.CEL |
- 1.263 |
- 134.78 |
- 62.60% |
- 36.10% |
- 1.40% |
- 1.44 |
- 0.78 |
- 2 |
- |
-
-
- | 68 |
- R2729E.3 |
- BXD27 |
- R2729E.3.CEL |
- 1 |
- 87 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.56 |
- 0.84 |
- 3 |
- Y |
-
-
- | 69 |
- R2562E.3 |
- BXD28 |
- R2562E.3.CEL |
- 1.65 |
- 116 |
- 59.90% |
- 38.40% |
- 1.70% |
- 1.37 |
- 0.79 |
- 3 |
- Y |
-
-
- | 70 |
- R2721E.2 |
- BXD28 |
- R2721E.2.CEL |
- 2.065 |
- 157.39 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 71 |
- R2561E.3 |
- BXD29 |
- R2561E.3.CEL |
- 1 |
- 77 |
- 53.30% |
- 45.40% |
- 1.40% |
- 3.36 |
- 19.66 |
- 3 |
- |
-
-
- | 72 |
- R1258E.2 |
- BXD31 |
- R1258E.2.CEL |
- 2.063 |
- 117.09 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.54 |
- 0.78 |
- 2 |
- |
-
-
- | 73 |
- R2597E.1 |
- BXD31 |
- R2597E.1.CEL |
- 2.37 |
- 94 |
- 60.30% |
- 38.30% |
- 1.50% |
- 1.34 |
- 0.77 |
- 1 |
- Y |
-
-
- | 74 |
- R2563E.1 |
- BXD32 |
- R2563E.1.CEL |
- 1.55 |
- 102 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.5 |
- 0.8 |
- 1 |
- |
-
-
- | 75 |
- R1216E.2 |
- BXD32 |
- R1216E.2.CEL |
- 2.23 |
- 111.99 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.35 |
- 0.79 |
- 2 |
- |
-
-
- | 76 |
- R2542E.1 |
- BXD33 |
- R2542E.1.CEL |
- 2.13 |
- 97 |
- 56.50% |
- 41.80% |
- 1.60% |
- 1.91 |
- 0.93 |
- 1 |
- |
-
-
- | 77 |
- R857E.2 |
- BXD33 |
- R857E.2.CEL |
- 1.737 |
- 113.98 |
- 61.90% |
- 36.70% |
- 1.30% |
- 1.6 |
- 0.77 |
- 2 |
- |
-
-
- | 78 |
- R1451E.2 |
- BXD34 |
- R1451E.2.CEL |
- 1.843 |
- 140.05 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.42 |
- 0.81 |
- 2 |
- Y |
-
-
- | 79 |
- R2585E.1 |
- BXD34 |
- R2585E.1.CEL |
- 2.64 |
- 75 |
- 58.30% |
- 40.00% |
- 1.70% |
- 1.25 |
- 0.77 |
- 1 |
- |
-
-
- | 80 |
- R2698E.3 |
- BXD36 |
- R2698E.3.CEL |
- 1 |
- 86 |
- 59.70% |
- 39.00% |
- 1.30% |
- 1.46 |
- 0.78 |
- 3 |
- |
-
-
- | 81 |
- R2705E.3 |
- BXD36 |
- R2705E.3.CEL |
- 1 |
- 86 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.46 |
- 0.77 |
- 3 |
- |
-
-
- | 82 |
- R2710E.2 |
- BXD38 |
- R2710E.2.CEL |
- 2.112 |
- 122.1 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.37 |
- 0.78 |
- 2 |
- |
-
-
- | 83 |
- R2532E.1 |
- BXD38 |
- R2532E.1.CEL |
- 2.04 |
- 94 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.37 |
- 0.8 |
- 1 |
- Y |
-
-
- | 84 |
- R2574E.1 |
- BXD39 |
- R2574E.1.CEL |
- 1.98 |
- 91 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.39 |
- 0.78 |
- 1 |
- |
-
-
- | 85 |
- R2695E.2 |
- BXD39 |
- R2695E.2.CEL |
- 1.638 |
- 122.7 |
- 60.80% |
- 37.80% |
- 1.50% |
- 1.42 |
- 0.8 |
- 2 |
- |
-
-
- | 86 |
- R2699E.2 |
- BXD40 |
- R2699E.2.CEL |
- 1.827 |
- 105.23 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 87 |
- R2590E.1 |
- BXD40 |
- R2590E.1.CEL |
- 2.71 |
- 77 |
- 59.10% |
- 39.30% |
- 1.50% |
- 1.4 |
- 0.77 |
- 1 |
- Y |
-
-
- | 88 |
- R2696E.2 |
- BXD42 |
- R2696E.2.CEL |
- 1.622 |
- 118.95 |
- 62.00% |
- 36.60% |
- 1.50% |
- 1.53 |
- 0.79 |
- 2 |
- |
-
-
- | 89 |
- R2596E.1 |
- BXD42 |
- R2596E.1.CEL |
- 2.63 |
- 108 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 90 |
- R994E.2 |
- BXD43 |
- R994E.2.CEL |
- 1.966 |
- 113.12 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.66 |
- 0.8 |
- 2 |
- |
-
-
- | 91 |
- R2607E.1 |
- BXD43 |
- R2607E.1.CEL |
- 2.43 |
- 115 |
- 58.60% |
- 40.00% |
- 1.40% |
- 1.31 |
- 0.76 |
- 1 |
- Y |
-
-
- | 92 |
- R2594E.1 |
- BXD44 |
- R2594E.1.CEL |
- 1.77 |
- 117 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.35 |
- 0.85 |
- 1 |
- |
-
-
- | 93 |
- R2610E.2 |
- BXD44 |
- R2610E.2.CEL |
- 1.814 |
- 142.91 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.35 |
- 0.8 |
- 2 |
- |
-
-
- | 94 |
- R2732E.2 |
- BXD45 |
- R2732E.2.CEL |
- 2.154 |
- 122.45 |
- 56.50% |
- 42.10% |
- 1.40% |
- 1.8 |
- 0.83 |
- 2 |
- |
-
-
- | 95 |
- R2592E.1 |
- BXD45 |
- R2592E.1.CEL |
- 1.85 |
- 106 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.43 |
- 0.85 |
- 1 |
- Y |
-
-
- | 96 |
- R967E.2 |
- BXD48 |
- R967E.2.CEL |
- 1.948 |
- 130.95 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.63 |
- 0.81 |
- 2 |
- |
-
-
- | 97 |
- R2606E.1 |
- BXD48 |
- R2606E.1.CEL |
- 2.56 |
- 106 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.35 |
- 0.83 |
- 1 |
- Y |
-
-
- | 98 |
- R2933E.3 |
- BXD50 |
- R2933E.3.CEL |
- 1 |
- 72 |
- 52.90% |
- 45.60% |
- 1.50% |
- 2.45 |
- 0.98 |
- 3 |
- |
-
-
- | 99 |
- R2937E.3 |
- BXD50 |
- R2937E.3.CEL |
- 1 |
- 89 |
- 56.90% |
- 41.60% |
- 1.40% |
- 1.81 |
- 0.82 |
- 3 |
- |
-
-
- | 100 |
- R2603E.1 |
- BXD51 |
- R2603E.1.CEL |
- 2.49 |
- 115 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.24 |
- 0.79 |
- 1 |
- |
-
-
- | 101 |
- R1042E.2 |
- BXD51 |
- R1042E.2.CEL |
- 2.352 |
- 104.12 |
- 58.70% |
- 39.90% |
- 1.40% |
- 1.53 |
- 0.82 |
- 2 |
- |
-
-
- | 102 |
- R2980E.3 |
- BXD55 |
- R2980E.3.CEL |
- 1 |
- 82 |
- 56.90% |
- 41.70% |
- 1.50% |
- 1.77 |
- 0.84 |
- 3 |
- |
-
-
- | 103 |
- R2690E.2 |
- BXD55 |
- R2690E.2.CEL |
- 1.887 |
- 164.01 |
- 56.10% |
- 42.30% |
- 1.60% |
- 1.43 |
- 0.8 |
- 2 |
- |
-
-
- | 104 |
- R4176E |
- BXD56 |
- R4176E.CEL |
- 4.75 |
- 43.08 |
- 63.00% |
- 35.60% |
- 1.30% |
- 1.39 |
- 0.81 |
- 4 |
- Y |
-
-
- | 105 |
- R4175E |
- BXD56 |
- R4175E.CEL |
- 6 |
- 38.49 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.47 |
- 0.81 |
- 4 |
- Y |
-
-
- | 106 |
- R1006E.3 |
- BXD60 |
- R1006E.3.CEL |
- 1 |
- 98 |
- 54.90% |
- 43.70% |
- 1.50% |
- 2.7 |
- 0.86 |
- 3 |
- |
-
-
- | 107 |
- R2725E.2 |
- BXD60 |
- R2725E.2.CEL |
- 1.551 |
- 148.01 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 108 |
- R1074E.3 |
- BXD60 |
- R1074E.3.CEL |
- 1 |
- 118 |
- 55.50% |
- 43.10% |
- 1.40% |
- 1.96 |
- 0.81 |
- 3 |
- |
-
-
- | 109 |
- R2534E2.1 |
- BXD61 |
- R2534E2.1.CEL |
- 2.47 |
- 118 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.42 |
- 0.79 |
- 1 |
- |
-
-
- | 110 |
- R2684E.2 |
- BXD61 |
- R2684E.2.CEL |
- 2.01 |
- 131.03 |
- 57.00% |
- 41.50% |
- 1.50% |
- 1.34 |
- 0.78 |
- 2 |
- |
-
-
- | 111 |
- R1107E.3 |
- BXD62 |
- R1107E.3.CEL |
- 1 |
- 83 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.43 |
- 0.93 |
- 3 |
- |
-
-
- | 112 |
- R2681E.2 |
- BXD62 |
- R2681E.2.CEL |
- 2.086 |
- 148.24 |
- 57.20% |
- 41.30% |
- 1.50% |
- 1.29 |
- 0.81 |
- 2 |
- |
-
-
- | 113 |
- R965E.3 |
- BXD62 |
- R965E.3.CEL |
- 1 |
- 93.55 |
- 53.30% |
- 45.20% |
- 1.50% |
- 3.11 |
- 0.94 |
- 3 |
- |
-
-
- | 114 |
- R1425E.2 |
- BXD63 |
- R1425E.2.CEL |
- 1.7 |
- 136 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.43 |
- 0.82 |
- 2 |
- |
-
-
- | 115 |
- R2576E.3 |
- BXD63 |
- R2576E.3.CEL |
- 1 |
- 84 |
- 61.30% |
- 37.40% |
- 1.40% |
- 1.48 |
- 0.76 |
- 3 |
- |
-
-
- | 116 |
- R943E-2.2 |
- BXD64 |
- R943E-2.2.CEL |
- 1.591 |
- 141.34 |
- 60.10% |
- 38.40% |
- 1.50% |
- 1.32 |
- 0.76 |
- 2 |
- |
-
-
- | 117 |
- R2611E.1 |
- BXD64 |
- R2611E.1.CEL |
- 2.29 |
- 92 |
- 58.00% |
- 40.50% |
- 1.50% |
- 1.57 |
- 1.06 |
- 1 |
- |
-
-
- | 118 |
- R2689E.2 |
- BXD65 |
- R2689E.2.CEL |
- 1.721 |
- 142.44 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.38 |
- 0.76 |
- 2 |
- |
-
-
- | 119 |
- R2583E.1 |
- BXD65 |
- R2583E.1.CEL |
- 2.49 |
- 70 |
- 56.90% |
- 41.50% |
- 1.60% |
- 1.67 |
- 1.01 |
- 1 |
- |
-
-
- | 120 |
- R2728E.2 |
- BXD66 |
- R2728E.2.CEL |
- 1.714 |
- 137.45 |
- 59.40% |
- 39.00% |
- 1.60% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 121 |
- R2536E2.1 |
- BXD66 |
- R2536E2.1.CEL |
- 2.74 |
- 109 |
- 56.10% |
- 42.30% |
- 1.70% |
- 1.28 |
- 0.79 |
- 1 |
- |
-
-
- | 122 |
- R1207E.2 |
- BXD66 |
- R1207E.2.CEL |
- 1.681 |
- 136.86 |
- 60.40% |
- 38.10% |
- 1.50% |
- 1.45 |
- 0.77 |
- 2 |
- |
-
-
- | 123 |
- R1192E.2 |
- BXD67 |
- R1192E.2.CEL |
- 2.126 |
- 123.37 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 124 |
- R2727E.3 |
- BXD67 |
- R2727E.3.CEL |
- 1 |
- 82.55 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.97 |
- 0.87 |
- 2 |
- |
-
-
- | 125 |
- R2691E.3 |
- BXD67 |
- R2691E.3.CEL |
- 1 |
- 90 |
- 54.80% |
- 43.80% |
- 1.50% |
- 2.61 |
- 0.81 |
- 3 |
- |
-
-
- | 126 |
- R2551E.1 |
- BXD68 |
- R2551E.1.CEL |
- 2.49 |
- 92 |
- 54.30% |
- 44.10% |
- 1.60% |
- 2.91 |
- 1.55 |
- 1 |
- |
-
-
- | 127 |
- R2726E.2 |
- BXD68 |
- R2726E.2.CEL |
- 1.811 |
- 153.09 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.39 |
- 0.78 |
- 2 |
- |
-
-
- | 128 |
- R2593E.1 |
- BXD69 |
- R2593E.1.CEL |
- 1.67 |
- 128 |
- 59.20% |
- 39.50% |
- 1.30% |
- 1.47 |
- 0.92 |
- 1 |
- Y |
-
-
- | 129 |
- R975E.2 |
- BXD70 |
- R975E.2.CEL |
- 1.841 |
- 137.97 |
- 58.00% |
- 40.50% |
- 1.40% |
- 1.36 |
- 0.79 |
- 2 |
- |
-
-
- | 130 |
- R2537E2.1 |
- BXD70 |
- R2537E2.1.CEL |
- 2.93 |
- 99 |
- 58.00% |
- 40.50% |
- 1.60% |
- 1.29 |
- 0.75 |
- 1 |
- |
-
-
- | 131 |
- R4531E |
- BXD71 |
- R4531E.CEL |
- 4.77 |
- 43.48 |
- 62.40% |
- 36.30% |
- 1.40% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 132 |
- R4532E |
- BXD71 |
- R4532E.CEL |
- 5.89 |
- 40.68 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.24 |
- 0.79 |
- 4 |
- Y |
-
-
- | 133 |
- R2779E.2 |
- BXD73 |
- R2779E.2.CEL |
- 1.746 |
- 121.11 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 134 |
- R3024E.3 |
- BXD73 |
- R3024E.3.CEL |
- 1 |
- 78.05 |
- 51.70% |
- 46.60% |
- 1.70% |
- 2.3 |
- 0.94 |
- 3 |
- |
-
-
- | 135 |
- R2565E.1 |
- BXD75 |
- R2565E.1.CEL |
- 1.79 |
- 102 |
- 58.00% |
- 40.50% |
- 1.50% |
- 2.31 |
- 3.47 |
- 1 |
- |
-
-
- | 136 |
- R1397E-re.2 |
- BXD75 |
- R1397E-re.2.CEL |
- 1.449 |
- 189.71 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 137 |
- R2687E.3 |
- BXD77 |
- R2687E.3.CEL |
- 1 |
- 80 |
- 58.00% |
- 40.60% |
- 1.40% |
- 1.57 |
- 0.8 |
- 3 |
- Y |
-
-
- | 138 |
- R2717E.2 |
- BXD77 |
- R2717E.2.CEL |
- 1.797 |
- 84.43 |
- 61.60% |
- 36.90% |
- 1.40% |
- 1.49 |
- 0.76 |
- 2 |
- |
-
-
- | 139 |
- R1421E.3 |
- BXD77 |
- R1421E.3.CEL |
- 1 |
- 94 |
- 52.40% |
- 46.20% |
- 1.40% |
- 2.29 |
- 0.82 |
- 3 |
- |
-
-
- | 140 |
- R2579E.1 |
- BXD80 |
- R2579E.1.CEL |
- 2.42 |
- 72 |
- 59.20% |
- 39.40% |
- 1.50% |
- 1.73 |
- 0.82 |
- 1 |
- |
-
-
- | 141 |
- R2686E.2 |
- BXD80 |
- R2686E.2.CEL |
- 2.342 |
- 119.63 |
- 56.00% |
- 42.60% |
- 1.50% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 142 |
- R2956E.3 |
- BXD83 |
- R2956E.3.CEL |
- 1 |
- 84 |
- 55.40% |
- 43.20% |
- 1.40% |
- 1.39 |
- 0.84 |
- 3 |
- |
-
-
- | 143 |
- R2960E.3 |
- BXD83 |
- R2960E.3.CEL |
- 1 |
- 80 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.5 |
- 0.82 |
- 3 |
- Y |
-
-
- | 144 |
- R2922E.3 |
- BXD84 |
- R2922E.3.CEL |
- 1 |
- 91 |
- 57.80% |
- 40.80% |
- 1.50% |
- 1.47 |
- 0.83 |
- 3 |
- Y |
-
-
- | 145 |
- R2895E.3 |
- BXD84 |
- R2895E.3.CEL |
- 1 |
- 75 |
- 58.30% |
- 40.20% |
- 1.50% |
- 1.56 |
- 0.77 |
- 3 |
- Y |
-
-
- | 146 |
- R2692E.2 |
- BXD85 |
- R2692E.2.CEL |
- 1.423 |
- 160.87 |
- 60.20% |
- 38.30% |
- 1.40% |
- 1.46 |
- 0.79 |
- 2 |
- |
-
-
- | 147 |
- R2715E.2 |
- BXD85 |
- R2715E.2.CEL |
- 1.488 |
- 142.6 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.5 |
- 0.78 |
- 2 |
- |
-
-
- | 148 |
- R1405E.2 |
- BXD86 |
- R1405E.2.CEL |
- 2.351 |
- 119.34 |
- 56.40% |
- 42.20% |
- 1.40% |
- 1.64 |
- 0.81 |
- 2 |
- |
-
-
- | 149 |
- R1225E.3 |
- BXD86 |
- R1225E.3.CEL |
- 1 |
- 71 |
- 53.90% |
- 44.60% |
- 1.40% |
- 3.2 |
- 1.61 |
- 3 |
- |
-
-
- | 150 |
- R2724E.2 |
- BXD87 |
- R2724E.2.CEL |
- 1.906 |
- 113.71 |
- 60.70% |
- 37.90% |
- 1.40% |
- 1.45 |
- 0.79 |
- 2 |
- |
-
-
- | 151 |
- R2540E.1 |
- BXD87 |
- R2540E.1.CEL |
- 2.33 |
- 93 |
- 61.10% |
- 37.40% |
- 1.40% |
- 1.22 |
- 0.81 |
- 1 |
- Y |
-
-
- | 152 |
- R1433E.2 |
- BXD89 |
- R1433E.2.CEL |
- 1 |
- 2.241 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.41 |
- 0.78 |
- 2 |
- |
-
-
- | 153 |
- R2546E.1 |
- BXD89 |
- R2546E.1.CEL |
- 1.99 |
- 96 |
- 58.60% |
- 39.70% |
- 1.70% |
- 1.47 |
- 0.78 |
- 1 |
- |
-
-
- | 154 |
- R2578E2.1 |
- BXD90 |
- R2578E2.1.CEL |
- 2.79 |
- 92 |
- 58.60% |
- 39.80% |
- 1.60% |
- 1.52 |
- 0.77 |
- 1 |
- Y |
-
-
- | 155 |
- R859E.2 |
- BXD90 |
- R859E.2.CEL |
- 1.847 |
- 152.22 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.36 |
- 0.77 |
- 2 |
- |
-
-
- | 156 |
- R2682E.2 |
- BXD92 |
- R2682E.2.CEL |
- 1.547 |
- 156.31 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.37 |
- 0.77 |
- 2 |
- |
-
-
- | 157 |
- R1388E.3 |
- BXD92 |
- R1388E.3.CEL |
- 1 |
- 63 |
- 60.00% |
- 38.60% |
- 1.40% |
- 1.85 |
- 1.03 |
- 3 |
- |
-
-
- | 158 |
- R1322E.3 |
- BXD92 |
- R1322E.3.CEL |
- 1 |
- 80 |
- 55.90% |
- 42.60% |
- 1.50% |
- 1.75 |
- 0.74 |
- 3 |
- |
-
-
- | 159 |
- R2733E.2 |
- BXD96 |
- R2733E.2.CEL |
- 1.7 |
- 113.99 |
- 62.10% |
- 36.60% |
- 1.30% |
- 1.4 |
- 0.78 |
- 2 |
- |
-
-
- | 160 |
- R2554E.1 |
- BXD96 |
- R2554E.1.CEL |
- 2.18 |
- 93 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 161 |
- R2649E.2 |
- BXD97 |
- R2649E.2.CEL |
- 2.343 |
- 119.04 |
- 57.50% |
- 41.20% |
- 1.40% |
- 1.53 |
- 0.8 |
- 2 |
- |
-
-
- | 162 |
- R2577E.1 |
- BXD97 |
- R2577E.1.CEL |
- 2.07 |
- 77 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.87 |
- 1.29 |
- 1 |
- |
-
-
- | 163 |
- R2645E.3 |
- BXD98 |
- R2645E.3.CEL |
- 1 |
- 88 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.59 |
- 0.81 |
- 3 |
- Y |
-
-
- | 164 |
- R2688E.2 |
- BXD98 |
- R2688E.2.CEL |
- 1.772 |
- 145.24 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.48 |
- 0.81 |
- 2 |
- |
-
-
- | 165 |
- R4533E |
- BXD99 |
- R4533E.CEL |
- 1 |
- 37.69 |
- 60.30% |
- 38.20% |
- 1.40% |
- 1.33 |
- 0.89 |
- 4 |
- Y |
-
-
- | 166 |
- R4534E |
- BXD99 |
- R4534E.CEL |
- 5.69 |
- 36.62 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.16 |
- 0.8 |
- 4 |
- Y |
-
-
- | 167 |
- R2885E.3 |
- BXSB/MpJ |
- R2885E.3.CEL |
- 1 |
- 76 |
- 58.10% |
- 40.60% |
- 1.30% |
- 1.88 |
- 1.06 |
- 3 |
- |
-
-
- | 168 |
- R2883E.3 |
- BXSB/MpJ |
- R2883E.3.CEL |
- 1 |
- 71 |
- 56.40% |
- 42.00% |
- 1.50% |
- 1.59 |
- 0.84 |
- 3 |
- Y |
-
-
- | 169 |
- R1700E.1 |
- C3H/HeJ |
- R1700E.1.CEL |
- 2.98 |
- 69 |
- 60.80% |
- 37.90% |
- 1.40% |
- 1.48 |
- 0.78 |
- 1 |
- |
-
-
- | 170 |
- R1704E.1 |
- C3H/HeJ |
- R1704E.1.CEL |
- 2.58 |
- 88 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.38 |
- 0.84 |
- 1 |
- |
-
-
- | 171 |
- R2605E.1 |
- C57BL/6J |
- R2605E.1.CEL |
- 1.82 |
- 131 |
- 60.50% |
- 38.20% |
- 1.30% |
- 1.32 |
- 0.8 |
- 1 |
- Y |
-
-
- | 172 |
- R0871E |
- C57BL/6J |
- R0871E.CEL |
- 6.24 |
- 37.38 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.41 |
- 0.8 |
- 4 |
- Y |
-
-
- | 173 |
- R0872E.1 |
- C57BL/6J |
- R0872E.1.CEL |
- 3.13 |
- 89 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 174 |
- R0872E |
- C57BL/6J |
- R0872E.CEL |
- 3.128 |
- 88.58 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- |
-
-
- | 175 |
- R4507E |
- C57BL/6J-Nyx |
- R4507E.CEL |
- 8.13 |
- 37.5 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.32 |
- 0.8 |
- 4 |
- Y |
-
-
- | 176 |
- R4508E |
- C57BL/6J-Nyx |
- R4508E.CEL |
- 6.33 |
- 37.26 |
- 60.90% |
- 37.80% |
- 1.30% |
- 1.24 |
- 0.82 |
- 4 |
- Y |
-
-
- | 177 |
- R4505E |
- C57BL/6J-Rpe65 |
- R4505E.CEL |
- 5.98 |
- 37.48 |
- 61.80% |
- 36.80% |
- 1.40% |
- 1.45 |
- 0.85 |
- 4 |
- Y |
-
-
- | 178 |
- R4506E |
- C57BL/6J-Rpe65 |
- R4506E.CEL |
- 6.94 |
- 37.9 |
- 61.10% |
- 37.50% |
- 1.30% |
- 1.5 |
- 0.83 |
- 4 |
- Y |
-
-
- | 179 |
- R4535E |
- C57BLKS/J |
- R4535E.CEL |
- 6.59 |
- 37.28 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.26 |
- 0.83 |
- 4 |
- Y |
-
-
- | 180 |
- R4536E |
- C57BLKS/J |
- R4536E.CEL |
- 1 |
- 40.71 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.25 |
- 0.77 |
- 4 |
- Y |
-
-
- | 181 |
- R2564E.1 |
- CAST/EiJ |
- R2564E.1.CEL |
- 1.94 |
- 89 |
- 58.50% |
- 39.90% |
- 1.60% |
- 1.6 |
- 0.77 |
- 1 |
- |
-
-
- | 182 |
- R2580E.1 |
- CAST/EiJ |
- R2580E.1.CEL |
- 2.09 |
- 95 |
- 58.20% |
- 40.10% |
- 1.70% |
- 1.4 |
- 0.76 |
- 1 |
- |
-
-
- | 183 |
- R4537E |
- CBA/CaJ |
- R4537E.CEL |
- 1 |
- 38.45 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.63 |
- 0.82 |
- 4 |
- Y |
-
-
- | 184 |
- R4538E |
- CBA/CaJ |
- R4538E.CEL |
- 5.89 |
- 39.18 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.45 |
- 0.8 |
- 4 |
- Y |
-
-
- | 185 |
- R4539E |
- CZECHII/EiJ |
- R4539E.CEL |
- 7.73 |
- 37.1 |
- 58.30% |
- 40.10% |
- 1.50% |
- 1.7 |
- 0.95 |
- 4 |
- Y |
-
-
- | 186 |
- R4540E |
- CZECHII/EiJ |
- R4540E.CEL |
- 11.04 |
- 36.69 |
- 53.00% |
- 45.30% |
- 1.70% |
- 1.83 |
- 1.32 |
- 4 |
- |
-
-
- | 187 |
- R2600E.1 |
- D2B6F1 |
- R2600E.1.CEL |
- 2.47 |
- 95 |
- 58.10% |
- 40.20% |
- 1.70% |
- 1.41 |
- 0.78 |
- 1 |
- Y |
-
-
- | 188 |
- R2604E.1 |
- D2B6F1 |
- R2604E.1.CEL |
- 2.66 |
- 90 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.28 |
- 0.79 |
- 1 |
- Y |
-
-
- | 189 |
- R1002E.3 |
- DBA/2J |
- R1002E.3.CEL |
- 1 |
- 102 |
- 54.80% |
- 43.70% |
- 1.50% |
- 2.84 |
- 0.83 |
- 3 |
- |
-
-
- | 190 |
- R4541E |
- DBA/2J |
- R4541E.CEL |
- 1 |
- 43.4 |
- 61.40% |
- 37.00% |
- 1.50% |
- 1.37 |
- 0.73 |
- 4 |
- Y |
-
-
- | 191 |
- R959E.3 |
- DBA/2J |
- R959E.3.CEL |
- 1 |
- 89.97 |
- 53.20% |
- 45.30% |
- 1.50% |
- 3.66 |
- 1.09 |
- 4 |
- |
-
-
- | 192 |
- R2572E.1 |
- DBA/2J |
- R2572E.1.CEL |
- 2.41 |
- 79 |
- 55.50% |
- 42.90% |
- 1.60% |
- 1.37 |
- 0.79 |
- 1 |
- |
-
-
- | 193 |
- R4542E |
- DBA/2J |
- R4542E.CEL |
- 5.7 |
- 39.95 |
- 61.00% |
- 37.40% |
- 1.50% |
- 1.23 |
- 0.81 |
- 4 |
- Y |
-
-
- | 194 |
- R2771E.3 |
- FVB/NJ |
- R2771E.3.CEL |
- 1 |
- 70 |
- 55.30% |
- 43.20% |
- 1.50% |
- 1.69 |
- 0.83 |
- 3 |
- |
-
-
- | 195 |
- R2772E.3 |
- FVB/NJ |
- R2772E.3.CEL |
- 1 |
- 76 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.13 |
- 1.02 |
- 3 |
- |
-
-
- | 196 |
- R2636E.1 |
- KK/HlJ |
- R2636E.1.CEL |
- 2.61 |
- 93 |
- 58.90% |
- 39.50% |
- 1.50% |
- 1.39 |
- 0.76 |
- 1 |
- Y |
-
-
- | 197 |
- R2637E.1 |
- KK/HlJ |
- R2637E.1.CEL |
- 2.19 |
- 103 |
- 59.40% |
- 39.00% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 198 |
- R0999E.1 |
- LG/J |
- R0999E.1.CEL |
- 2.45 |
- 82 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 199 |
- R1004E.1 |
- LG/J |
- R1004E.1.CEL |
- 2.44 |
- 92 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 200 |
- R4543E |
- LP/J |
- R4543E.CEL |
- 6.57 |
- 41.99 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.28 |
- 0.75 |
- 4 |
- Y |
-
-
- | 201 |
- R4544E |
- LP/J |
- R4544E.CEL |
- 4.56 |
- 39.9 |
- 62.40% |
- 36.10% |
- 1.50% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 202 |
- R2858E.3 |
- MOLF/EiJ |
- R2858E.3.CEL |
- 1 |
- 64 |
- 53.80% |
- 44.70% |
- 1.50% |
- 1.59 |
- 0.95 |
- 3 |
- |
-
-
- | 203 |
- R2919.3 |
- MOLF/EiJ |
- R2919.3.CEL |
- 1 |
- 64 |
- 52.40% |
- 46.00% |
- 1.60% |
- 2.15 |
- 1.07 |
- 3 |
- |
-
-
- | 204 |
- R1688E.1 |
- NOD/LtJ |
- R1688E.1.CEL |
- 2.66 |
- 98 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 205 |
- R2566E-2.1 |
- NOD/LtJ |
- R2566E-2.1.CEL |
- 3.03 |
- 69 |
- 59.80% |
- 38.80% |
- 1.50% |
- 1.38 |
- 0.75 |
- 1 |
- Y |
-
-
- | 206 |
- R4545E |
- NZB/BlNJ |
- R4545E.CEL |
- 4.23 |
- 43.48 |
- 62.10% |
- 36.40% |
- 1.50% |
- 1.33 |
- 0.76 |
- 4 |
- Y |
-
-
- | 207 |
- R4546E |
- NZB/BlNJ |
- R4546E.CEL |
- 6.27 |
- 44.22 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.17 |
- 0.82 |
- 4 |
- Y |
-
-
- | 208 |
- R2535E.1 |
- NZO/HlLtJ |
- R2535E.1.CEL |
- 1.89 |
- 86 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.41 |
- 0.85 |
- 1 |
- |
-
-
- | 209 |
- R2550E.1 |
- NZO/HlLtJ |
- R2550E.1.CEL |
- 1.79 |
- 87 |
- 60.70% |
- 37.80% |
- 1.50% |
- 1.52 |
- 0.82 |
- 1 |
- |
-
-
- | 210 |
- R2817E.3 |
- NZW/LacJ |
- R2817E.3.CEL |
- 1 |
- 59 |
- 50.90% |
- 47.60% |
- 1.50% |
- 3.59 |
- 1.48 |
- 3 |
- |
-
-
- | 211 |
- R2810E |
- NZW/LacJ |
- R2810E.CEL |
- |
- |
- |
- |
- |
- |
- |
- 3 |
- |
-
-
- | 212 |
- R2810E.3 |
- NZW/LacJ |
- R2810E.3.CEL |
- 1 |
- 74 |
- 57.00% |
- 41.70% |
- 1.40% |
- 2.15 |
- 1.03 |
- 4 |
- Y |
-
-
- | 213 |
- R4547E |
- PANCEVO/EiJ |
- R4547E.CEL |
- 5.27 |
- 51.34 |
- 57.20% |
- 41.10% |
- 1.70% |
- 1.7 |
- 0.83 |
- 4 |
- |
-
-
- | 214 |
- R4548E |
- PANCEVO/EiJ |
- R4548E.CEL |
- 10.54 |
- 37.39 |
- 50.30% |
- 48.00% |
- 1.70% |
- 1.68 |
- 1.09 |
- 4 |
- |
-
-
- | 215 |
- R2635E.1 |
- PWD/PhJ |
- R2635E.1.CEL |
- 3.72 |
- 80 |
- 54.20% |
- 44.10% |
- 1.70% |
- 1.53 |
- 0.85 |
- 1 |
- |
-
-
- | 216 |
- R2634E.1 |
- PWD/PhJ |
- R2634E.1.CEL |
- 3.29 |
- 90 |
- 55.90% |
- 42.50% |
- 1.60% |
- 1.57 |
- 0.81 |
- 1 |
- |
-
-
- | 217 |
- R2544E.1 |
- PWK/PhJ |
- R2544E.1.CEL |
- 2.2 |
- 108 |
- 54.90% |
- 43.50% |
- 1.70% |
- 1.36 |
- 0.82 |
- 1 |
- |
-
-
- | 218 |
- R2549E.1 |
- PWK/PhJ |
- R2549E.1.CEL |
- 2.28 |
- 84 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.57 |
- 0.83 |
- 1 |
- |
-
-
- | 219 |
- R4550E |
- SJL/J |
- R4550E.CEL |
- 5.35 |
- 40.44 |
- 62.30% |
- 36.20% |
- 1.40% |
- 1.24 |
- 0.79 |
- 4 |
- |
-
-
- | 220 |
- R2368E.1 |
- WSB/EiJ |
- R2368E.1.CEL |
- 2.57 |
- 86 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.29 |
- 0.74 |
- 1 |
- Y |
-
-
- | 221 |
- R2547E.1 |
- WSB/EiJ |
- R2547E.1.CEL |
- 2.14 |
- 90 |
- 58.20% |
- 40.10% |
- 1.60% |
- 1.32 |
- 0.77 |
- 1 |
- Y |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_NB/summary.rtf b/general/datasets/Eye_M2_0908_R_NB/summary.rtf
deleted file mode 100644
index 44b7e23..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/summary.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-FINAL RECOMMENDED EYE DATA SET. The HEIMED September 2008 RMA data release provides estimates of gene expression in whole eyes of 103 lines of young adult mice generated using 221 Affymetrix M430 2.0 arrays. This data set is intended for exploration of the genetics and genomics of the mouse eye, retina, lens, retinal pigment epithelium, cornea, iris and choroid. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
diff --git a/general/datasets/Eye_M2_0908_R_NB/tissue.rtf b/general/datasets/Eye_M2_0908_R_NB/tissue.rtf
deleted file mode 100644
index 9b6ee0f..0000000
--- a/general/datasets/Eye_M2_0908_R_NB/tissue.rtf
+++ /dev/null
@@ -1,2058 +0,0 @@
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.
-
-Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well balanced sample of males and females, in general without within-strain-by-sex replication. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.
-
-Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.
-
-Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.
-
-
- - Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
- - Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
- - Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
- - Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
-
-
-Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Group |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- R2595E.1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- UTHSC RW |
-
-
- | 2 |
- R2533E.1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- UTHSC RW |
-
-
- | 3 |
- R0754E.1 |
- GDP |
- A/J |
- 60 |
- M |
- JAX |
-
-
- | 4 |
- R4521E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 5 |
- R4522E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 6 |
- R4523E |
- KO |
- B6129P2F2N1-Clcn3 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 7 |
- R4526E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- F |
- TChoi_Deltagen |
-
-
- | 8 |
- R4509E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- M |
- TChoi_Deltagen |
-
-
- | 9 |
- R4510E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 10 |
- R4511E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 20 |
- M |
- TChoi_Deltagen |
-
-
- | 11 |
- R4524E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 12 |
- R4525E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 13 |
- R4515E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 14 |
- R4516E |
- KO |
- B6129P2F2N1-Gabra1 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 15 |
- R4517E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 16 |
- R4512E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- F |
- TChoi_Deltagen |
-
-
- | 17 |
- R4513E |
- KO |
- B6129P2F2N1-Gnb5 |
- 25 |
- M |
- TChoi_Deltagen |
-
-
- | 18 |
- R4514E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 19 |
- R4518E |
- KO |
- B6129P2F2N1-Gpr19 |
- 70 |
- M |
- TChoi_Deltagen |
-
-
- | 20 |
- R4519E |
- KO |
- B6129P2F2N1-Gpr19 |
- 68 |
- M |
- TChoi_Deltagen |
-
-
- | 21 |
- R2601E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 22 |
- R2602E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 23 |
- R1676E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- JAX |
-
-
- | 24 |
- R1672E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- JAX |
-
-
- | 25 |
- R4530E |
- GDP |
- BALB/cJ |
- 66 |
- F |
- JAX |
-
-
- | 26 |
- R4529E |
- GDP |
- BALB/cJ |
- 66 |
- M |
- JAX |
-
-
- | 27 |
- R2704E.2 |
- BXD |
- BXD1 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 28 |
- R2707E.3 |
- BXD |
- BXD1 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 29 |
- R1231E.2 |
- BXD |
- BXD2 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 30 |
- R2598E.1 |
- BXD |
- BXD2 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 31 |
- R2591E.1 |
- BXD |
- BXD5 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 32 |
- R2714E.2 |
- BXD |
- BXD5 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 33 |
- R2570E.1 |
- BXD |
- BXD6 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 34 |
- R2694E.2 |
- BXD |
- BXD6 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 35 |
- R2538E.1 |
- BXD |
- BXD8 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 36 |
- R2709E.2 |
- BXD |
- BXD8 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 37 |
- R2708E.2 |
- BXD |
- BXD9 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 38 |
- R2569E.1 |
- BXD |
- BXD9 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 39 |
- R2581E.1 |
- BXD |
- BXD11 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 40 |
- R2612E.2 |
- BXD |
- BXD11 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 41 |
- R2742E.2 |
- BXD |
- BXD12 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 42 |
- R2543E.1 |
- BXD |
- BXD12 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 43 |
- R2586E.1 |
- BXD |
- BXD13 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 44 |
- R877E.2 |
- BXD |
- BXD13 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 45 |
- R2557E.1 |
- BXD |
- BXD14 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 46 |
- R1128E.2 |
- BXD |
- BXD14 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 47 |
- R2701E.3 |
- BXD |
- BXD15 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 48 |
- R2716E.2 |
- BXD |
- BXD15 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 49 |
- R2711E.2 |
- BXD |
- BXD16 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 50 |
- R2567E.1 |
- BXD |
- BXD16 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 51 |
- R2720E.2 |
- BXD |
- BXD18 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 52 |
- R2559E.1 |
- BXD |
- BXD18 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 53 |
- R2560E.1 |
- BXD |
- BXD19 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 54 |
- R2713E.2 |
- BXD |
- BXD19 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 55 |
- R2584E.1 |
- BXD |
- BXD20 |
- 59 |
- F |
- BIDMC GR |
-
-
- | 56 |
- R2731E.2 |
- BXD |
- BXD20 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 57 |
- R2702E.2 |
- BXD |
- BXD21 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 58 |
- R2541E2.1 |
- BXD |
- BXD21 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 59 |
- R2553E.1 |
- BXD |
- BXD22 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 60 |
- R2700E.2 |
- BXD |
- BXD22 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 61 |
- R2558E-2.1 |
- BXD |
- BXD23 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 62 |
- R1086E.2 |
- BXD |
- BXD23 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 63 |
- R2719E.2 |
- BXD |
- BXD24 |
- 123 |
- F |
- UTHSC RW |
-
-
- | 64 |
- R2589E2.1 |
- BXD |
- BXD24 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 65 |
- R2573E-2.1 |
- BXD |
- BXD25 |
- 67 |
- F |
- UAB |
-
-
- | 66 |
- R2683E.2 |
- BXD |
- BXD25 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 67 |
- R2703E.2 |
- BXD |
- BXD27 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 68 |
- R2729E.3 |
- BXD |
- BXD27 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 69 |
- R2562E.3 |
- BXD |
- BXD28 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 70 |
- R2721E.2 |
- BXD |
- BXD28 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 71 |
- R2561E.3 |
- BXD |
- BXD29 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 72 |
- R1258E.2 |
- BXD |
- BXD31 |
- 57 |
- F |
- UTHSC RW |
-
-
- | 73 |
- R2597E.1 |
- BXD |
- BXD31 |
- 61 |
- M |
- BIDMC GR |
-
-
- | 74 |
- R2563E.1 |
- BXD |
- BXD32 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 75 |
- R1216E.2 |
- BXD |
- BXD32 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 76 |
- R2542E.1 |
- BXD |
- BXD33 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- R857E.2 |
- BXD |
- BXD33 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 78 |
- R1451E.2 |
- BXD |
- BXD34 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 79 |
- R2585E.1 |
- BXD |
- BXD34 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 80 |
- R2698E.3 |
- BXD |
- BXD36 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 81 |
- R2705E.3 |
- BXD |
- BXD36 |
- 57 |
- M |
- BIDMC GR |
-
-
- | 82 |
- R2710E.2 |
- BXD |
- BXD38 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 83 |
- R2532E.1 |
- BXD |
- BXD38 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 84 |
- R2574E.1 |
- BXD |
- BXD39 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 85 |
- R2695E.2 |
- BXD |
- BXD39 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 86 |
- R2699E.2 |
- BXD |
- BXD40 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 87 |
- R2590E.1 |
- BXD |
- BXD40 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 88 |
- R2696E.2 |
- BXD |
- BXD42 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 89 |
- R2596E.1 |
- BXD |
- BXD42 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 90 |
- R994E.2 |
- BXD |
- BXD43 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 91 |
- R2607E.1 |
- BXD |
- BXD43 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 92 |
- R2594E.1 |
- BXD |
- BXD44 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 93 |
- R2610E.2 |
- BXD |
- BXD44 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 94 |
- R2732E.2 |
- BXD |
- BXD45 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 95 |
- R2592E.1 |
- BXD |
- BXD45 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- R967E.2 |
- BXD |
- BXD48 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 97 |
- R2606E.1 |
- BXD |
- BXD48 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 98 |
- R2933E.3 |
- BXD |
- BXD50 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 99 |
- R2937E.3 |
- BXD |
- BXD50 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 100 |
- R2603E.1 |
- BXD |
- BXD51 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 101 |
- R1042E.2 |
- BXD |
- BXD51 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 102 |
- R2980E.3 |
- BXD |
- BXD55 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 103 |
- R2690E.2 |
- BXD |
- BXD55 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 104 |
- R4176E |
- BXD |
- BXD56 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 105 |
- R4175E |
- BXD |
- BXD56 |
- 53 |
- M |
- UTHSC RW |
-
-
- | 106 |
- R1006E.3 |
- BXD |
- BXD60 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 107 |
- R2725E.2 |
- BXD |
- BXD60 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 108 |
- R1074E.3 |
- BXD |
- BXD60 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 109 |
- R2534E2.1 |
- BXD |
- BXD61 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 110 |
- R2684E.2 |
- BXD |
- BXD61 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 111 |
- R1107E.3 |
- BXD |
- BXD62 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 112 |
- R2681E.2 |
- BXD |
- BXD62 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 113 |
- R965E.3 |
- BXD |
- BXD62 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 114 |
- R1425E.2 |
- BXD |
- BXD63 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 115 |
- R2576E.3 |
- BXD |
- BXD63 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 116 |
- R943E-2.2 |
- BXD |
- BXD64 |
- 56 |
- F |
- UTHSC RW |
-
-
- | 117 |
- R2611E.1 |
- BXD |
- BXD64 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 118 |
- R2689E.2 |
- BXD |
- BXD65 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 119 |
- R2583E.1 |
- BXD |
- BXD65 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 120 |
- R2728E.2 |
- BXD |
- BXD66 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 121 |
- R2536E2.1 |
- BXD |
- BXD66 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 122 |
- R1207E.2 |
- BXD |
- BXD66 |
- 83 |
- M |
- UTHSC RW |
-
-
- | 123 |
- R1192E.2 |
- BXD |
- BXD67 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 124 |
- R2727E.3 |
- BXD |
- BXD67 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 125 |
- R2691E.3 |
- BXD |
- BXD67 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 126 |
- R2551E.1 |
- BXD |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 127 |
- R2726E.2 |
- BXD |
- BXD68 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 128 |
- R2593E.1 |
- BXD |
- BXD69 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 129 |
- R975E.2 |
- BXD |
- BXD70 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 130 |
- R2537E2.1 |
- BXD |
- BXD70 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 131 |
- R4531E |
- BXD |
- BXD71 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 132 |
- R4532E |
- BXD |
- BXD71 |
- 86 |
- M |
- UTHSC RW |
-
-
- | 133 |
- R2779E.2 |
- BXD |
- BXD73 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 134 |
- R3024E.3 |
- BXD |
- BXD73 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 135 |
- R2565E.1 |
- BXD |
- BXD75 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 136 |
- R1397E-re.2 |
- BXD |
- BXD75 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 137 |
- R2687E.3 |
- BXD |
- BXD77 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 138 |
- R2717E.2 |
- BXD |
- BXD77 |
- 107 |
- M |
- UTHSC RW |
-
-
- | 139 |
- R1421E.3 |
- BXD |
- BXD77 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 140 |
- R2579E.1 |
- BXD |
- BXD80 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 141 |
- R2686E.2 |
- BXD |
- BXD80 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 142 |
- R2956E.3 |
- BXD |
- BXD83 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 143 |
- R2960E.3 |
- BXD |
- BXD83 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 144 |
- R2922E.3 |
- BXD |
- BXD84 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 145 |
- R2895E.3 |
- BXD |
- BXD84 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- R2692E.2 |
- BXD |
- BXD85 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 147 |
- R2715E.2 |
- BXD |
- BXD85 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 148 |
- R1405E.2 |
- BXD |
- BXD86 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 149 |
- R1225E.3 |
- BXD |
- BXD86 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 150 |
- R2724E.2 |
- BXD |
- BXD87 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 151 |
- R2540E.1 |
- BXD |
- BXD87 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 152 |
- R1433E.2 |
- BXD |
- BXD89 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 153 |
- R2546E.1 |
- BXD |
- BXD89 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 154 |
- R2578E2.1 |
- BXD |
- BXD90 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 155 |
- R859E.2 |
- BXD |
- BXD90 |
- 72 |
- M |
- UTHSC RW |
-
-
- | 156 |
- R2682E.2 |
- BXD |
- BXD92 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 157 |
- R1388E.3 |
- BXD |
- BXD92 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 158 |
- R1322E.3 |
- BXD |
- BXD92 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 159 |
- R2733E.2 |
- BXD |
- BXD96 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 160 |
- R2554E.1 |
- BXD |
- BXD96 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 161 |
- R2649E.2 |
- BXD |
- BXD97 |
- 74 |
- F |
- UTHSC RW |
-
-
- | 162 |
- R2577E.1 |
- BXD |
- BXD97 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 163 |
- R2645E.3 |
- BXD |
- BXD98 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 164 |
- R2688E.2 |
- BXD |
- BXD98 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 165 |
- R4533E |
- BXD |
- BXD99 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 166 |
- R4534E |
- BXD |
- BXD99 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 167 |
- R2885E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 168 |
- R2883E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- M |
- BIDMC GR |
-
-
- | 169 |
- R1700E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- UTHSC RW |
-
-
- | 170 |
- R1704E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- UTHSC RW |
-
-
- | 171 |
- R2605E.1 |
- GDP BXD |
- C57BL/6J |
- 79 |
- F |
- UTHSC RW |
-
-
- | 172 |
- R0871E |
- GDP BXD |
- C57BL/6J |
- 65 |
- F |
- UTHSC RW |
-
-
- | 173 |
- R0872E.1 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 174 |
- R0872E |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 175 |
- R4507E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 176 |
- R4508E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 177 |
- R4505E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 178 |
- R4506E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 179 |
- R4535E |
- GDP |
- C57BLKS/J |
- 66 |
- F |
- JAX |
-
-
- | 180 |
- R4536E |
- GDP |
- C57BLKS/J |
- 66 |
- M |
- JAX |
-
-
- | 181 |
- R2564E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- F |
- JAX |
-
-
- | 182 |
- R2580E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- M |
- JAX |
-
-
- | 183 |
- R4537E |
- GDP |
- CBA/CaJ |
- 66 |
- F |
- JAX |
-
-
- | 184 |
- R4538E |
- GDP |
- CBA/CaJ |
- 66 |
- M |
- JAX |
-
-
- | 185 |
- R4539E |
- GDP |
- CZECHII/EiJ |
- 66 |
- F |
- JAX |
-
-
- | 186 |
- R4540E |
- GDP |
- CZECHII/EiJ |
- 66 |
- M |
- JAX |
-
-
- | 187 |
- R2600E.1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- UTHSC RW |
-
-
- | 188 |
- R2604E.1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- UTHSC RW |
-
-
- | 189 |
- R1002E.3 |
- GDP BXD |
- DBA/2J |
- 72 |
- F |
- UTHSC RW |
-
-
- | 190 |
- R4541E |
- GDP BXD |
- DBA/2J |
- 65 |
- F |
- JAX |
-
-
- | 191 |
- R959E.3 |
- GDP BXD |
- DBA/2J |
- 60 |
- M |
- UTHSC RW |
-
-
- | 192 |
- R2572E.1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 193 |
- R4542E |
- GDP BXD |
- DBA/2J |
- 59 |
- M |
- JAX |
-
-
- | 194 |
- R2771E.3 |
- GDP |
- FVB/NJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 195 |
- R2772E.3 |
- GDP |
- FVB/NJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 196 |
- R2636E.1 |
- GDP |
- KK/HlJ |
- 64 |
- F |
- UTHSC RW |
-
-
- | 197 |
- R2637E.1 |
- GDP |
- KK/HlJ |
- 64 |
- M |
- UTHSC RW |
-
-
- | 198 |
- R0999E.1 |
- GDP |
- LG/J |
- 57 |
- F |
- UTHSC RW |
-
-
- | 199 |
- R1004E.1 |
- GDP |
- LG/J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 200 |
- R4543E |
- GDP |
- LP/J |
- 65 |
- F |
- JAX |
-
-
- | 201 |
- R4544E |
- GDP |
- LP/J |
- 65 |
- M |
- JAX |
-
-
- | 202 |
- R2858E.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 203 |
- R2919.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 204 |
- R1688E.1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- JAX |
-
-
- | 205 |
- R2566E-2.1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- UTHSC RW |
-
-
- | 206 |
- R4545E |
- GDP |
- NZB/BlNJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 207 |
- R4546E |
- GDP |
- NZB/BlNJ |
- 58 |
- M |
- BIDMC GR |
-
-
- | 208 |
- R2535E.1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- JAX |
-
-
- | 209 |
- R2550E.1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- JAX |
-
-
- | 210 |
- R2817E.3 |
- GDP |
- NZW/LacJ |
- 65 |
- F |
- BIDMC GR |
-
-
- | 211 |
- R2810E |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 212 |
- R2810E.3 |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 213 |
- R4547E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- F |
- JAX |
-
-
- | 214 |
- R4548E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- M |
- JAX |
-
-
- | 215 |
- R2635E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- JAX |
-
-
- | 216 |
- R2634E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- JAX |
-
-
- | 217 |
- R2544E.1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- JAX |
-
-
- | 218 |
- R2549E.1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- JAX |
-
-
- | 219 |
- R4550E |
- GDP |
- SJL/J |
- 65 |
- M+F |
- JAX |
-
-
- | 220 |
- R2368E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- UTHSC RW |
-
-
- | 221 |
- R2547E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- UTHSC RW |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_ND/acknowledgment.rtf b/general/datasets/Eye_M2_0908_R_ND/acknowledgment.rtf
deleted file mode 100644
index 5098d32..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant and from funds from NEI grant to Dr. Eldon Geisert (R01EY017841), an NEI Vision Core grant (EY14080) and an Unrestricted Grant from Research To Prevent Blindness.
-
-We thank Dr. Ted Choi, Chief Scientific Director of Predictive Biology, Inc. (past director of molecular genetics at Deltagen Inc.) for providing us with eye samples from several interesting DeltaGen knockouts.
diff --git a/general/datasets/Eye_M2_0908_R_ND/cases.rtf b/general/datasets/Eye_M2_0908_R_ND/cases.rtf
deleted file mode 100644
index 552d4a5..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/cases.rtf
+++ /dev/null
@@ -1,57 +0,0 @@
-This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:
-
-
- - 68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.
- - 35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common Mus musculus domesticus inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (Mus musculus domesticus, e.g, WSB/EiJ; M. musculus musculus, e.g., CZECHII/EiJ; M. musculus molossinus, e.g., MOLF/EiJ; M. musculus castaneus, e.g., CAST/EiJ); and even one different species of mouse (Mus spicilegus, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the Nyx-nob mutant:
- - 6 knockouts (KO), including a KO of Rpe65, and 5 DeltaGen Inc. knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: Gabra1, Gabbr1, Gnb1, Gpr19, and Clcn3. We also included one spontaneous mutant of the nyctalopin (Nyx no b wave "nob") gene (Pardue et al., 1998) that is on a BALB/cByJ background.
-
-
-Rod photoreceptor degeneration in inbred mice: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the retinal degeneration 1 (rd1) mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (Pde6b). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.
-
-As expected (Dickerson LW et al., 2002) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, Clcn3) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of Gnat2, a gene associated with cones and achromatopsia in mice and humans.
-
-Lines of mice were selected using the following criteria:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - representation of a fairly wide variety of different subspecies of Mus
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - interesting mutations or knockouts affecting genes with high expression in the eye
- - general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.
-
-
-We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see Perlegen's excellent data resources and browser).
-
-
- - 129S1/SvImJ : Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a cone photoreceptor function loss 3 mutant (Cpfl3 allele) of the Gnat2 gene that is a model for achromatopsia (JAX Stock Number: 002448)
- - A/J: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (Tyr c allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: 000646)
- - BALB/cByJ: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Small brain, not aggressive (JAX Stock Number: 001026)
- - BALB/cJ: Phenome Project A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Large brain and aggressive (JAX Stock Number: 000651)
- - BXSB/MpJ: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the Yaa gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: 000740)
- - C3H/HeJ: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a Pdeb6 rd1 mutant with near total photoreceptor loss at as early as postnatal day 30. Also a Tlr4 mutant that is endotoxin resistant. (JAX Stock Number: 000659)
- - C57BL/6J: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: 000664)
- - C57BLKS/J: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: 000662)
- - CAST/EiJ: A wild-derived inbred Mus musculus castaneus strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: 000928)
- - CBA/CaJ: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: 000654)
- - CZECHII/EiJ: Czech 2 is a wild-derived inbred strain M. musculus musculus strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: 001144).
- - DBA/2J: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. A myosin 5a (Myo5a d) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: 000671)
- - FVB/NJ: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. Tyr c locus albino and a Pdeb6 rd1 mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: 001800).
- - KK/HlJ: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: 002106)
- - LG/J: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A Tyr c locus albino strain. (JAX Stock Number: 000675)
- - LP/J: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B Ednrb gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: 000676)
- - MOLF/EiJ: A wild-derived inbred strain derived from M. musculus molossinus samples camputered in Fukuoka, Japan. This strain has the retinal degeneration rd1 allele in Pde6b. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: 000550)
- - NOD/LtJ: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. (JAX Stock Number: 001976)
- - NZO/HlLtJ: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: 002105)
- - NZB/BlNJ: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: 000648)
- - NZW/LacJ: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the Tyr c locus albino mutation, the pink-eye dilution mutation in the Oca2 or p locus, and the brown allele at Tyrp1. (JAX Stock Number: 001058)
- - PANCEVO/EiJ: PANCEVO/EiJ is a wild-derived inbred strain from the Mus spicilegus samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier 10103). M. spicilegus is a colonial mound-building species. No known ocular or retina mutations, but the expression level of Gnat2 is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: 001384)
- - PWD/PhJ: A wild-derived Mus musculus musculus agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: 004660)
- - PWK/PhJ: A wild-derived Mus musculus musculus inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: 003715)
- - SJL/J: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration rd1 allele in Pde6b. It also carries both the Tyr c albino mutation and the pink-eye dilution mutation in the Oca2 or p locus. Highly aggressive males. (JAX Stock Number: 000686)
- - WSB/EiJ: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived Mus musculus domesticus inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: 001145)
- - B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J 100006)
-
-
-Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, 2008 and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (Tyr, or human OCA1), the brown allele of the tyrosinase related protein 1 (Tyrp1), the pink-eye dilution allele of Oca2 (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein Asip, the steel allele of Kitlg, the dilute allele of Myo5a (probe set 1419754), and the piebald allele of Ednrb. In some of these cases, effects of the mutation are easily detected at the transcript level (Tyrp1, Oca2, and Myo5a), but in the other cases (Tyr, Asip, Ednrb, and Kitlg), mutations do not leave a strong imprint on expression.
diff --git a/general/datasets/Eye_M2_0908_R_ND/experiment-design.rtf b/general/datasets/Eye_M2_0908_R_ND/experiment-design.rtf
deleted file mode 100644
index 1ebe0ad..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression profiling by array
diff --git a/general/datasets/Eye_M2_0908_R_ND/notes.rtf b/general/datasets/Eye_M2_0908_R_ND/notes.rtf
deleted file mode 100644
index 7a26eb5..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Eye_M2_0908_R_ND/platform.rtf b/general/datasets/Eye_M2_0908_R_ND/platform.rtf
deleted file mode 100644
index 9024a99..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/platform.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many probes overlap and target the same transcript). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
-As part of the development of HEIMED, we have manually annotated individual probe sets by sequence alignment to the mouse genome and transcriptome. Approximately 13,000 probe sets that have comparatively high expression in eye and CNS were curated by one of the authors (RWW) and now have specific information on the part of the transcript targeted by each probe set. The other 33,000 transcripts have corresponding data that was generated by Xusheng Wang using computational methods (BLAT analysis combined with annotated genome sequence).
-
-One example may help explain how to exploit this annotation. The four probe sets for rhodopsin include information on the target location. Only the first probe set targets the last two coding exons. The other three probe sets target different parts of the 3’ UTR (mid, distal, and far distal regions). The probe sets can be reordered by from high to low expression using the Sort By function in Search Results pages. In the case of rhodopsin, the probe set that targets that last two coding exons and proximal parts of the 3’ UTR also has the highest expression . Finally, the HEIMED gene descriptions have been customized to help vision researchers. In the case of rhodopsin, the description appended after the gene name reads “rod photoreceptor pigment, retinitis pigmentosa-associated”. For less well known genes this kind of annotation can be extremely useful. For example, the more verbose annotation for Cerkl reads “neuronal survival and apoptosis-related, retinal ganglion cell expressed, retinitis pigmentosa 26); alternative 3' UTR of short form message, intron 2”.
-
-
-
-
-
-Legend: Distribution of expression values for all probe sets in HEIMED.
diff --git a/general/datasets/Eye_M2_0908_R_ND/processing.rtf b/general/datasets/Eye_M2_0908_R_ND/processing.rtf
deleted file mode 100644
index 4349e60..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/processing.rtf
+++ /dev/null
@@ -1,3381 +0,0 @@
-Range of Gene Expression in the Eye. Expression of transcripts in the HEIMED and most other GN data sets is measured on a log2 scale. Each unit corresponding approximately to a 2-fold difference in hybridization signal intensity. To simplify comparisons among different data sets and cases, log2 RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units (variance stabilized). Values of all 45,101 probe sets in this data set range from a low of 4.8 (Tcf15, probe set 1420281_at) to a high of 15.5 (crystallin gamma C, Crygc, probe set 1422674_s_at). This corresponds to 10.7 units or a 1 to 1700 dynamic range of expression (2^10.73).
-
-We used pooled RNA samples of whole eyes, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-We calibrated this log intensity scale using Affymetrix spike-in control probe sets. These 18 control probe sets target exogenous bacterial mRNAs that are added to each sample (a graded dose spike cocktail) during preparation at concentrations of 1.5, 5, 25, and 100 pM. (To find these probe sets, search GN’s ALL search field using the string “AFFX pM”.) A value of 6 or less is equivalent to an mRNA concentration of under 0.4 pM, a value of 8 is equivalent to ~1.5 pM, 9.5 is equivalent to ~5 pM, 11.5 is equivalent to ~25 pM, 13.5 is equivalent to ~100 pM, and a value of 15.5 is equivalent to an mRNA concentration of 400 pM or greater.
-
-This range can be converted to the mRNA molecules per cell in the eye assuming that a value of 8 is equivalent to about 1 mRNA copy per cell (Kanno et al. 2006, see http://www.biomedcentral.com/1471-2164/7/64). Since the expression of rhodopsin mRNA is normally 15 units, we predict that there are 27 or ~128 Rho mRNAs per cell in the whole eye and ~256 in rods themselves (assuming that rods make up about half of all cells in the eye). For this purpose it may be useful to know that a normal mouse eye contains between 6 and 8 million rod photoreceptors (Guo, Lu, and Williams; GN BXD Phenotype ID 11024).
-
-Note that some probe sets with very low expression still provide reliable data. For example, probe set 1440397_at (Cacna2d1) has expression of only 5.5 units (a value that would be declared as "absent" using conventional Affymetrix procedures), but the values for this calcium channel transcript are associated with a very strong cis QTL with an LRS of 79 (LOD = 17). This strong linkage is definitely not due to chance since the probability of the expression data mapping precisely to the location of the parent gene itself is about 10e-16. This indicates a high signal to noise ratio and the detection of significant strain variation of the correct transcript.
-
-The standard error of the mean for the HEIMED data set is computed for 2 to 6 biological replicates. The standard error of such small samples tends to systematically underestimate the population standard error. With n = 2 the underestimate is about 25%, whereas for n = 6 the underestimate is 5%. Gurland and Tripathi (1971) provide a correction and equation for this effect (see Sokal and Rohlf, Biometry, 2nd ed., 1981, p 53 for an equation of the correction factor for small samples of n < 20.) Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the first three batches together. The last batch was processed separately and merged as described below.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing using Biobase affy10 build running under R version 2.7.1, all array data sets were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (FVB/NJ, NOD/LtJ, MOLF/EiJ, C3H/HeJ and BXD24), samples from wild subspecies such as WSB/EiJ, CAST/EiJ, PWD/PhJ, and PWK/PhJ, and knockouts. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. The assumption is that anomolous data are much more likely due to experimental and technical errors than to informative biological variation. Approximately 10% of arrays were discarded.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We reviewed the data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g., 1800) represented the QTL harvest for the full data set. We then dropped a single array from the data set, recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 1750 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs. Values ranged from approximately -90 (good arrays) to +40 (bad arrays). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a method to polish a data set.
-
-During this process we discovered that nearly 20 arrays in the batch 2 had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of high quality.
-
-A third batch of approximately 40 arrays were processed by Yan Jiao and Weikuan Gu in August 2006. These complete data set assembled by Hongqiang Li. This process again included a correction for a batch effect.
-
-For the June 2006 data set Hongqiang Li used a new batch correction method that stabilizes the range of expression in each batch. For each of the three large batches, we extracted the minumum and maximum raw probe expression (CEL file level) value. We then adjusted raw probe values in each batch to have the same range as the first and largest batch (batch 1) using a simple linear interpolation. These procedures generated new correct CEL files which were then used with RMA to generate final probe set estimates.
-
-For the final fourth batch of arrays (Sept 2008) Arthur Centeno and Rob Williams corrected for a systematic difference in probe set expression values between original arrays run in 2005 and 2006 and the new arrays added in 2008 (n = 45 acceptable arrays). This difference is due to unknown technical batch effects that are probably associated with labeling, hybridization, and scanning. We performed a simple correction to normalize values of the new set of arrays to those of the old set (batches 1 through 3). No changes were made to any values of the previous three batches. We corrected only the probe set level (RMA) values and not the CEL files. For this final batch, we corrected for the difference (offset) in probe set expression between the first three batches arrays run in 2005 and 2006 (a total of 174 acceptable arrays) and the new batch (n = 47 acceptable arrays). This difference is due to unknown technical effects that are probably related to various steps in labeling, hybridization, and scanning. The correction was applied as follows: (1) RWW selected 51 high quality arrays with similar expression characteristics (r = 0.97 or better between pairs of arrays) in the old data set (from batches 1, 2, and 3) and 34 high quality arrays in the final batch. RWW used scatterplots of full RMA transcriptome data sets to review many pairs of arrays within these new and old array batches. Strains with retinal degeneration or unusual eye gene expression characteristics were excluded from these selected subsets. The average expression values for each probe set were then computed for both the old and new array subsets. The offset value (old minus new) was added to each probe set across all 47 new arrays. This processes forces the average probe set in the new arrays to be very close to that of the previous arrays.
-
-Table 2: Sample tube ID, strain, original CEL filename, and Affymetrix quality control values. Columns labeled Scale factor, Background Average, Present, Absent, Marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Strain |
- Original CEL |
- Scale factor |
- Background Average |
- Present |
- Absent |
- Marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- Batch Id |
- Used for batch control |
-
-
- | 1 |
- R2595E.1 |
- 129S1/SvImJ |
- R2595E.1.CEL |
- 1.79 |
- 115 |
- 61.00% |
- 37.50% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 2 |
- R2533E.1 |
- 129S1/SvImJ |
- R2533E.1.CEL |
- 2.11 |
- 94 |
- 57.90% |
- 40.50% |
- 1.60% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 3 |
- R0754E.1 |
- A/J |
- R0754E.1.CEL |
- 2.72 |
- 86 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.36 |
- 0.76 |
- 1 |
- Y |
-
-
- | 4 |
- R4521E |
- B6129P2F2N1-Clcn3 |
- R4521E.CEL |
- 4.83 |
- 38.7 |
- 63.30% |
- 35.30% |
- 1.40% |
- 1.25 |
- 0.77 |
- 4 |
- |
-
-
- | 5 |
- R4522E |
- B6129P2F2N1-Clcn3 |
- R4522E.CEL |
- 5.76 |
- 37.36 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.37 |
- 0.83 |
- 4 |
- |
-
-
- | 6 |
- R4523E |
- B6129P2F2N1-Clcn3 |
- R4523E.CEL |
- 4.88 |
- 40.42 |
- 63.90% |
- 34.70% |
- 1.40% |
- 1.27 |
- 0.77 |
- 4 |
- |
-
-
- | 7 |
- R4526E |
- B6129P2F2N1-Gabbr1 |
- R4526E.CEL |
- 3.84 |
- 44.18 |
- 65.00% |
- 33.70% |
- 1.30% |
- 1.34 |
- 0.78 |
- 4 |
- Y |
-
-
- | 8 |
- R4509E |
- B6129P2F2N1-Gabbr1 |
- R4509E.CEL |
- 7.45 |
- 34.76 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.45 |
- 0.83 |
- 4 |
- |
-
-
- | 9 |
- R4510E |
- B6129P2F2N1-Gabbr1 |
- R4510E.CEL |
- 8.44 |
- 37.44 |
- 57.40% |
- 41.10% |
- 1.50% |
- 1.35 |
- 0.83 |
- 4 |
- |
-
-
- | 10 |
- R4511E |
- B6129P2F2N1-Gabbr1 |
- R4511E.CEL |
- 5.91 |
- 42.02 |
- 61.40% |
- 37.20% |
- 1.40% |
- 1.41 |
- 0.83 |
- 4 |
- |
-
-
- | 11 |
- R4524E |
- B6129P2F2N1-Gabbr1 |
- R4524E.CEL |
- 5.49 |
- 42.34 |
- 62.40% |
- 36.20% |
- 1.40% |
- 1.29 |
- 0.78 |
- 4 |
- Y |
-
-
- | 12 |
- R4525E |
- B6129P2F2N1-Gabbr1 |
- R4525E.CEL |
- 4.69 |
- 41.3 |
- 63.10% |
- 35.50% |
- 1.40% |
- 1.27 |
- 0.8 |
- 4 |
- Y |
-
-
- | 13 |
- R4515E |
- B6129P2F2N1-Gabra1 |
- R4515E.CEL |
- 5.75 |
- 41.76 |
- 62.80% |
- 35.80% |
- 1.40% |
- 1.41 |
- 0.81 |
- 4 |
- Y |
-
-
- | 14 |
- R4516E |
- B6129P2F2N1-Gabra1 |
- R4516E.CEL |
- 7.07 |
- 40.73 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.32 |
- 0.87 |
- 4 |
- Y |
-
-
- | 15 |
- R4517E |
- B6129P2F2N1-Gabra1 |
- R4517E.CEL |
- 5.45 |
- 38.09 |
- 62.70% |
- 35.80% |
- 1.40% |
- 1.34 |
- 0.82 |
- 4 |
- Y |
-
-
- | 16 |
- R4512E |
- B6129P2F2N1-Gnb5 |
- R4512E.CEL |
- 6.56 |
- 38.02 |
- 59.90% |
- 38.70% |
- 1.50% |
- 1.33 |
- 0.83 |
- 4 |
- |
-
-
- | 17 |
- R4513E |
- B6129P2F2N1-Gnb5 |
- R4513E.CEL |
- 4.15 |
- 41.6 |
- 63.40% |
- 35.10% |
- 1.50% |
- 1.34 |
- 0.82 |
- 4 |
- |
-
-
- | 18 |
- R4514E |
- B6129P2F2N1-Gnb5 |
- R4514E.CEL |
- 5.86 |
- 39.2 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.34 |
- 0.81 |
- 4 |
- |
-
-
- | 19 |
- R4518E |
- B6129P2F2N1-Gpr19 |
- R4518E.CEL |
- 5.58 |
- 38.9 |
- 62.60% |
- 36.00% |
- 1.30% |
- 1.39 |
- 0.79 |
- 4 |
- Y |
-
-
- | 20 |
- R4519E |
- B6129P2F2N1-Gpr19 |
- R4519E.CEL |
- 5.95 |
- 41.91 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.35 |
- 0.84 |
- 4 |
- Y |
-
-
- | 21 |
- R2601E.1 |
- B6D2F1 |
- R2601E.1.CEL |
- 2.55 |
- 92 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.44 |
- 0.78 |
- 1 |
- Y |
-
-
- | 22 |
- R2602E.1 |
- B6D2F1 |
- R2602E.1.CEL |
- 2.6 |
- 84 |
- 59.70% |
- 38.80% |
- 1.50% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 23 |
- R1676E.1 |
- BALB/cByJ |
- R1676E.1.CEL |
- 2.69 |
- 98 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.46 |
- 0.74 |
- 1 |
- |
-
-
- | 24 |
- R1672E.1 |
- BALB/cByJ |
- R1672E.1.CEL |
- 2.22 |
- 111 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 25 |
- R4530E |
- BALB/cJ |
- R4530E.CEL |
- 6.37 |
- 37.53 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.3 |
- 0.84 |
- 4 |
- Y |
-
-
- | 26 |
- R4529E |
- BALB/cJ |
- R4529E.CEL |
- 5.71 |
- 41.33 |
- 60.50% |
- 38.00% |
- 1.50% |
- 1.48 |
- 0.8 |
- 4 |
- Y |
-
-
- | 27 |
- R2704E.2 |
- BXD1 |
- R2704E.2.CEL |
- 2.066 |
- 139.61 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 28 |
- R2707E.3 |
- BXD1 |
- R2707E.3.CEL |
- 1 |
- 80 |
- 56.40% |
- 42.10% |
- 1.50% |
- 1.43 |
- 0.79 |
- 3 |
- |
-
-
- | 29 |
- R1231E.2 |
- BXD2 |
- R1231E.2.CEL |
- 2.197 |
- 138.73 |
- 57.30% |
- 41.30% |
- 1.40% |
- 1.41 |
- 0.77 |
- 2 |
- |
-
-
- | 30 |
- R2598E.1 |
- BXD2 |
- R2598E.1.CEL |
- 1.99 |
- 106 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 31 |
- R2591E.1 |
- BXD5 |
- R2591E.1.CEL |
- 1.7 |
- 136 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.33 |
- 0.78 |
- 1 |
- Y |
-
-
- | 32 |
- R2714E.2 |
- BXD5 |
- R2714E.2.CEL |
- 1.404 |
- 144.35 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 33 |
- R2570E.1 |
- BXD6 |
- R2570E.1.CEL |
- 1.99 |
- 87 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.46 |
- 0.76 |
- 1 |
- Y |
-
-
- | 34 |
- R2694E.2 |
- BXD6 |
- R2694E.2.CEL |
- 1.983 |
- 97.23 |
- 61.60% |
- 37.10% |
- 1.30% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 35 |
- R2538E.1 |
- BXD8 |
- R2538E.1.CEL |
- 1.91 |
- 102 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.52 |
- 0.79 |
- 1 |
- Y |
-
-
- | 36 |
- R2709E.2 |
- BXD8 |
- R2709E.2.CEL |
- 1.99 |
- 99.79 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.42 |
- 0.76 |
- 2 |
- |
-
-
- | 37 |
- R2708E.2 |
- BXD9 |
- R2708E.2.CEL |
- 1.966 |
- 126.46 |
- 57.70% |
- 40.70% |
- 1.50% |
- 1.4 |
- 0.84 |
- 2 |
- |
-
-
- | 38 |
- R2569E.1 |
- BXD9 |
- R2569E.1.CEL |
- 1.75 |
- 87 |
- 55.10% |
- 43.40% |
- 1.50% |
- 2.82 |
- 3.14 |
- 1 |
- |
-
-
- | 39 |
- R2581E.1 |
- BXD11 |
- R2581E.1.CEL |
- 1.94 |
- 89 |
- 62.10% |
- 36.40% |
- 1.60% |
- 1.55 |
- 0.81 |
- 1 |
- Y |
-
-
- | 40 |
- R2612E.2 |
- BXD11 |
- R2612E.2.CEL |
- 1.83 |
- 142.03 |
- 58.20% |
- 40.50% |
- 1.40% |
- 1.78 |
- 0.81 |
- 2 |
- |
-
-
- | 41 |
- R2742E.2 |
- BXD12 |
- R2742E.2.CEL |
- 2.127 |
- 134.14 |
- 57.00% |
- 41.60% |
- 1.40% |
- 1.64 |
- 0.78 |
- 2 |
- |
-
-
- | 42 |
- R2543E.1 |
- BXD12 |
- R2543E.1.CEL |
- 1.61 |
- 118 |
- 58.60% |
- 39.90% |
- 1.60% |
- 1.43 |
- 0.77 |
- 1 |
- Y |
-
-
- | 43 |
- R2586E.1 |
- BXD13 |
- R2586E.1.CEL |
- 2.01 |
- 74 |
- 56.40% |
- 42.00% |
- 1.60% |
- 2.85 |
- 3.81 |
- 1 |
- |
-
-
- | 44 |
- R877E.2 |
- BXD13 |
- R877E.2.CEL |
- 1.558 |
- 125.63 |
- 61.20% |
- 37.50% |
- 1.20% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 45 |
- R2557E.1 |
- BXD14 |
- R2557E.1.CEL |
- 1.83 |
- 99 |
- 62.50% |
- 36.10% |
- 1.40% |
- 1.31 |
- 0.78 |
- 1 |
- Y |
-
-
- | 46 |
- R1128E.2 |
- BXD14 |
- R1128E.2.CEL |
- 1.91 |
- 115 |
- 59.90% |
- 38.80% |
- 1.40% |
- 1.2 |
- 0.82 |
- 1 |
- Y |
-
-
- | 47 |
- R2701E.3 |
- BXD15 |
- R2701E.3.CEL |
- 1 |
- 88 |
- 60.60% |
- 37.90% |
- 1.40% |
- 1.5 |
- 0.77 |
- 3 |
- |
-
-
- | 48 |
- R2716E.2 |
- BXD15 |
- R2716E.2.CEL |
- 2.015 |
- 150.83 |
- 56.40% |
- 42.10% |
- 1.60% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 49 |
- R2711E.2 |
- BXD16 |
- R2711E.2.CEL |
- 1.953 |
- 118.53 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 50 |
- R2567E.1 |
- BXD16 |
- R2567E.1.CEL |
- 2.24 |
- 82 |
- 56.70% |
- 41.60% |
- 1.70% |
- 1.37 |
- 0.75 |
- 1 |
- |
-
-
- | 51 |
- R2720E.2 |
- BXD18 |
- R2720E.2.CEL |
- 2.32 |
- 99.93 |
- 59.50% |
- 39.00% |
- 1.50% |
- 1.33 |
- 0.77 |
- 2 |
- |
-
-
- | 52 |
- R2559E.1 |
- BXD18 |
- R2559E.1.CEL |
- 1.65 |
- 104 |
- 60.80% |
- 37.70% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 53 |
- R2560E.1 |
- BXD19 |
- R2560E.1.CEL |
- 1.79 |
- 98 |
- 60.90% |
- 37.50% |
- 1.60% |
- 1.35 |
- 0.8 |
- 1 |
- Y |
-
-
- | 54 |
- R2713E.2 |
- BXD19 |
- R2713E.2.CEL |
- 1.67 |
- 120.82 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 55 |
- R2584E.1 |
- BXD20 |
- R2584E.1.CEL |
- 2.07 |
- 84 |
- 59.30% |
- 39.10% |
- 1.60% |
- 1.4 |
- 0.76 |
- 1 |
- Y |
-
-
- | 56 |
- R2731E.2 |
- BXD20 |
- R2731E.2.CEL |
- 1.825 |
- 147 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.4 |
- 0.8 |
- 2 |
- |
-
-
- | 57 |
- R2702E.2 |
- BXD21 |
- R2702E.2.CEL |
- 1.811 |
- 128.65 |
- 59.40% |
- 39.10% |
- 1.40% |
- 1.26 |
- 0.8 |
- 2 |
- |
-
-
- | 58 |
- R2541E2.1 |
- BXD21 |
- R2541E2.1.CEL |
- 2.63 |
- 125 |
- 56.00% |
- 42.40% |
- 1.50% |
- 1.29 |
- 0.78 |
- 1 |
- |
-
-
- | 59 |
- R2553E.1 |
- BXD22 |
- R2553E.1.CEL |
- 1.95 |
- 111 |
- 59.90% |
- 38.50% |
- 1.50% |
- 1.28 |
- 0.76 |
- 1 |
- Y |
-
-
- | 60 |
- R2700E.2 |
- BXD22 |
- R2700E.2.CEL |
- 1.858 |
- 102.96 |
- 61.50% |
- 37.10% |
- 1.30% |
- 1.48 |
- 0.79 |
- 2 |
- |
-
-
- | 61 |
- R2558E-2.1 |
- BXD23 |
- R2558E-2.1.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 62 |
- R1086E.2 |
- BXD23 |
- R1086E.2.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 63 |
- R2719E.2 |
- BXD24 |
- R2719E.2.CEL |
- 1.47 |
- 140.38 |
- 61.50% |
- 37.20% |
- 1.30% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 64 |
- R2589E2.1 |
- BXD24 |
- R2589E2.1.CEL |
- 2.61 |
- 112 |
- 57.50% |
- 40.90% |
- 1.60% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 65 |
- R2573E-2.1 |
- BXD25 |
- R2573E-2.1.CEL |
- 3.15 |
- 72 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.77 |
- 0.97 |
- 1 |
- |
-
-
- | 66 |
- R2683E.2 |
- BXD25 |
- R2683E.2.CEL |
- 1.777 |
- 115.64 |
- 58.30% |
- 40.30% |
- 1.40% |
- 2.01 |
- 0.79 |
- 2 |
- |
-
-
- | 67 |
- R2703E.2 |
- BXD27 |
- R2703E.2.CEL |
- 1.263 |
- 134.78 |
- 62.60% |
- 36.10% |
- 1.40% |
- 1.44 |
- 0.78 |
- 2 |
- |
-
-
- | 68 |
- R2729E.3 |
- BXD27 |
- R2729E.3.CEL |
- 1 |
- 87 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.56 |
- 0.84 |
- 3 |
- Y |
-
-
- | 69 |
- R2562E.3 |
- BXD28 |
- R2562E.3.CEL |
- 1.65 |
- 116 |
- 59.90% |
- 38.40% |
- 1.70% |
- 1.37 |
- 0.79 |
- 3 |
- Y |
-
-
- | 70 |
- R2721E.2 |
- BXD28 |
- R2721E.2.CEL |
- 2.065 |
- 157.39 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 71 |
- R2561E.3 |
- BXD29 |
- R2561E.3.CEL |
- 1 |
- 77 |
- 53.30% |
- 45.40% |
- 1.40% |
- 3.36 |
- 19.66 |
- 3 |
- |
-
-
- | 72 |
- R1258E.2 |
- BXD31 |
- R1258E.2.CEL |
- 2.063 |
- 117.09 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.54 |
- 0.78 |
- 2 |
- |
-
-
- | 73 |
- R2597E.1 |
- BXD31 |
- R2597E.1.CEL |
- 2.37 |
- 94 |
- 60.30% |
- 38.30% |
- 1.50% |
- 1.34 |
- 0.77 |
- 1 |
- Y |
-
-
- | 74 |
- R2563E.1 |
- BXD32 |
- R2563E.1.CEL |
- 1.55 |
- 102 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.5 |
- 0.8 |
- 1 |
- |
-
-
- | 75 |
- R1216E.2 |
- BXD32 |
- R1216E.2.CEL |
- 2.23 |
- 111.99 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.35 |
- 0.79 |
- 2 |
- |
-
-
- | 76 |
- R2542E.1 |
- BXD33 |
- R2542E.1.CEL |
- 2.13 |
- 97 |
- 56.50% |
- 41.80% |
- 1.60% |
- 1.91 |
- 0.93 |
- 1 |
- |
-
-
- | 77 |
- R857E.2 |
- BXD33 |
- R857E.2.CEL |
- 1.737 |
- 113.98 |
- 61.90% |
- 36.70% |
- 1.30% |
- 1.6 |
- 0.77 |
- 2 |
- |
-
-
- | 78 |
- R1451E.2 |
- BXD34 |
- R1451E.2.CEL |
- 1.843 |
- 140.05 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.42 |
- 0.81 |
- 2 |
- Y |
-
-
- | 79 |
- R2585E.1 |
- BXD34 |
- R2585E.1.CEL |
- 2.64 |
- 75 |
- 58.30% |
- 40.00% |
- 1.70% |
- 1.25 |
- 0.77 |
- 1 |
- |
-
-
- | 80 |
- R2698E.3 |
- BXD36 |
- R2698E.3.CEL |
- 1 |
- 86 |
- 59.70% |
- 39.00% |
- 1.30% |
- 1.46 |
- 0.78 |
- 3 |
- |
-
-
- | 81 |
- R2705E.3 |
- BXD36 |
- R2705E.3.CEL |
- 1 |
- 86 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.46 |
- 0.77 |
- 3 |
- |
-
-
- | 82 |
- R2710E.2 |
- BXD38 |
- R2710E.2.CEL |
- 2.112 |
- 122.1 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.37 |
- 0.78 |
- 2 |
- |
-
-
- | 83 |
- R2532E.1 |
- BXD38 |
- R2532E.1.CEL |
- 2.04 |
- 94 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.37 |
- 0.8 |
- 1 |
- Y |
-
-
- | 84 |
- R2574E.1 |
- BXD39 |
- R2574E.1.CEL |
- 1.98 |
- 91 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.39 |
- 0.78 |
- 1 |
- |
-
-
- | 85 |
- R2695E.2 |
- BXD39 |
- R2695E.2.CEL |
- 1.638 |
- 122.7 |
- 60.80% |
- 37.80% |
- 1.50% |
- 1.42 |
- 0.8 |
- 2 |
- |
-
-
- | 86 |
- R2699E.2 |
- BXD40 |
- R2699E.2.CEL |
- 1.827 |
- 105.23 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 87 |
- R2590E.1 |
- BXD40 |
- R2590E.1.CEL |
- 2.71 |
- 77 |
- 59.10% |
- 39.30% |
- 1.50% |
- 1.4 |
- 0.77 |
- 1 |
- Y |
-
-
- | 88 |
- R2696E.2 |
- BXD42 |
- R2696E.2.CEL |
- 1.622 |
- 118.95 |
- 62.00% |
- 36.60% |
- 1.50% |
- 1.53 |
- 0.79 |
- 2 |
- |
-
-
- | 89 |
- R2596E.1 |
- BXD42 |
- R2596E.1.CEL |
- 2.63 |
- 108 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 90 |
- R994E.2 |
- BXD43 |
- R994E.2.CEL |
- 1.966 |
- 113.12 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.66 |
- 0.8 |
- 2 |
- |
-
-
- | 91 |
- R2607E.1 |
- BXD43 |
- R2607E.1.CEL |
- 2.43 |
- 115 |
- 58.60% |
- 40.00% |
- 1.40% |
- 1.31 |
- 0.76 |
- 1 |
- Y |
-
-
- | 92 |
- R2594E.1 |
- BXD44 |
- R2594E.1.CEL |
- 1.77 |
- 117 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.35 |
- 0.85 |
- 1 |
- |
-
-
- | 93 |
- R2610E.2 |
- BXD44 |
- R2610E.2.CEL |
- 1.814 |
- 142.91 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.35 |
- 0.8 |
- 2 |
- |
-
-
- | 94 |
- R2732E.2 |
- BXD45 |
- R2732E.2.CEL |
- 2.154 |
- 122.45 |
- 56.50% |
- 42.10% |
- 1.40% |
- 1.8 |
- 0.83 |
- 2 |
- |
-
-
- | 95 |
- R2592E.1 |
- BXD45 |
- R2592E.1.CEL |
- 1.85 |
- 106 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.43 |
- 0.85 |
- 1 |
- Y |
-
-
- | 96 |
- R967E.2 |
- BXD48 |
- R967E.2.CEL |
- 1.948 |
- 130.95 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.63 |
- 0.81 |
- 2 |
- |
-
-
- | 97 |
- R2606E.1 |
- BXD48 |
- R2606E.1.CEL |
- 2.56 |
- 106 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.35 |
- 0.83 |
- 1 |
- Y |
-
-
- | 98 |
- R2933E.3 |
- BXD50 |
- R2933E.3.CEL |
- 1 |
- 72 |
- 52.90% |
- 45.60% |
- 1.50% |
- 2.45 |
- 0.98 |
- 3 |
- |
-
-
- | 99 |
- R2937E.3 |
- BXD50 |
- R2937E.3.CEL |
- 1 |
- 89 |
- 56.90% |
- 41.60% |
- 1.40% |
- 1.81 |
- 0.82 |
- 3 |
- |
-
-
- | 100 |
- R2603E.1 |
- BXD51 |
- R2603E.1.CEL |
- 2.49 |
- 115 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.24 |
- 0.79 |
- 1 |
- |
-
-
- | 101 |
- R1042E.2 |
- BXD51 |
- R1042E.2.CEL |
- 2.352 |
- 104.12 |
- 58.70% |
- 39.90% |
- 1.40% |
- 1.53 |
- 0.82 |
- 2 |
- |
-
-
- | 102 |
- R2980E.3 |
- BXD55 |
- R2980E.3.CEL |
- 1 |
- 82 |
- 56.90% |
- 41.70% |
- 1.50% |
- 1.77 |
- 0.84 |
- 3 |
- |
-
-
- | 103 |
- R2690E.2 |
- BXD55 |
- R2690E.2.CEL |
- 1.887 |
- 164.01 |
- 56.10% |
- 42.30% |
- 1.60% |
- 1.43 |
- 0.8 |
- 2 |
- |
-
-
- | 104 |
- R4176E |
- BXD56 |
- R4176E.CEL |
- 4.75 |
- 43.08 |
- 63.00% |
- 35.60% |
- 1.30% |
- 1.39 |
- 0.81 |
- 4 |
- Y |
-
-
- | 105 |
- R4175E |
- BXD56 |
- R4175E.CEL |
- 6 |
- 38.49 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.47 |
- 0.81 |
- 4 |
- Y |
-
-
- | 106 |
- R1006E.3 |
- BXD60 |
- R1006E.3.CEL |
- 1 |
- 98 |
- 54.90% |
- 43.70% |
- 1.50% |
- 2.7 |
- 0.86 |
- 3 |
- |
-
-
- | 107 |
- R2725E.2 |
- BXD60 |
- R2725E.2.CEL |
- 1.551 |
- 148.01 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 108 |
- R1074E.3 |
- BXD60 |
- R1074E.3.CEL |
- 1 |
- 118 |
- 55.50% |
- 43.10% |
- 1.40% |
- 1.96 |
- 0.81 |
- 3 |
- |
-
-
- | 109 |
- R2534E2.1 |
- BXD61 |
- R2534E2.1.CEL |
- 2.47 |
- 118 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.42 |
- 0.79 |
- 1 |
- |
-
-
- | 110 |
- R2684E.2 |
- BXD61 |
- R2684E.2.CEL |
- 2.01 |
- 131.03 |
- 57.00% |
- 41.50% |
- 1.50% |
- 1.34 |
- 0.78 |
- 2 |
- |
-
-
- | 111 |
- R1107E.3 |
- BXD62 |
- R1107E.3.CEL |
- 1 |
- 83 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.43 |
- 0.93 |
- 3 |
- |
-
-
- | 112 |
- R2681E.2 |
- BXD62 |
- R2681E.2.CEL |
- 2.086 |
- 148.24 |
- 57.20% |
- 41.30% |
- 1.50% |
- 1.29 |
- 0.81 |
- 2 |
- |
-
-
- | 113 |
- R965E.3 |
- BXD62 |
- R965E.3.CEL |
- 1 |
- 93.55 |
- 53.30% |
- 45.20% |
- 1.50% |
- 3.11 |
- 0.94 |
- 3 |
- |
-
-
- | 114 |
- R1425E.2 |
- BXD63 |
- R1425E.2.CEL |
- 1.7 |
- 136 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.43 |
- 0.82 |
- 2 |
- |
-
-
- | 115 |
- R2576E.3 |
- BXD63 |
- R2576E.3.CEL |
- 1 |
- 84 |
- 61.30% |
- 37.40% |
- 1.40% |
- 1.48 |
- 0.76 |
- 3 |
- |
-
-
- | 116 |
- R943E-2.2 |
- BXD64 |
- R943E-2.2.CEL |
- 1.591 |
- 141.34 |
- 60.10% |
- 38.40% |
- 1.50% |
- 1.32 |
- 0.76 |
- 2 |
- |
-
-
- | 117 |
- R2611E.1 |
- BXD64 |
- R2611E.1.CEL |
- 2.29 |
- 92 |
- 58.00% |
- 40.50% |
- 1.50% |
- 1.57 |
- 1.06 |
- 1 |
- |
-
-
- | 118 |
- R2689E.2 |
- BXD65 |
- R2689E.2.CEL |
- 1.721 |
- 142.44 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.38 |
- 0.76 |
- 2 |
- |
-
-
- | 119 |
- R2583E.1 |
- BXD65 |
- R2583E.1.CEL |
- 2.49 |
- 70 |
- 56.90% |
- 41.50% |
- 1.60% |
- 1.67 |
- 1.01 |
- 1 |
- |
-
-
- | 120 |
- R2728E.2 |
- BXD66 |
- R2728E.2.CEL |
- 1.714 |
- 137.45 |
- 59.40% |
- 39.00% |
- 1.60% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 121 |
- R2536E2.1 |
- BXD66 |
- R2536E2.1.CEL |
- 2.74 |
- 109 |
- 56.10% |
- 42.30% |
- 1.70% |
- 1.28 |
- 0.79 |
- 1 |
- |
-
-
- | 122 |
- R1207E.2 |
- BXD66 |
- R1207E.2.CEL |
- 1.681 |
- 136.86 |
- 60.40% |
- 38.10% |
- 1.50% |
- 1.45 |
- 0.77 |
- 2 |
- |
-
-
- | 123 |
- R1192E.2 |
- BXD67 |
- R1192E.2.CEL |
- 2.126 |
- 123.37 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 124 |
- R2727E.3 |
- BXD67 |
- R2727E.3.CEL |
- 1 |
- 82.55 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.97 |
- 0.87 |
- 2 |
- |
-
-
- | 125 |
- R2691E.3 |
- BXD67 |
- R2691E.3.CEL |
- 1 |
- 90 |
- 54.80% |
- 43.80% |
- 1.50% |
- 2.61 |
- 0.81 |
- 3 |
- |
-
-
- | 126 |
- R2551E.1 |
- BXD68 |
- R2551E.1.CEL |
- 2.49 |
- 92 |
- 54.30% |
- 44.10% |
- 1.60% |
- 2.91 |
- 1.55 |
- 1 |
- |
-
-
- | 127 |
- R2726E.2 |
- BXD68 |
- R2726E.2.CEL |
- 1.811 |
- 153.09 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.39 |
- 0.78 |
- 2 |
- |
-
-
- | 128 |
- R2593E.1 |
- BXD69 |
- R2593E.1.CEL |
- 1.67 |
- 128 |
- 59.20% |
- 39.50% |
- 1.30% |
- 1.47 |
- 0.92 |
- 1 |
- Y |
-
-
- | 129 |
- R975E.2 |
- BXD70 |
- R975E.2.CEL |
- 1.841 |
- 137.97 |
- 58.00% |
- 40.50% |
- 1.40% |
- 1.36 |
- 0.79 |
- 2 |
- |
-
-
- | 130 |
- R2537E2.1 |
- BXD70 |
- R2537E2.1.CEL |
- 2.93 |
- 99 |
- 58.00% |
- 40.50% |
- 1.60% |
- 1.29 |
- 0.75 |
- 1 |
- |
-
-
- | 131 |
- R4531E |
- BXD71 |
- R4531E.CEL |
- 4.77 |
- 43.48 |
- 62.40% |
- 36.30% |
- 1.40% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 132 |
- R4532E |
- BXD71 |
- R4532E.CEL |
- 5.89 |
- 40.68 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.24 |
- 0.79 |
- 4 |
- Y |
-
-
- | 133 |
- R2779E.2 |
- BXD73 |
- R2779E.2.CEL |
- 1.746 |
- 121.11 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 134 |
- R3024E.3 |
- BXD73 |
- R3024E.3.CEL |
- 1 |
- 78.05 |
- 51.70% |
- 46.60% |
- 1.70% |
- 2.3 |
- 0.94 |
- 3 |
- |
-
-
- | 135 |
- R2565E.1 |
- BXD75 |
- R2565E.1.CEL |
- 1.79 |
- 102 |
- 58.00% |
- 40.50% |
- 1.50% |
- 2.31 |
- 3.47 |
- 1 |
- |
-
-
- | 136 |
- R1397E-re.2 |
- BXD75 |
- R1397E-re.2.CEL |
- 1.449 |
- 189.71 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 137 |
- R2687E.3 |
- BXD77 |
- R2687E.3.CEL |
- 1 |
- 80 |
- 58.00% |
- 40.60% |
- 1.40% |
- 1.57 |
- 0.8 |
- 3 |
- Y |
-
-
- | 138 |
- R2717E.2 |
- BXD77 |
- R2717E.2.CEL |
- 1.797 |
- 84.43 |
- 61.60% |
- 36.90% |
- 1.40% |
- 1.49 |
- 0.76 |
- 2 |
- |
-
-
- | 139 |
- R1421E.3 |
- BXD77 |
- R1421E.3.CEL |
- 1 |
- 94 |
- 52.40% |
- 46.20% |
- 1.40% |
- 2.29 |
- 0.82 |
- 3 |
- |
-
-
- | 140 |
- R2579E.1 |
- BXD80 |
- R2579E.1.CEL |
- 2.42 |
- 72 |
- 59.20% |
- 39.40% |
- 1.50% |
- 1.73 |
- 0.82 |
- 1 |
- |
-
-
- | 141 |
- R2686E.2 |
- BXD80 |
- R2686E.2.CEL |
- 2.342 |
- 119.63 |
- 56.00% |
- 42.60% |
- 1.50% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 142 |
- R2956E.3 |
- BXD83 |
- R2956E.3.CEL |
- 1 |
- 84 |
- 55.40% |
- 43.20% |
- 1.40% |
- 1.39 |
- 0.84 |
- 3 |
- |
-
-
- | 143 |
- R2960E.3 |
- BXD83 |
- R2960E.3.CEL |
- 1 |
- 80 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.5 |
- 0.82 |
- 3 |
- Y |
-
-
- | 144 |
- R2922E.3 |
- BXD84 |
- R2922E.3.CEL |
- 1 |
- 91 |
- 57.80% |
- 40.80% |
- 1.50% |
- 1.47 |
- 0.83 |
- 3 |
- Y |
-
-
- | 145 |
- R2895E.3 |
- BXD84 |
- R2895E.3.CEL |
- 1 |
- 75 |
- 58.30% |
- 40.20% |
- 1.50% |
- 1.56 |
- 0.77 |
- 3 |
- Y |
-
-
- | 146 |
- R2692E.2 |
- BXD85 |
- R2692E.2.CEL |
- 1.423 |
- 160.87 |
- 60.20% |
- 38.30% |
- 1.40% |
- 1.46 |
- 0.79 |
- 2 |
- |
-
-
- | 147 |
- R2715E.2 |
- BXD85 |
- R2715E.2.CEL |
- 1.488 |
- 142.6 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.5 |
- 0.78 |
- 2 |
- |
-
-
- | 148 |
- R1405E.2 |
- BXD86 |
- R1405E.2.CEL |
- 2.351 |
- 119.34 |
- 56.40% |
- 42.20% |
- 1.40% |
- 1.64 |
- 0.81 |
- 2 |
- |
-
-
- | 149 |
- R1225E.3 |
- BXD86 |
- R1225E.3.CEL |
- 1 |
- 71 |
- 53.90% |
- 44.60% |
- 1.40% |
- 3.2 |
- 1.61 |
- 3 |
- |
-
-
- | 150 |
- R2724E.2 |
- BXD87 |
- R2724E.2.CEL |
- 1.906 |
- 113.71 |
- 60.70% |
- 37.90% |
- 1.40% |
- 1.45 |
- 0.79 |
- 2 |
- |
-
-
- | 151 |
- R2540E.1 |
- BXD87 |
- R2540E.1.CEL |
- 2.33 |
- 93 |
- 61.10% |
- 37.40% |
- 1.40% |
- 1.22 |
- 0.81 |
- 1 |
- Y |
-
-
- | 152 |
- R1433E.2 |
- BXD89 |
- R1433E.2.CEL |
- 1 |
- 2.241 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.41 |
- 0.78 |
- 2 |
- |
-
-
- | 153 |
- R2546E.1 |
- BXD89 |
- R2546E.1.CEL |
- 1.99 |
- 96 |
- 58.60% |
- 39.70% |
- 1.70% |
- 1.47 |
- 0.78 |
- 1 |
- |
-
-
- | 154 |
- R2578E2.1 |
- BXD90 |
- R2578E2.1.CEL |
- 2.79 |
- 92 |
- 58.60% |
- 39.80% |
- 1.60% |
- 1.52 |
- 0.77 |
- 1 |
- Y |
-
-
- | 155 |
- R859E.2 |
- BXD90 |
- R859E.2.CEL |
- 1.847 |
- 152.22 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.36 |
- 0.77 |
- 2 |
- |
-
-
- | 156 |
- R2682E.2 |
- BXD92 |
- R2682E.2.CEL |
- 1.547 |
- 156.31 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.37 |
- 0.77 |
- 2 |
- |
-
-
- | 157 |
- R1388E.3 |
- BXD92 |
- R1388E.3.CEL |
- 1 |
- 63 |
- 60.00% |
- 38.60% |
- 1.40% |
- 1.85 |
- 1.03 |
- 3 |
- |
-
-
- | 158 |
- R1322E.3 |
- BXD92 |
- R1322E.3.CEL |
- 1 |
- 80 |
- 55.90% |
- 42.60% |
- 1.50% |
- 1.75 |
- 0.74 |
- 3 |
- |
-
-
- | 159 |
- R2733E.2 |
- BXD96 |
- R2733E.2.CEL |
- 1.7 |
- 113.99 |
- 62.10% |
- 36.60% |
- 1.30% |
- 1.4 |
- 0.78 |
- 2 |
- |
-
-
- | 160 |
- R2554E.1 |
- BXD96 |
- R2554E.1.CEL |
- 2.18 |
- 93 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 161 |
- R2649E.2 |
- BXD97 |
- R2649E.2.CEL |
- 2.343 |
- 119.04 |
- 57.50% |
- 41.20% |
- 1.40% |
- 1.53 |
- 0.8 |
- 2 |
- |
-
-
- | 162 |
- R2577E.1 |
- BXD97 |
- R2577E.1.CEL |
- 2.07 |
- 77 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.87 |
- 1.29 |
- 1 |
- |
-
-
- | 163 |
- R2645E.3 |
- BXD98 |
- R2645E.3.CEL |
- 1 |
- 88 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.59 |
- 0.81 |
- 3 |
- Y |
-
-
- | 164 |
- R2688E.2 |
- BXD98 |
- R2688E.2.CEL |
- 1.772 |
- 145.24 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.48 |
- 0.81 |
- 2 |
- |
-
-
- | 165 |
- R4533E |
- BXD99 |
- R4533E.CEL |
- 1 |
- 37.69 |
- 60.30% |
- 38.20% |
- 1.40% |
- 1.33 |
- 0.89 |
- 4 |
- Y |
-
-
- | 166 |
- R4534E |
- BXD99 |
- R4534E.CEL |
- 5.69 |
- 36.62 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.16 |
- 0.8 |
- 4 |
- Y |
-
-
- | 167 |
- R2885E.3 |
- BXSB/MpJ |
- R2885E.3.CEL |
- 1 |
- 76 |
- 58.10% |
- 40.60% |
- 1.30% |
- 1.88 |
- 1.06 |
- 3 |
- |
-
-
- | 168 |
- R2883E.3 |
- BXSB/MpJ |
- R2883E.3.CEL |
- 1 |
- 71 |
- 56.40% |
- 42.00% |
- 1.50% |
- 1.59 |
- 0.84 |
- 3 |
- Y |
-
-
- | 169 |
- R1700E.1 |
- C3H/HeJ |
- R1700E.1.CEL |
- 2.98 |
- 69 |
- 60.80% |
- 37.90% |
- 1.40% |
- 1.48 |
- 0.78 |
- 1 |
- |
-
-
- | 170 |
- R1704E.1 |
- C3H/HeJ |
- R1704E.1.CEL |
- 2.58 |
- 88 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.38 |
- 0.84 |
- 1 |
- |
-
-
- | 171 |
- R2605E.1 |
- C57BL/6J |
- R2605E.1.CEL |
- 1.82 |
- 131 |
- 60.50% |
- 38.20% |
- 1.30% |
- 1.32 |
- 0.8 |
- 1 |
- Y |
-
-
- | 172 |
- R0871E |
- C57BL/6J |
- R0871E.CEL |
- 6.24 |
- 37.38 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.41 |
- 0.8 |
- 4 |
- Y |
-
-
- | 173 |
- R0872E.1 |
- C57BL/6J |
- R0872E.1.CEL |
- 3.13 |
- 89 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 174 |
- R0872E |
- C57BL/6J |
- R0872E.CEL |
- 3.128 |
- 88.58 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- |
-
-
- | 175 |
- R4507E |
- C57BL/6J-Nyx |
- R4507E.CEL |
- 8.13 |
- 37.5 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.32 |
- 0.8 |
- 4 |
- Y |
-
-
- | 176 |
- R4508E |
- C57BL/6J-Nyx |
- R4508E.CEL |
- 6.33 |
- 37.26 |
- 60.90% |
- 37.80% |
- 1.30% |
- 1.24 |
- 0.82 |
- 4 |
- Y |
-
-
- | 177 |
- R4505E |
- C57BL/6J-Rpe65 |
- R4505E.CEL |
- 5.98 |
- 37.48 |
- 61.80% |
- 36.80% |
- 1.40% |
- 1.45 |
- 0.85 |
- 4 |
- Y |
-
-
- | 178 |
- R4506E |
- C57BL/6J-Rpe65 |
- R4506E.CEL |
- 6.94 |
- 37.9 |
- 61.10% |
- 37.50% |
- 1.30% |
- 1.5 |
- 0.83 |
- 4 |
- Y |
-
-
- | 179 |
- R4535E |
- C57BLKS/J |
- R4535E.CEL |
- 6.59 |
- 37.28 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.26 |
- 0.83 |
- 4 |
- Y |
-
-
- | 180 |
- R4536E |
- C57BLKS/J |
- R4536E.CEL |
- 1 |
- 40.71 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.25 |
- 0.77 |
- 4 |
- Y |
-
-
- | 181 |
- R2564E.1 |
- CAST/EiJ |
- R2564E.1.CEL |
- 1.94 |
- 89 |
- 58.50% |
- 39.90% |
- 1.60% |
- 1.6 |
- 0.77 |
- 1 |
- |
-
-
- | 182 |
- R2580E.1 |
- CAST/EiJ |
- R2580E.1.CEL |
- 2.09 |
- 95 |
- 58.20% |
- 40.10% |
- 1.70% |
- 1.4 |
- 0.76 |
- 1 |
- |
-
-
- | 183 |
- R4537E |
- CBA/CaJ |
- R4537E.CEL |
- 1 |
- 38.45 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.63 |
- 0.82 |
- 4 |
- Y |
-
-
- | 184 |
- R4538E |
- CBA/CaJ |
- R4538E.CEL |
- 5.89 |
- 39.18 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.45 |
- 0.8 |
- 4 |
- Y |
-
-
- | 185 |
- R4539E |
- CZECHII/EiJ |
- R4539E.CEL |
- 7.73 |
- 37.1 |
- 58.30% |
- 40.10% |
- 1.50% |
- 1.7 |
- 0.95 |
- 4 |
- Y |
-
-
- | 186 |
- R4540E |
- CZECHII/EiJ |
- R4540E.CEL |
- 11.04 |
- 36.69 |
- 53.00% |
- 45.30% |
- 1.70% |
- 1.83 |
- 1.32 |
- 4 |
- |
-
-
- | 187 |
- R2600E.1 |
- D2B6F1 |
- R2600E.1.CEL |
- 2.47 |
- 95 |
- 58.10% |
- 40.20% |
- 1.70% |
- 1.41 |
- 0.78 |
- 1 |
- Y |
-
-
- | 188 |
- R2604E.1 |
- D2B6F1 |
- R2604E.1.CEL |
- 2.66 |
- 90 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.28 |
- 0.79 |
- 1 |
- Y |
-
-
- | 189 |
- R1002E.3 |
- DBA/2J |
- R1002E.3.CEL |
- 1 |
- 102 |
- 54.80% |
- 43.70% |
- 1.50% |
- 2.84 |
- 0.83 |
- 3 |
- |
-
-
- | 190 |
- R4541E |
- DBA/2J |
- R4541E.CEL |
- 1 |
- 43.4 |
- 61.40% |
- 37.00% |
- 1.50% |
- 1.37 |
- 0.73 |
- 4 |
- Y |
-
-
- | 191 |
- R959E.3 |
- DBA/2J |
- R959E.3.CEL |
- 1 |
- 89.97 |
- 53.20% |
- 45.30% |
- 1.50% |
- 3.66 |
- 1.09 |
- 4 |
- |
-
-
- | 192 |
- R2572E.1 |
- DBA/2J |
- R2572E.1.CEL |
- 2.41 |
- 79 |
- 55.50% |
- 42.90% |
- 1.60% |
- 1.37 |
- 0.79 |
- 1 |
- |
-
-
- | 193 |
- R4542E |
- DBA/2J |
- R4542E.CEL |
- 5.7 |
- 39.95 |
- 61.00% |
- 37.40% |
- 1.50% |
- 1.23 |
- 0.81 |
- 4 |
- Y |
-
-
- | 194 |
- R2771E.3 |
- FVB/NJ |
- R2771E.3.CEL |
- 1 |
- 70 |
- 55.30% |
- 43.20% |
- 1.50% |
- 1.69 |
- 0.83 |
- 3 |
- |
-
-
- | 195 |
- R2772E.3 |
- FVB/NJ |
- R2772E.3.CEL |
- 1 |
- 76 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.13 |
- 1.02 |
- 3 |
- |
-
-
- | 196 |
- R2636E.1 |
- KK/HlJ |
- R2636E.1.CEL |
- 2.61 |
- 93 |
- 58.90% |
- 39.50% |
- 1.50% |
- 1.39 |
- 0.76 |
- 1 |
- Y |
-
-
- | 197 |
- R2637E.1 |
- KK/HlJ |
- R2637E.1.CEL |
- 2.19 |
- 103 |
- 59.40% |
- 39.00% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 198 |
- R0999E.1 |
- LG/J |
- R0999E.1.CEL |
- 2.45 |
- 82 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 199 |
- R1004E.1 |
- LG/J |
- R1004E.1.CEL |
- 2.44 |
- 92 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 200 |
- R4543E |
- LP/J |
- R4543E.CEL |
- 6.57 |
- 41.99 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.28 |
- 0.75 |
- 4 |
- Y |
-
-
- | 201 |
- R4544E |
- LP/J |
- R4544E.CEL |
- 4.56 |
- 39.9 |
- 62.40% |
- 36.10% |
- 1.50% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 202 |
- R2858E.3 |
- MOLF/EiJ |
- R2858E.3.CEL |
- 1 |
- 64 |
- 53.80% |
- 44.70% |
- 1.50% |
- 1.59 |
- 0.95 |
- 3 |
- |
-
-
- | 203 |
- R2919.3 |
- MOLF/EiJ |
- R2919.3.CEL |
- 1 |
- 64 |
- 52.40% |
- 46.00% |
- 1.60% |
- 2.15 |
- 1.07 |
- 3 |
- |
-
-
- | 204 |
- R1688E.1 |
- NOD/LtJ |
- R1688E.1.CEL |
- 2.66 |
- 98 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 205 |
- R2566E-2.1 |
- NOD/LtJ |
- R2566E-2.1.CEL |
- 3.03 |
- 69 |
- 59.80% |
- 38.80% |
- 1.50% |
- 1.38 |
- 0.75 |
- 1 |
- Y |
-
-
- | 206 |
- R4545E |
- NZB/BlNJ |
- R4545E.CEL |
- 4.23 |
- 43.48 |
- 62.10% |
- 36.40% |
- 1.50% |
- 1.33 |
- 0.76 |
- 4 |
- Y |
-
-
- | 207 |
- R4546E |
- NZB/BlNJ |
- R4546E.CEL |
- 6.27 |
- 44.22 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.17 |
- 0.82 |
- 4 |
- Y |
-
-
- | 208 |
- R2535E.1 |
- NZO/HlLtJ |
- R2535E.1.CEL |
- 1.89 |
- 86 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.41 |
- 0.85 |
- 1 |
- |
-
-
- | 209 |
- R2550E.1 |
- NZO/HlLtJ |
- R2550E.1.CEL |
- 1.79 |
- 87 |
- 60.70% |
- 37.80% |
- 1.50% |
- 1.52 |
- 0.82 |
- 1 |
- |
-
-
- | 210 |
- R2817E.3 |
- NZW/LacJ |
- R2817E.3.CEL |
- 1 |
- 59 |
- 50.90% |
- 47.60% |
- 1.50% |
- 3.59 |
- 1.48 |
- 3 |
- |
-
-
- | 211 |
- R2810E |
- NZW/LacJ |
- R2810E.CEL |
- |
- |
- |
- |
- |
- |
- |
- 3 |
- |
-
-
- | 212 |
- R2810E.3 |
- NZW/LacJ |
- R2810E.3.CEL |
- 1 |
- 74 |
- 57.00% |
- 41.70% |
- 1.40% |
- 2.15 |
- 1.03 |
- 4 |
- Y |
-
-
- | 213 |
- R4547E |
- PANCEVO/EiJ |
- R4547E.CEL |
- 5.27 |
- 51.34 |
- 57.20% |
- 41.10% |
- 1.70% |
- 1.7 |
- 0.83 |
- 4 |
- |
-
-
- | 214 |
- R4548E |
- PANCEVO/EiJ |
- R4548E.CEL |
- 10.54 |
- 37.39 |
- 50.30% |
- 48.00% |
- 1.70% |
- 1.68 |
- 1.09 |
- 4 |
- |
-
-
- | 215 |
- R2635E.1 |
- PWD/PhJ |
- R2635E.1.CEL |
- 3.72 |
- 80 |
- 54.20% |
- 44.10% |
- 1.70% |
- 1.53 |
- 0.85 |
- 1 |
- |
-
-
- | 216 |
- R2634E.1 |
- PWD/PhJ |
- R2634E.1.CEL |
- 3.29 |
- 90 |
- 55.90% |
- 42.50% |
- 1.60% |
- 1.57 |
- 0.81 |
- 1 |
- |
-
-
- | 217 |
- R2544E.1 |
- PWK/PhJ |
- R2544E.1.CEL |
- 2.2 |
- 108 |
- 54.90% |
- 43.50% |
- 1.70% |
- 1.36 |
- 0.82 |
- 1 |
- |
-
-
- | 218 |
- R2549E.1 |
- PWK/PhJ |
- R2549E.1.CEL |
- 2.28 |
- 84 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.57 |
- 0.83 |
- 1 |
- |
-
-
- | 219 |
- R4550E |
- SJL/J |
- R4550E.CEL |
- 5.35 |
- 40.44 |
- 62.30% |
- 36.20% |
- 1.40% |
- 1.24 |
- 0.79 |
- 4 |
- |
-
-
- | 220 |
- R2368E.1 |
- WSB/EiJ |
- R2368E.1.CEL |
- 2.57 |
- 86 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.29 |
- 0.74 |
- 1 |
- Y |
-
-
- | 221 |
- R2547E.1 |
- WSB/EiJ |
- R2547E.1.CEL |
- 2.14 |
- 90 |
- 58.20% |
- 40.10% |
- 1.60% |
- 1.32 |
- 0.77 |
- 1 |
- Y |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_ND/summary.rtf b/general/datasets/Eye_M2_0908_R_ND/summary.rtf
deleted file mode 100644
index 44b7e23..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/summary.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-FINAL RECOMMENDED EYE DATA SET. The HEIMED September 2008 RMA data release provides estimates of gene expression in whole eyes of 103 lines of young adult mice generated using 221 Affymetrix M430 2.0 arrays. This data set is intended for exploration of the genetics and genomics of the mouse eye, retina, lens, retinal pigment epithelium, cornea, iris and choroid. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
diff --git a/general/datasets/Eye_M2_0908_R_ND/tissue.rtf b/general/datasets/Eye_M2_0908_R_ND/tissue.rtf
deleted file mode 100644
index 9b6ee0f..0000000
--- a/general/datasets/Eye_M2_0908_R_ND/tissue.rtf
+++ /dev/null
@@ -1,2058 +0,0 @@
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.
-
-Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well balanced sample of males and females, in general without within-strain-by-sex replication. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.
-
-Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.
-
-Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.
-
-
- - Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
- - Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
- - Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
- - Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
-
-
-Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Group |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- R2595E.1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- UTHSC RW |
-
-
- | 2 |
- R2533E.1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- UTHSC RW |
-
-
- | 3 |
- R0754E.1 |
- GDP |
- A/J |
- 60 |
- M |
- JAX |
-
-
- | 4 |
- R4521E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 5 |
- R4522E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 6 |
- R4523E |
- KO |
- B6129P2F2N1-Clcn3 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 7 |
- R4526E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- F |
- TChoi_Deltagen |
-
-
- | 8 |
- R4509E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- M |
- TChoi_Deltagen |
-
-
- | 9 |
- R4510E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 10 |
- R4511E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 20 |
- M |
- TChoi_Deltagen |
-
-
- | 11 |
- R4524E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 12 |
- R4525E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 13 |
- R4515E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 14 |
- R4516E |
- KO |
- B6129P2F2N1-Gabra1 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 15 |
- R4517E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 16 |
- R4512E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- F |
- TChoi_Deltagen |
-
-
- | 17 |
- R4513E |
- KO |
- B6129P2F2N1-Gnb5 |
- 25 |
- M |
- TChoi_Deltagen |
-
-
- | 18 |
- R4514E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 19 |
- R4518E |
- KO |
- B6129P2F2N1-Gpr19 |
- 70 |
- M |
- TChoi_Deltagen |
-
-
- | 20 |
- R4519E |
- KO |
- B6129P2F2N1-Gpr19 |
- 68 |
- M |
- TChoi_Deltagen |
-
-
- | 21 |
- R2601E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 22 |
- R2602E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 23 |
- R1676E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- JAX |
-
-
- | 24 |
- R1672E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- JAX |
-
-
- | 25 |
- R4530E |
- GDP |
- BALB/cJ |
- 66 |
- F |
- JAX |
-
-
- | 26 |
- R4529E |
- GDP |
- BALB/cJ |
- 66 |
- M |
- JAX |
-
-
- | 27 |
- R2704E.2 |
- BXD |
- BXD1 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 28 |
- R2707E.3 |
- BXD |
- BXD1 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 29 |
- R1231E.2 |
- BXD |
- BXD2 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 30 |
- R2598E.1 |
- BXD |
- BXD2 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 31 |
- R2591E.1 |
- BXD |
- BXD5 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 32 |
- R2714E.2 |
- BXD |
- BXD5 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 33 |
- R2570E.1 |
- BXD |
- BXD6 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 34 |
- R2694E.2 |
- BXD |
- BXD6 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 35 |
- R2538E.1 |
- BXD |
- BXD8 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 36 |
- R2709E.2 |
- BXD |
- BXD8 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 37 |
- R2708E.2 |
- BXD |
- BXD9 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 38 |
- R2569E.1 |
- BXD |
- BXD9 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 39 |
- R2581E.1 |
- BXD |
- BXD11 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 40 |
- R2612E.2 |
- BXD |
- BXD11 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 41 |
- R2742E.2 |
- BXD |
- BXD12 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 42 |
- R2543E.1 |
- BXD |
- BXD12 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 43 |
- R2586E.1 |
- BXD |
- BXD13 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 44 |
- R877E.2 |
- BXD |
- BXD13 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 45 |
- R2557E.1 |
- BXD |
- BXD14 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 46 |
- R1128E.2 |
- BXD |
- BXD14 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 47 |
- R2701E.3 |
- BXD |
- BXD15 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 48 |
- R2716E.2 |
- BXD |
- BXD15 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 49 |
- R2711E.2 |
- BXD |
- BXD16 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 50 |
- R2567E.1 |
- BXD |
- BXD16 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 51 |
- R2720E.2 |
- BXD |
- BXD18 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 52 |
- R2559E.1 |
- BXD |
- BXD18 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 53 |
- R2560E.1 |
- BXD |
- BXD19 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 54 |
- R2713E.2 |
- BXD |
- BXD19 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 55 |
- R2584E.1 |
- BXD |
- BXD20 |
- 59 |
- F |
- BIDMC GR |
-
-
- | 56 |
- R2731E.2 |
- BXD |
- BXD20 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 57 |
- R2702E.2 |
- BXD |
- BXD21 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 58 |
- R2541E2.1 |
- BXD |
- BXD21 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 59 |
- R2553E.1 |
- BXD |
- BXD22 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 60 |
- R2700E.2 |
- BXD |
- BXD22 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 61 |
- R2558E-2.1 |
- BXD |
- BXD23 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 62 |
- R1086E.2 |
- BXD |
- BXD23 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 63 |
- R2719E.2 |
- BXD |
- BXD24 |
- 123 |
- F |
- UTHSC RW |
-
-
- | 64 |
- R2589E2.1 |
- BXD |
- BXD24 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 65 |
- R2573E-2.1 |
- BXD |
- BXD25 |
- 67 |
- F |
- UAB |
-
-
- | 66 |
- R2683E.2 |
- BXD |
- BXD25 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 67 |
- R2703E.2 |
- BXD |
- BXD27 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 68 |
- R2729E.3 |
- BXD |
- BXD27 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 69 |
- R2562E.3 |
- BXD |
- BXD28 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 70 |
- R2721E.2 |
- BXD |
- BXD28 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 71 |
- R2561E.3 |
- BXD |
- BXD29 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 72 |
- R1258E.2 |
- BXD |
- BXD31 |
- 57 |
- F |
- UTHSC RW |
-
-
- | 73 |
- R2597E.1 |
- BXD |
- BXD31 |
- 61 |
- M |
- BIDMC GR |
-
-
- | 74 |
- R2563E.1 |
- BXD |
- BXD32 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 75 |
- R1216E.2 |
- BXD |
- BXD32 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 76 |
- R2542E.1 |
- BXD |
- BXD33 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- R857E.2 |
- BXD |
- BXD33 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 78 |
- R1451E.2 |
- BXD |
- BXD34 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 79 |
- R2585E.1 |
- BXD |
- BXD34 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 80 |
- R2698E.3 |
- BXD |
- BXD36 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 81 |
- R2705E.3 |
- BXD |
- BXD36 |
- 57 |
- M |
- BIDMC GR |
-
-
- | 82 |
- R2710E.2 |
- BXD |
- BXD38 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 83 |
- R2532E.1 |
- BXD |
- BXD38 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 84 |
- R2574E.1 |
- BXD |
- BXD39 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 85 |
- R2695E.2 |
- BXD |
- BXD39 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 86 |
- R2699E.2 |
- BXD |
- BXD40 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 87 |
- R2590E.1 |
- BXD |
- BXD40 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 88 |
- R2696E.2 |
- BXD |
- BXD42 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 89 |
- R2596E.1 |
- BXD |
- BXD42 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 90 |
- R994E.2 |
- BXD |
- BXD43 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 91 |
- R2607E.1 |
- BXD |
- BXD43 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 92 |
- R2594E.1 |
- BXD |
- BXD44 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 93 |
- R2610E.2 |
- BXD |
- BXD44 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 94 |
- R2732E.2 |
- BXD |
- BXD45 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 95 |
- R2592E.1 |
- BXD |
- BXD45 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- R967E.2 |
- BXD |
- BXD48 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 97 |
- R2606E.1 |
- BXD |
- BXD48 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 98 |
- R2933E.3 |
- BXD |
- BXD50 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 99 |
- R2937E.3 |
- BXD |
- BXD50 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 100 |
- R2603E.1 |
- BXD |
- BXD51 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 101 |
- R1042E.2 |
- BXD |
- BXD51 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 102 |
- R2980E.3 |
- BXD |
- BXD55 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 103 |
- R2690E.2 |
- BXD |
- BXD55 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 104 |
- R4176E |
- BXD |
- BXD56 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 105 |
- R4175E |
- BXD |
- BXD56 |
- 53 |
- M |
- UTHSC RW |
-
-
- | 106 |
- R1006E.3 |
- BXD |
- BXD60 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 107 |
- R2725E.2 |
- BXD |
- BXD60 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 108 |
- R1074E.3 |
- BXD |
- BXD60 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 109 |
- R2534E2.1 |
- BXD |
- BXD61 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 110 |
- R2684E.2 |
- BXD |
- BXD61 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 111 |
- R1107E.3 |
- BXD |
- BXD62 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 112 |
- R2681E.2 |
- BXD |
- BXD62 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 113 |
- R965E.3 |
- BXD |
- BXD62 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 114 |
- R1425E.2 |
- BXD |
- BXD63 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 115 |
- R2576E.3 |
- BXD |
- BXD63 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 116 |
- R943E-2.2 |
- BXD |
- BXD64 |
- 56 |
- F |
- UTHSC RW |
-
-
- | 117 |
- R2611E.1 |
- BXD |
- BXD64 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 118 |
- R2689E.2 |
- BXD |
- BXD65 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 119 |
- R2583E.1 |
- BXD |
- BXD65 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 120 |
- R2728E.2 |
- BXD |
- BXD66 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 121 |
- R2536E2.1 |
- BXD |
- BXD66 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 122 |
- R1207E.2 |
- BXD |
- BXD66 |
- 83 |
- M |
- UTHSC RW |
-
-
- | 123 |
- R1192E.2 |
- BXD |
- BXD67 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 124 |
- R2727E.3 |
- BXD |
- BXD67 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 125 |
- R2691E.3 |
- BXD |
- BXD67 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 126 |
- R2551E.1 |
- BXD |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 127 |
- R2726E.2 |
- BXD |
- BXD68 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 128 |
- R2593E.1 |
- BXD |
- BXD69 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 129 |
- R975E.2 |
- BXD |
- BXD70 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 130 |
- R2537E2.1 |
- BXD |
- BXD70 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 131 |
- R4531E |
- BXD |
- BXD71 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 132 |
- R4532E |
- BXD |
- BXD71 |
- 86 |
- M |
- UTHSC RW |
-
-
- | 133 |
- R2779E.2 |
- BXD |
- BXD73 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 134 |
- R3024E.3 |
- BXD |
- BXD73 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 135 |
- R2565E.1 |
- BXD |
- BXD75 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 136 |
- R1397E-re.2 |
- BXD |
- BXD75 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 137 |
- R2687E.3 |
- BXD |
- BXD77 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 138 |
- R2717E.2 |
- BXD |
- BXD77 |
- 107 |
- M |
- UTHSC RW |
-
-
- | 139 |
- R1421E.3 |
- BXD |
- BXD77 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 140 |
- R2579E.1 |
- BXD |
- BXD80 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 141 |
- R2686E.2 |
- BXD |
- BXD80 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 142 |
- R2956E.3 |
- BXD |
- BXD83 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 143 |
- R2960E.3 |
- BXD |
- BXD83 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 144 |
- R2922E.3 |
- BXD |
- BXD84 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 145 |
- R2895E.3 |
- BXD |
- BXD84 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- R2692E.2 |
- BXD |
- BXD85 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 147 |
- R2715E.2 |
- BXD |
- BXD85 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 148 |
- R1405E.2 |
- BXD |
- BXD86 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 149 |
- R1225E.3 |
- BXD |
- BXD86 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 150 |
- R2724E.2 |
- BXD |
- BXD87 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 151 |
- R2540E.1 |
- BXD |
- BXD87 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 152 |
- R1433E.2 |
- BXD |
- BXD89 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 153 |
- R2546E.1 |
- BXD |
- BXD89 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 154 |
- R2578E2.1 |
- BXD |
- BXD90 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 155 |
- R859E.2 |
- BXD |
- BXD90 |
- 72 |
- M |
- UTHSC RW |
-
-
- | 156 |
- R2682E.2 |
- BXD |
- BXD92 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 157 |
- R1388E.3 |
- BXD |
- BXD92 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 158 |
- R1322E.3 |
- BXD |
- BXD92 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 159 |
- R2733E.2 |
- BXD |
- BXD96 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 160 |
- R2554E.1 |
- BXD |
- BXD96 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 161 |
- R2649E.2 |
- BXD |
- BXD97 |
- 74 |
- F |
- UTHSC RW |
-
-
- | 162 |
- R2577E.1 |
- BXD |
- BXD97 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 163 |
- R2645E.3 |
- BXD |
- BXD98 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 164 |
- R2688E.2 |
- BXD |
- BXD98 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 165 |
- R4533E |
- BXD |
- BXD99 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 166 |
- R4534E |
- BXD |
- BXD99 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 167 |
- R2885E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 168 |
- R2883E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- M |
- BIDMC GR |
-
-
- | 169 |
- R1700E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- UTHSC RW |
-
-
- | 170 |
- R1704E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- UTHSC RW |
-
-
- | 171 |
- R2605E.1 |
- GDP BXD |
- C57BL/6J |
- 79 |
- F |
- UTHSC RW |
-
-
- | 172 |
- R0871E |
- GDP BXD |
- C57BL/6J |
- 65 |
- F |
- UTHSC RW |
-
-
- | 173 |
- R0872E.1 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 174 |
- R0872E |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 175 |
- R4507E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 176 |
- R4508E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 177 |
- R4505E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 178 |
- R4506E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 179 |
- R4535E |
- GDP |
- C57BLKS/J |
- 66 |
- F |
- JAX |
-
-
- | 180 |
- R4536E |
- GDP |
- C57BLKS/J |
- 66 |
- M |
- JAX |
-
-
- | 181 |
- R2564E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- F |
- JAX |
-
-
- | 182 |
- R2580E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- M |
- JAX |
-
-
- | 183 |
- R4537E |
- GDP |
- CBA/CaJ |
- 66 |
- F |
- JAX |
-
-
- | 184 |
- R4538E |
- GDP |
- CBA/CaJ |
- 66 |
- M |
- JAX |
-
-
- | 185 |
- R4539E |
- GDP |
- CZECHII/EiJ |
- 66 |
- F |
- JAX |
-
-
- | 186 |
- R4540E |
- GDP |
- CZECHII/EiJ |
- 66 |
- M |
- JAX |
-
-
- | 187 |
- R2600E.1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- UTHSC RW |
-
-
- | 188 |
- R2604E.1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- UTHSC RW |
-
-
- | 189 |
- R1002E.3 |
- GDP BXD |
- DBA/2J |
- 72 |
- F |
- UTHSC RW |
-
-
- | 190 |
- R4541E |
- GDP BXD |
- DBA/2J |
- 65 |
- F |
- JAX |
-
-
- | 191 |
- R959E.3 |
- GDP BXD |
- DBA/2J |
- 60 |
- M |
- UTHSC RW |
-
-
- | 192 |
- R2572E.1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 193 |
- R4542E |
- GDP BXD |
- DBA/2J |
- 59 |
- M |
- JAX |
-
-
- | 194 |
- R2771E.3 |
- GDP |
- FVB/NJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 195 |
- R2772E.3 |
- GDP |
- FVB/NJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 196 |
- R2636E.1 |
- GDP |
- KK/HlJ |
- 64 |
- F |
- UTHSC RW |
-
-
- | 197 |
- R2637E.1 |
- GDP |
- KK/HlJ |
- 64 |
- M |
- UTHSC RW |
-
-
- | 198 |
- R0999E.1 |
- GDP |
- LG/J |
- 57 |
- F |
- UTHSC RW |
-
-
- | 199 |
- R1004E.1 |
- GDP |
- LG/J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 200 |
- R4543E |
- GDP |
- LP/J |
- 65 |
- F |
- JAX |
-
-
- | 201 |
- R4544E |
- GDP |
- LP/J |
- 65 |
- M |
- JAX |
-
-
- | 202 |
- R2858E.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 203 |
- R2919.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 204 |
- R1688E.1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- JAX |
-
-
- | 205 |
- R2566E-2.1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- UTHSC RW |
-
-
- | 206 |
- R4545E |
- GDP |
- NZB/BlNJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 207 |
- R4546E |
- GDP |
- NZB/BlNJ |
- 58 |
- M |
- BIDMC GR |
-
-
- | 208 |
- R2535E.1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- JAX |
-
-
- | 209 |
- R2550E.1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- JAX |
-
-
- | 210 |
- R2817E.3 |
- GDP |
- NZW/LacJ |
- 65 |
- F |
- BIDMC GR |
-
-
- | 211 |
- R2810E |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 212 |
- R2810E.3 |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 213 |
- R4547E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- F |
- JAX |
-
-
- | 214 |
- R4548E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- M |
- JAX |
-
-
- | 215 |
- R2635E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- JAX |
-
-
- | 216 |
- R2634E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- JAX |
-
-
- | 217 |
- R2544E.1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- JAX |
-
-
- | 218 |
- R2549E.1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- JAX |
-
-
- | 219 |
- R4550E |
- GDP |
- SJL/J |
- 65 |
- M+F |
- JAX |
-
-
- | 220 |
- R2368E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- UTHSC RW |
-
-
- | 221 |
- R2547E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- UTHSC RW |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_WT/acknowledgment.rtf b/general/datasets/Eye_M2_0908_R_WT/acknowledgment.rtf
deleted file mode 100644
index 5098d32..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant and from funds from NEI grant to Dr. Eldon Geisert (R01EY017841), an NEI Vision Core grant (EY14080) and an Unrestricted Grant from Research To Prevent Blindness.
-
-We thank Dr. Ted Choi, Chief Scientific Director of Predictive Biology, Inc. (past director of molecular genetics at Deltagen Inc.) for providing us with eye samples from several interesting DeltaGen knockouts.
diff --git a/general/datasets/Eye_M2_0908_R_WT/cases.rtf b/general/datasets/Eye_M2_0908_R_WT/cases.rtf
deleted file mode 100644
index 552d4a5..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/cases.rtf
+++ /dev/null
@@ -1,57 +0,0 @@
-This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:
-
-
- - 68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.
- - 35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common Mus musculus domesticus inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (Mus musculus domesticus, e.g, WSB/EiJ; M. musculus musculus, e.g., CZECHII/EiJ; M. musculus molossinus, e.g., MOLF/EiJ; M. musculus castaneus, e.g., CAST/EiJ); and even one different species of mouse (Mus spicilegus, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the Nyx-nob mutant:
- - 6 knockouts (KO), including a KO of Rpe65, and 5 DeltaGen Inc. knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: Gabra1, Gabbr1, Gnb1, Gpr19, and Clcn3. We also included one spontaneous mutant of the nyctalopin (Nyx no b wave "nob") gene (Pardue et al., 1998) that is on a BALB/cByJ background.
-
-
-Rod photoreceptor degeneration in inbred mice: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the retinal degeneration 1 (rd1) mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (Pde6b). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.
-
-As expected (Dickerson LW et al., 2002) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, Clcn3) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of Gnat2, a gene associated with cones and achromatopsia in mice and humans.
-
-Lines of mice were selected using the following criteria:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - representation of a fairly wide variety of different subspecies of Mus
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - interesting mutations or knockouts affecting genes with high expression in the eye
- - general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.
-
-
-We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see Perlegen's excellent data resources and browser).
-
-
- - 129S1/SvImJ : Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a cone photoreceptor function loss 3 mutant (Cpfl3 allele) of the Gnat2 gene that is a model for achromatopsia (JAX Stock Number: 002448)
- - A/J: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (Tyr c allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: 000646)
- - BALB/cByJ: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Small brain, not aggressive (JAX Stock Number: 001026)
- - BALB/cJ: Phenome Project A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Large brain and aggressive (JAX Stock Number: 000651)
- - BXSB/MpJ: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the Yaa gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: 000740)
- - C3H/HeJ: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a Pdeb6 rd1 mutant with near total photoreceptor loss at as early as postnatal day 30. Also a Tlr4 mutant that is endotoxin resistant. (JAX Stock Number: 000659)
- - C57BL/6J: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: 000664)
- - C57BLKS/J: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: 000662)
- - CAST/EiJ: A wild-derived inbred Mus musculus castaneus strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: 000928)
- - CBA/CaJ: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: 000654)
- - CZECHII/EiJ: Czech 2 is a wild-derived inbred strain M. musculus musculus strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: 001144).
- - DBA/2J: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. A myosin 5a (Myo5a d) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: 000671)
- - FVB/NJ: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. Tyr c locus albino and a Pdeb6 rd1 mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: 001800).
- - KK/HlJ: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: 002106)
- - LG/J: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A Tyr c locus albino strain. (JAX Stock Number: 000675)
- - LP/J: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B Ednrb gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: 000676)
- - MOLF/EiJ: A wild-derived inbred strain derived from M. musculus molossinus samples camputered in Fukuoka, Japan. This strain has the retinal degeneration rd1 allele in Pde6b. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: 000550)
- - NOD/LtJ: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. (JAX Stock Number: 001976)
- - NZO/HlLtJ: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: 002105)
- - NZB/BlNJ: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: 000648)
- - NZW/LacJ: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the Tyr c locus albino mutation, the pink-eye dilution mutation in the Oca2 or p locus, and the brown allele at Tyrp1. (JAX Stock Number: 001058)
- - PANCEVO/EiJ: PANCEVO/EiJ is a wild-derived inbred strain from the Mus spicilegus samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier 10103). M. spicilegus is a colonial mound-building species. No known ocular or retina mutations, but the expression level of Gnat2 is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: 001384)
- - PWD/PhJ: A wild-derived Mus musculus musculus agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: 004660)
- - PWK/PhJ: A wild-derived Mus musculus musculus inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: 003715)
- - SJL/J: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration rd1 allele in Pde6b. It also carries both the Tyr c albino mutation and the pink-eye dilution mutation in the Oca2 or p locus. Highly aggressive males. (JAX Stock Number: 000686)
- - WSB/EiJ: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived Mus musculus domesticus inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: 001145)
- - B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J 100006)
-
-
-Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, 2008 and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (Tyr, or human OCA1), the brown allele of the tyrosinase related protein 1 (Tyrp1), the pink-eye dilution allele of Oca2 (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein Asip, the steel allele of Kitlg, the dilute allele of Myo5a (probe set 1419754), and the piebald allele of Ednrb. In some of these cases, effects of the mutation are easily detected at the transcript level (Tyrp1, Oca2, and Myo5a), but in the other cases (Tyr, Asip, Ednrb, and Kitlg), mutations do not leave a strong imprint on expression.
diff --git a/general/datasets/Eye_M2_0908_R_WT/experiment-design.rtf b/general/datasets/Eye_M2_0908_R_WT/experiment-design.rtf
deleted file mode 100644
index 1ebe0ad..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression profiling by array
diff --git a/general/datasets/Eye_M2_0908_R_WT/notes.rtf b/general/datasets/Eye_M2_0908_R_WT/notes.rtf
deleted file mode 100644
index 7a26eb5..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Eye_M2_0908_R_WT/platform.rtf b/general/datasets/Eye_M2_0908_R_WT/platform.rtf
deleted file mode 100644
index 9024a99..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/platform.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many probes overlap and target the same transcript). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
-As part of the development of HEIMED, we have manually annotated individual probe sets by sequence alignment to the mouse genome and transcriptome. Approximately 13,000 probe sets that have comparatively high expression in eye and CNS were curated by one of the authors (RWW) and now have specific information on the part of the transcript targeted by each probe set. The other 33,000 transcripts have corresponding data that was generated by Xusheng Wang using computational methods (BLAT analysis combined with annotated genome sequence).
-
-One example may help explain how to exploit this annotation. The four probe sets for rhodopsin include information on the target location. Only the first probe set targets the last two coding exons. The other three probe sets target different parts of the 3’ UTR (mid, distal, and far distal regions). The probe sets can be reordered by from high to low expression using the Sort By function in Search Results pages. In the case of rhodopsin, the probe set that targets that last two coding exons and proximal parts of the 3’ UTR also has the highest expression . Finally, the HEIMED gene descriptions have been customized to help vision researchers. In the case of rhodopsin, the description appended after the gene name reads “rod photoreceptor pigment, retinitis pigmentosa-associated”. For less well known genes this kind of annotation can be extremely useful. For example, the more verbose annotation for Cerkl reads “neuronal survival and apoptosis-related, retinal ganglion cell expressed, retinitis pigmentosa 26); alternative 3' UTR of short form message, intron 2”.
-
-
-
-
-
-Legend: Distribution of expression values for all probe sets in HEIMED.
diff --git a/general/datasets/Eye_M2_0908_R_WT/processing.rtf b/general/datasets/Eye_M2_0908_R_WT/processing.rtf
deleted file mode 100644
index 4349e60..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/processing.rtf
+++ /dev/null
@@ -1,3381 +0,0 @@
-Range of Gene Expression in the Eye. Expression of transcripts in the HEIMED and most other GN data sets is measured on a log2 scale. Each unit corresponding approximately to a 2-fold difference in hybridization signal intensity. To simplify comparisons among different data sets and cases, log2 RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units (variance stabilized). Values of all 45,101 probe sets in this data set range from a low of 4.8 (Tcf15, probe set 1420281_at) to a high of 15.5 (crystallin gamma C, Crygc, probe set 1422674_s_at). This corresponds to 10.7 units or a 1 to 1700 dynamic range of expression (2^10.73).
-
-We used pooled RNA samples of whole eyes, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-We calibrated this log intensity scale using Affymetrix spike-in control probe sets. These 18 control probe sets target exogenous bacterial mRNAs that are added to each sample (a graded dose spike cocktail) during preparation at concentrations of 1.5, 5, 25, and 100 pM. (To find these probe sets, search GN’s ALL search field using the string “AFFX pM”.) A value of 6 or less is equivalent to an mRNA concentration of under 0.4 pM, a value of 8 is equivalent to ~1.5 pM, 9.5 is equivalent to ~5 pM, 11.5 is equivalent to ~25 pM, 13.5 is equivalent to ~100 pM, and a value of 15.5 is equivalent to an mRNA concentration of 400 pM or greater.
-
-This range can be converted to the mRNA molecules per cell in the eye assuming that a value of 8 is equivalent to about 1 mRNA copy per cell (Kanno et al. 2006, see http://www.biomedcentral.com/1471-2164/7/64). Since the expression of rhodopsin mRNA is normally 15 units, we predict that there are 27 or ~128 Rho mRNAs per cell in the whole eye and ~256 in rods themselves (assuming that rods make up about half of all cells in the eye). For this purpose it may be useful to know that a normal mouse eye contains between 6 and 8 million rod photoreceptors (Guo, Lu, and Williams; GN BXD Phenotype ID 11024).
-
-Note that some probe sets with very low expression still provide reliable data. For example, probe set 1440397_at (Cacna2d1) has expression of only 5.5 units (a value that would be declared as "absent" using conventional Affymetrix procedures), but the values for this calcium channel transcript are associated with a very strong cis QTL with an LRS of 79 (LOD = 17). This strong linkage is definitely not due to chance since the probability of the expression data mapping precisely to the location of the parent gene itself is about 10e-16. This indicates a high signal to noise ratio and the detection of significant strain variation of the correct transcript.
-
-The standard error of the mean for the HEIMED data set is computed for 2 to 6 biological replicates. The standard error of such small samples tends to systematically underestimate the population standard error. With n = 2 the underestimate is about 25%, whereas for n = 6 the underestimate is 5%. Gurland and Tripathi (1971) provide a correction and equation for this effect (see Sokal and Rohlf, Biometry, 2nd ed., 1981, p 53 for an equation of the correction factor for small samples of n < 20.) Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the first three batches together. The last batch was processed separately and merged as described below.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing using Biobase affy10 build running under R version 2.7.1, all array data sets were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (FVB/NJ, NOD/LtJ, MOLF/EiJ, C3H/HeJ and BXD24), samples from wild subspecies such as WSB/EiJ, CAST/EiJ, PWD/PhJ, and PWK/PhJ, and knockouts. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. The assumption is that anomolous data are much more likely due to experimental and technical errors than to informative biological variation. Approximately 10% of arrays were discarded.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We reviewed the data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g., 1800) represented the QTL harvest for the full data set. We then dropped a single array from the data set, recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 1750 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs. Values ranged from approximately -90 (good arrays) to +40 (bad arrays). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a method to polish a data set.
-
-During this process we discovered that nearly 20 arrays in the batch 2 had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of high quality.
-
-A third batch of approximately 40 arrays were processed by Yan Jiao and Weikuan Gu in August 2006. These complete data set assembled by Hongqiang Li. This process again included a correction for a batch effect.
-
-For the June 2006 data set Hongqiang Li used a new batch correction method that stabilizes the range of expression in each batch. For each of the three large batches, we extracted the minumum and maximum raw probe expression (CEL file level) value. We then adjusted raw probe values in each batch to have the same range as the first and largest batch (batch 1) using a simple linear interpolation. These procedures generated new correct CEL files which were then used with RMA to generate final probe set estimates.
-
-For the final fourth batch of arrays (Sept 2008) Arthur Centeno and Rob Williams corrected for a systematic difference in probe set expression values between original arrays run in 2005 and 2006 and the new arrays added in 2008 (n = 45 acceptable arrays). This difference is due to unknown technical batch effects that are probably associated with labeling, hybridization, and scanning. We performed a simple correction to normalize values of the new set of arrays to those of the old set (batches 1 through 3). No changes were made to any values of the previous three batches. We corrected only the probe set level (RMA) values and not the CEL files. For this final batch, we corrected for the difference (offset) in probe set expression between the first three batches arrays run in 2005 and 2006 (a total of 174 acceptable arrays) and the new batch (n = 47 acceptable arrays). This difference is due to unknown technical effects that are probably related to various steps in labeling, hybridization, and scanning. The correction was applied as follows: (1) RWW selected 51 high quality arrays with similar expression characteristics (r = 0.97 or better between pairs of arrays) in the old data set (from batches 1, 2, and 3) and 34 high quality arrays in the final batch. RWW used scatterplots of full RMA transcriptome data sets to review many pairs of arrays within these new and old array batches. Strains with retinal degeneration or unusual eye gene expression characteristics were excluded from these selected subsets. The average expression values for each probe set were then computed for both the old and new array subsets. The offset value (old minus new) was added to each probe set across all 47 new arrays. This processes forces the average probe set in the new arrays to be very close to that of the previous arrays.
-
-Table 2: Sample tube ID, strain, original CEL filename, and Affymetrix quality control values. Columns labeled Scale factor, Background Average, Present, Absent, Marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Strain |
- Original CEL |
- Scale factor |
- Background Average |
- Present |
- Absent |
- Marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- Batch Id |
- Used for batch control |
-
-
- | 1 |
- R2595E.1 |
- 129S1/SvImJ |
- R2595E.1.CEL |
- 1.79 |
- 115 |
- 61.00% |
- 37.50% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 2 |
- R2533E.1 |
- 129S1/SvImJ |
- R2533E.1.CEL |
- 2.11 |
- 94 |
- 57.90% |
- 40.50% |
- 1.60% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 3 |
- R0754E.1 |
- A/J |
- R0754E.1.CEL |
- 2.72 |
- 86 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.36 |
- 0.76 |
- 1 |
- Y |
-
-
- | 4 |
- R4521E |
- B6129P2F2N1-Clcn3 |
- R4521E.CEL |
- 4.83 |
- 38.7 |
- 63.30% |
- 35.30% |
- 1.40% |
- 1.25 |
- 0.77 |
- 4 |
- |
-
-
- | 5 |
- R4522E |
- B6129P2F2N1-Clcn3 |
- R4522E.CEL |
- 5.76 |
- 37.36 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.37 |
- 0.83 |
- 4 |
- |
-
-
- | 6 |
- R4523E |
- B6129P2F2N1-Clcn3 |
- R4523E.CEL |
- 4.88 |
- 40.42 |
- 63.90% |
- 34.70% |
- 1.40% |
- 1.27 |
- 0.77 |
- 4 |
- |
-
-
- | 7 |
- R4526E |
- B6129P2F2N1-Gabbr1 |
- R4526E.CEL |
- 3.84 |
- 44.18 |
- 65.00% |
- 33.70% |
- 1.30% |
- 1.34 |
- 0.78 |
- 4 |
- Y |
-
-
- | 8 |
- R4509E |
- B6129P2F2N1-Gabbr1 |
- R4509E.CEL |
- 7.45 |
- 34.76 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.45 |
- 0.83 |
- 4 |
- |
-
-
- | 9 |
- R4510E |
- B6129P2F2N1-Gabbr1 |
- R4510E.CEL |
- 8.44 |
- 37.44 |
- 57.40% |
- 41.10% |
- 1.50% |
- 1.35 |
- 0.83 |
- 4 |
- |
-
-
- | 10 |
- R4511E |
- B6129P2F2N1-Gabbr1 |
- R4511E.CEL |
- 5.91 |
- 42.02 |
- 61.40% |
- 37.20% |
- 1.40% |
- 1.41 |
- 0.83 |
- 4 |
- |
-
-
- | 11 |
- R4524E |
- B6129P2F2N1-Gabbr1 |
- R4524E.CEL |
- 5.49 |
- 42.34 |
- 62.40% |
- 36.20% |
- 1.40% |
- 1.29 |
- 0.78 |
- 4 |
- Y |
-
-
- | 12 |
- R4525E |
- B6129P2F2N1-Gabbr1 |
- R4525E.CEL |
- 4.69 |
- 41.3 |
- 63.10% |
- 35.50% |
- 1.40% |
- 1.27 |
- 0.8 |
- 4 |
- Y |
-
-
- | 13 |
- R4515E |
- B6129P2F2N1-Gabra1 |
- R4515E.CEL |
- 5.75 |
- 41.76 |
- 62.80% |
- 35.80% |
- 1.40% |
- 1.41 |
- 0.81 |
- 4 |
- Y |
-
-
- | 14 |
- R4516E |
- B6129P2F2N1-Gabra1 |
- R4516E.CEL |
- 7.07 |
- 40.73 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.32 |
- 0.87 |
- 4 |
- Y |
-
-
- | 15 |
- R4517E |
- B6129P2F2N1-Gabra1 |
- R4517E.CEL |
- 5.45 |
- 38.09 |
- 62.70% |
- 35.80% |
- 1.40% |
- 1.34 |
- 0.82 |
- 4 |
- Y |
-
-
- | 16 |
- R4512E |
- B6129P2F2N1-Gnb5 |
- R4512E.CEL |
- 6.56 |
- 38.02 |
- 59.90% |
- 38.70% |
- 1.50% |
- 1.33 |
- 0.83 |
- 4 |
- |
-
-
- | 17 |
- R4513E |
- B6129P2F2N1-Gnb5 |
- R4513E.CEL |
- 4.15 |
- 41.6 |
- 63.40% |
- 35.10% |
- 1.50% |
- 1.34 |
- 0.82 |
- 4 |
- |
-
-
- | 18 |
- R4514E |
- B6129P2F2N1-Gnb5 |
- R4514E.CEL |
- 5.86 |
- 39.2 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.34 |
- 0.81 |
- 4 |
- |
-
-
- | 19 |
- R4518E |
- B6129P2F2N1-Gpr19 |
- R4518E.CEL |
- 5.58 |
- 38.9 |
- 62.60% |
- 36.00% |
- 1.30% |
- 1.39 |
- 0.79 |
- 4 |
- Y |
-
-
- | 20 |
- R4519E |
- B6129P2F2N1-Gpr19 |
- R4519E.CEL |
- 5.95 |
- 41.91 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.35 |
- 0.84 |
- 4 |
- Y |
-
-
- | 21 |
- R2601E.1 |
- B6D2F1 |
- R2601E.1.CEL |
- 2.55 |
- 92 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.44 |
- 0.78 |
- 1 |
- Y |
-
-
- | 22 |
- R2602E.1 |
- B6D2F1 |
- R2602E.1.CEL |
- 2.6 |
- 84 |
- 59.70% |
- 38.80% |
- 1.50% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 23 |
- R1676E.1 |
- BALB/cByJ |
- R1676E.1.CEL |
- 2.69 |
- 98 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.46 |
- 0.74 |
- 1 |
- |
-
-
- | 24 |
- R1672E.1 |
- BALB/cByJ |
- R1672E.1.CEL |
- 2.22 |
- 111 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 25 |
- R4530E |
- BALB/cJ |
- R4530E.CEL |
- 6.37 |
- 37.53 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.3 |
- 0.84 |
- 4 |
- Y |
-
-
- | 26 |
- R4529E |
- BALB/cJ |
- R4529E.CEL |
- 5.71 |
- 41.33 |
- 60.50% |
- 38.00% |
- 1.50% |
- 1.48 |
- 0.8 |
- 4 |
- Y |
-
-
- | 27 |
- R2704E.2 |
- BXD1 |
- R2704E.2.CEL |
- 2.066 |
- 139.61 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 28 |
- R2707E.3 |
- BXD1 |
- R2707E.3.CEL |
- 1 |
- 80 |
- 56.40% |
- 42.10% |
- 1.50% |
- 1.43 |
- 0.79 |
- 3 |
- |
-
-
- | 29 |
- R1231E.2 |
- BXD2 |
- R1231E.2.CEL |
- 2.197 |
- 138.73 |
- 57.30% |
- 41.30% |
- 1.40% |
- 1.41 |
- 0.77 |
- 2 |
- |
-
-
- | 30 |
- R2598E.1 |
- BXD2 |
- R2598E.1.CEL |
- 1.99 |
- 106 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 31 |
- R2591E.1 |
- BXD5 |
- R2591E.1.CEL |
- 1.7 |
- 136 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.33 |
- 0.78 |
- 1 |
- Y |
-
-
- | 32 |
- R2714E.2 |
- BXD5 |
- R2714E.2.CEL |
- 1.404 |
- 144.35 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 33 |
- R2570E.1 |
- BXD6 |
- R2570E.1.CEL |
- 1.99 |
- 87 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.46 |
- 0.76 |
- 1 |
- Y |
-
-
- | 34 |
- R2694E.2 |
- BXD6 |
- R2694E.2.CEL |
- 1.983 |
- 97.23 |
- 61.60% |
- 37.10% |
- 1.30% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 35 |
- R2538E.1 |
- BXD8 |
- R2538E.1.CEL |
- 1.91 |
- 102 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.52 |
- 0.79 |
- 1 |
- Y |
-
-
- | 36 |
- R2709E.2 |
- BXD8 |
- R2709E.2.CEL |
- 1.99 |
- 99.79 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.42 |
- 0.76 |
- 2 |
- |
-
-
- | 37 |
- R2708E.2 |
- BXD9 |
- R2708E.2.CEL |
- 1.966 |
- 126.46 |
- 57.70% |
- 40.70% |
- 1.50% |
- 1.4 |
- 0.84 |
- 2 |
- |
-
-
- | 38 |
- R2569E.1 |
- BXD9 |
- R2569E.1.CEL |
- 1.75 |
- 87 |
- 55.10% |
- 43.40% |
- 1.50% |
- 2.82 |
- 3.14 |
- 1 |
- |
-
-
- | 39 |
- R2581E.1 |
- BXD11 |
- R2581E.1.CEL |
- 1.94 |
- 89 |
- 62.10% |
- 36.40% |
- 1.60% |
- 1.55 |
- 0.81 |
- 1 |
- Y |
-
-
- | 40 |
- R2612E.2 |
- BXD11 |
- R2612E.2.CEL |
- 1.83 |
- 142.03 |
- 58.20% |
- 40.50% |
- 1.40% |
- 1.78 |
- 0.81 |
- 2 |
- |
-
-
- | 41 |
- R2742E.2 |
- BXD12 |
- R2742E.2.CEL |
- 2.127 |
- 134.14 |
- 57.00% |
- 41.60% |
- 1.40% |
- 1.64 |
- 0.78 |
- 2 |
- |
-
-
- | 42 |
- R2543E.1 |
- BXD12 |
- R2543E.1.CEL |
- 1.61 |
- 118 |
- 58.60% |
- 39.90% |
- 1.60% |
- 1.43 |
- 0.77 |
- 1 |
- Y |
-
-
- | 43 |
- R2586E.1 |
- BXD13 |
- R2586E.1.CEL |
- 2.01 |
- 74 |
- 56.40% |
- 42.00% |
- 1.60% |
- 2.85 |
- 3.81 |
- 1 |
- |
-
-
- | 44 |
- R877E.2 |
- BXD13 |
- R877E.2.CEL |
- 1.558 |
- 125.63 |
- 61.20% |
- 37.50% |
- 1.20% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 45 |
- R2557E.1 |
- BXD14 |
- R2557E.1.CEL |
- 1.83 |
- 99 |
- 62.50% |
- 36.10% |
- 1.40% |
- 1.31 |
- 0.78 |
- 1 |
- Y |
-
-
- | 46 |
- R1128E.2 |
- BXD14 |
- R1128E.2.CEL |
- 1.91 |
- 115 |
- 59.90% |
- 38.80% |
- 1.40% |
- 1.2 |
- 0.82 |
- 1 |
- Y |
-
-
- | 47 |
- R2701E.3 |
- BXD15 |
- R2701E.3.CEL |
- 1 |
- 88 |
- 60.60% |
- 37.90% |
- 1.40% |
- 1.5 |
- 0.77 |
- 3 |
- |
-
-
- | 48 |
- R2716E.2 |
- BXD15 |
- R2716E.2.CEL |
- 2.015 |
- 150.83 |
- 56.40% |
- 42.10% |
- 1.60% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 49 |
- R2711E.2 |
- BXD16 |
- R2711E.2.CEL |
- 1.953 |
- 118.53 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 50 |
- R2567E.1 |
- BXD16 |
- R2567E.1.CEL |
- 2.24 |
- 82 |
- 56.70% |
- 41.60% |
- 1.70% |
- 1.37 |
- 0.75 |
- 1 |
- |
-
-
- | 51 |
- R2720E.2 |
- BXD18 |
- R2720E.2.CEL |
- 2.32 |
- 99.93 |
- 59.50% |
- 39.00% |
- 1.50% |
- 1.33 |
- 0.77 |
- 2 |
- |
-
-
- | 52 |
- R2559E.1 |
- BXD18 |
- R2559E.1.CEL |
- 1.65 |
- 104 |
- 60.80% |
- 37.70% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 53 |
- R2560E.1 |
- BXD19 |
- R2560E.1.CEL |
- 1.79 |
- 98 |
- 60.90% |
- 37.50% |
- 1.60% |
- 1.35 |
- 0.8 |
- 1 |
- Y |
-
-
- | 54 |
- R2713E.2 |
- BXD19 |
- R2713E.2.CEL |
- 1.67 |
- 120.82 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 55 |
- R2584E.1 |
- BXD20 |
- R2584E.1.CEL |
- 2.07 |
- 84 |
- 59.30% |
- 39.10% |
- 1.60% |
- 1.4 |
- 0.76 |
- 1 |
- Y |
-
-
- | 56 |
- R2731E.2 |
- BXD20 |
- R2731E.2.CEL |
- 1.825 |
- 147 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.4 |
- 0.8 |
- 2 |
- |
-
-
- | 57 |
- R2702E.2 |
- BXD21 |
- R2702E.2.CEL |
- 1.811 |
- 128.65 |
- 59.40% |
- 39.10% |
- 1.40% |
- 1.26 |
- 0.8 |
- 2 |
- |
-
-
- | 58 |
- R2541E2.1 |
- BXD21 |
- R2541E2.1.CEL |
- 2.63 |
- 125 |
- 56.00% |
- 42.40% |
- 1.50% |
- 1.29 |
- 0.78 |
- 1 |
- |
-
-
- | 59 |
- R2553E.1 |
- BXD22 |
- R2553E.1.CEL |
- 1.95 |
- 111 |
- 59.90% |
- 38.50% |
- 1.50% |
- 1.28 |
- 0.76 |
- 1 |
- Y |
-
-
- | 60 |
- R2700E.2 |
- BXD22 |
- R2700E.2.CEL |
- 1.858 |
- 102.96 |
- 61.50% |
- 37.10% |
- 1.30% |
- 1.48 |
- 0.79 |
- 2 |
- |
-
-
- | 61 |
- R2558E-2.1 |
- BXD23 |
- R2558E-2.1.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 62 |
- R1086E.2 |
- BXD23 |
- R1086E.2.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 63 |
- R2719E.2 |
- BXD24 |
- R2719E.2.CEL |
- 1.47 |
- 140.38 |
- 61.50% |
- 37.20% |
- 1.30% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 64 |
- R2589E2.1 |
- BXD24 |
- R2589E2.1.CEL |
- 2.61 |
- 112 |
- 57.50% |
- 40.90% |
- 1.60% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 65 |
- R2573E-2.1 |
- BXD25 |
- R2573E-2.1.CEL |
- 3.15 |
- 72 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.77 |
- 0.97 |
- 1 |
- |
-
-
- | 66 |
- R2683E.2 |
- BXD25 |
- R2683E.2.CEL |
- 1.777 |
- 115.64 |
- 58.30% |
- 40.30% |
- 1.40% |
- 2.01 |
- 0.79 |
- 2 |
- |
-
-
- | 67 |
- R2703E.2 |
- BXD27 |
- R2703E.2.CEL |
- 1.263 |
- 134.78 |
- 62.60% |
- 36.10% |
- 1.40% |
- 1.44 |
- 0.78 |
- 2 |
- |
-
-
- | 68 |
- R2729E.3 |
- BXD27 |
- R2729E.3.CEL |
- 1 |
- 87 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.56 |
- 0.84 |
- 3 |
- Y |
-
-
- | 69 |
- R2562E.3 |
- BXD28 |
- R2562E.3.CEL |
- 1.65 |
- 116 |
- 59.90% |
- 38.40% |
- 1.70% |
- 1.37 |
- 0.79 |
- 3 |
- Y |
-
-
- | 70 |
- R2721E.2 |
- BXD28 |
- R2721E.2.CEL |
- 2.065 |
- 157.39 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 71 |
- R2561E.3 |
- BXD29 |
- R2561E.3.CEL |
- 1 |
- 77 |
- 53.30% |
- 45.40% |
- 1.40% |
- 3.36 |
- 19.66 |
- 3 |
- |
-
-
- | 72 |
- R1258E.2 |
- BXD31 |
- R1258E.2.CEL |
- 2.063 |
- 117.09 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.54 |
- 0.78 |
- 2 |
- |
-
-
- | 73 |
- R2597E.1 |
- BXD31 |
- R2597E.1.CEL |
- 2.37 |
- 94 |
- 60.30% |
- 38.30% |
- 1.50% |
- 1.34 |
- 0.77 |
- 1 |
- Y |
-
-
- | 74 |
- R2563E.1 |
- BXD32 |
- R2563E.1.CEL |
- 1.55 |
- 102 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.5 |
- 0.8 |
- 1 |
- |
-
-
- | 75 |
- R1216E.2 |
- BXD32 |
- R1216E.2.CEL |
- 2.23 |
- 111.99 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.35 |
- 0.79 |
- 2 |
- |
-
-
- | 76 |
- R2542E.1 |
- BXD33 |
- R2542E.1.CEL |
- 2.13 |
- 97 |
- 56.50% |
- 41.80% |
- 1.60% |
- 1.91 |
- 0.93 |
- 1 |
- |
-
-
- | 77 |
- R857E.2 |
- BXD33 |
- R857E.2.CEL |
- 1.737 |
- 113.98 |
- 61.90% |
- 36.70% |
- 1.30% |
- 1.6 |
- 0.77 |
- 2 |
- |
-
-
- | 78 |
- R1451E.2 |
- BXD34 |
- R1451E.2.CEL |
- 1.843 |
- 140.05 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.42 |
- 0.81 |
- 2 |
- Y |
-
-
- | 79 |
- R2585E.1 |
- BXD34 |
- R2585E.1.CEL |
- 2.64 |
- 75 |
- 58.30% |
- 40.00% |
- 1.70% |
- 1.25 |
- 0.77 |
- 1 |
- |
-
-
- | 80 |
- R2698E.3 |
- BXD36 |
- R2698E.3.CEL |
- 1 |
- 86 |
- 59.70% |
- 39.00% |
- 1.30% |
- 1.46 |
- 0.78 |
- 3 |
- |
-
-
- | 81 |
- R2705E.3 |
- BXD36 |
- R2705E.3.CEL |
- 1 |
- 86 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.46 |
- 0.77 |
- 3 |
- |
-
-
- | 82 |
- R2710E.2 |
- BXD38 |
- R2710E.2.CEL |
- 2.112 |
- 122.1 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.37 |
- 0.78 |
- 2 |
- |
-
-
- | 83 |
- R2532E.1 |
- BXD38 |
- R2532E.1.CEL |
- 2.04 |
- 94 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.37 |
- 0.8 |
- 1 |
- Y |
-
-
- | 84 |
- R2574E.1 |
- BXD39 |
- R2574E.1.CEL |
- 1.98 |
- 91 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.39 |
- 0.78 |
- 1 |
- |
-
-
- | 85 |
- R2695E.2 |
- BXD39 |
- R2695E.2.CEL |
- 1.638 |
- 122.7 |
- 60.80% |
- 37.80% |
- 1.50% |
- 1.42 |
- 0.8 |
- 2 |
- |
-
-
- | 86 |
- R2699E.2 |
- BXD40 |
- R2699E.2.CEL |
- 1.827 |
- 105.23 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 87 |
- R2590E.1 |
- BXD40 |
- R2590E.1.CEL |
- 2.71 |
- 77 |
- 59.10% |
- 39.30% |
- 1.50% |
- 1.4 |
- 0.77 |
- 1 |
- Y |
-
-
- | 88 |
- R2696E.2 |
- BXD42 |
- R2696E.2.CEL |
- 1.622 |
- 118.95 |
- 62.00% |
- 36.60% |
- 1.50% |
- 1.53 |
- 0.79 |
- 2 |
- |
-
-
- | 89 |
- R2596E.1 |
- BXD42 |
- R2596E.1.CEL |
- 2.63 |
- 108 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 90 |
- R994E.2 |
- BXD43 |
- R994E.2.CEL |
- 1.966 |
- 113.12 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.66 |
- 0.8 |
- 2 |
- |
-
-
- | 91 |
- R2607E.1 |
- BXD43 |
- R2607E.1.CEL |
- 2.43 |
- 115 |
- 58.60% |
- 40.00% |
- 1.40% |
- 1.31 |
- 0.76 |
- 1 |
- Y |
-
-
- | 92 |
- R2594E.1 |
- BXD44 |
- R2594E.1.CEL |
- 1.77 |
- 117 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.35 |
- 0.85 |
- 1 |
- |
-
-
- | 93 |
- R2610E.2 |
- BXD44 |
- R2610E.2.CEL |
- 1.814 |
- 142.91 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.35 |
- 0.8 |
- 2 |
- |
-
-
- | 94 |
- R2732E.2 |
- BXD45 |
- R2732E.2.CEL |
- 2.154 |
- 122.45 |
- 56.50% |
- 42.10% |
- 1.40% |
- 1.8 |
- 0.83 |
- 2 |
- |
-
-
- | 95 |
- R2592E.1 |
- BXD45 |
- R2592E.1.CEL |
- 1.85 |
- 106 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.43 |
- 0.85 |
- 1 |
- Y |
-
-
- | 96 |
- R967E.2 |
- BXD48 |
- R967E.2.CEL |
- 1.948 |
- 130.95 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.63 |
- 0.81 |
- 2 |
- |
-
-
- | 97 |
- R2606E.1 |
- BXD48 |
- R2606E.1.CEL |
- 2.56 |
- 106 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.35 |
- 0.83 |
- 1 |
- Y |
-
-
- | 98 |
- R2933E.3 |
- BXD50 |
- R2933E.3.CEL |
- 1 |
- 72 |
- 52.90% |
- 45.60% |
- 1.50% |
- 2.45 |
- 0.98 |
- 3 |
- |
-
-
- | 99 |
- R2937E.3 |
- BXD50 |
- R2937E.3.CEL |
- 1 |
- 89 |
- 56.90% |
- 41.60% |
- 1.40% |
- 1.81 |
- 0.82 |
- 3 |
- |
-
-
- | 100 |
- R2603E.1 |
- BXD51 |
- R2603E.1.CEL |
- 2.49 |
- 115 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.24 |
- 0.79 |
- 1 |
- |
-
-
- | 101 |
- R1042E.2 |
- BXD51 |
- R1042E.2.CEL |
- 2.352 |
- 104.12 |
- 58.70% |
- 39.90% |
- 1.40% |
- 1.53 |
- 0.82 |
- 2 |
- |
-
-
- | 102 |
- R2980E.3 |
- BXD55 |
- R2980E.3.CEL |
- 1 |
- 82 |
- 56.90% |
- 41.70% |
- 1.50% |
- 1.77 |
- 0.84 |
- 3 |
- |
-
-
- | 103 |
- R2690E.2 |
- BXD55 |
- R2690E.2.CEL |
- 1.887 |
- 164.01 |
- 56.10% |
- 42.30% |
- 1.60% |
- 1.43 |
- 0.8 |
- 2 |
- |
-
-
- | 104 |
- R4176E |
- BXD56 |
- R4176E.CEL |
- 4.75 |
- 43.08 |
- 63.00% |
- 35.60% |
- 1.30% |
- 1.39 |
- 0.81 |
- 4 |
- Y |
-
-
- | 105 |
- R4175E |
- BXD56 |
- R4175E.CEL |
- 6 |
- 38.49 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.47 |
- 0.81 |
- 4 |
- Y |
-
-
- | 106 |
- R1006E.3 |
- BXD60 |
- R1006E.3.CEL |
- 1 |
- 98 |
- 54.90% |
- 43.70% |
- 1.50% |
- 2.7 |
- 0.86 |
- 3 |
- |
-
-
- | 107 |
- R2725E.2 |
- BXD60 |
- R2725E.2.CEL |
- 1.551 |
- 148.01 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 108 |
- R1074E.3 |
- BXD60 |
- R1074E.3.CEL |
- 1 |
- 118 |
- 55.50% |
- 43.10% |
- 1.40% |
- 1.96 |
- 0.81 |
- 3 |
- |
-
-
- | 109 |
- R2534E2.1 |
- BXD61 |
- R2534E2.1.CEL |
- 2.47 |
- 118 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.42 |
- 0.79 |
- 1 |
- |
-
-
- | 110 |
- R2684E.2 |
- BXD61 |
- R2684E.2.CEL |
- 2.01 |
- 131.03 |
- 57.00% |
- 41.50% |
- 1.50% |
- 1.34 |
- 0.78 |
- 2 |
- |
-
-
- | 111 |
- R1107E.3 |
- BXD62 |
- R1107E.3.CEL |
- 1 |
- 83 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.43 |
- 0.93 |
- 3 |
- |
-
-
- | 112 |
- R2681E.2 |
- BXD62 |
- R2681E.2.CEL |
- 2.086 |
- 148.24 |
- 57.20% |
- 41.30% |
- 1.50% |
- 1.29 |
- 0.81 |
- 2 |
- |
-
-
- | 113 |
- R965E.3 |
- BXD62 |
- R965E.3.CEL |
- 1 |
- 93.55 |
- 53.30% |
- 45.20% |
- 1.50% |
- 3.11 |
- 0.94 |
- 3 |
- |
-
-
- | 114 |
- R1425E.2 |
- BXD63 |
- R1425E.2.CEL |
- 1.7 |
- 136 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.43 |
- 0.82 |
- 2 |
- |
-
-
- | 115 |
- R2576E.3 |
- BXD63 |
- R2576E.3.CEL |
- 1 |
- 84 |
- 61.30% |
- 37.40% |
- 1.40% |
- 1.48 |
- 0.76 |
- 3 |
- |
-
-
- | 116 |
- R943E-2.2 |
- BXD64 |
- R943E-2.2.CEL |
- 1.591 |
- 141.34 |
- 60.10% |
- 38.40% |
- 1.50% |
- 1.32 |
- 0.76 |
- 2 |
- |
-
-
- | 117 |
- R2611E.1 |
- BXD64 |
- R2611E.1.CEL |
- 2.29 |
- 92 |
- 58.00% |
- 40.50% |
- 1.50% |
- 1.57 |
- 1.06 |
- 1 |
- |
-
-
- | 118 |
- R2689E.2 |
- BXD65 |
- R2689E.2.CEL |
- 1.721 |
- 142.44 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.38 |
- 0.76 |
- 2 |
- |
-
-
- | 119 |
- R2583E.1 |
- BXD65 |
- R2583E.1.CEL |
- 2.49 |
- 70 |
- 56.90% |
- 41.50% |
- 1.60% |
- 1.67 |
- 1.01 |
- 1 |
- |
-
-
- | 120 |
- R2728E.2 |
- BXD66 |
- R2728E.2.CEL |
- 1.714 |
- 137.45 |
- 59.40% |
- 39.00% |
- 1.60% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 121 |
- R2536E2.1 |
- BXD66 |
- R2536E2.1.CEL |
- 2.74 |
- 109 |
- 56.10% |
- 42.30% |
- 1.70% |
- 1.28 |
- 0.79 |
- 1 |
- |
-
-
- | 122 |
- R1207E.2 |
- BXD66 |
- R1207E.2.CEL |
- 1.681 |
- 136.86 |
- 60.40% |
- 38.10% |
- 1.50% |
- 1.45 |
- 0.77 |
- 2 |
- |
-
-
- | 123 |
- R1192E.2 |
- BXD67 |
- R1192E.2.CEL |
- 2.126 |
- 123.37 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 124 |
- R2727E.3 |
- BXD67 |
- R2727E.3.CEL |
- 1 |
- 82.55 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.97 |
- 0.87 |
- 2 |
- |
-
-
- | 125 |
- R2691E.3 |
- BXD67 |
- R2691E.3.CEL |
- 1 |
- 90 |
- 54.80% |
- 43.80% |
- 1.50% |
- 2.61 |
- 0.81 |
- 3 |
- |
-
-
- | 126 |
- R2551E.1 |
- BXD68 |
- R2551E.1.CEL |
- 2.49 |
- 92 |
- 54.30% |
- 44.10% |
- 1.60% |
- 2.91 |
- 1.55 |
- 1 |
- |
-
-
- | 127 |
- R2726E.2 |
- BXD68 |
- R2726E.2.CEL |
- 1.811 |
- 153.09 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.39 |
- 0.78 |
- 2 |
- |
-
-
- | 128 |
- R2593E.1 |
- BXD69 |
- R2593E.1.CEL |
- 1.67 |
- 128 |
- 59.20% |
- 39.50% |
- 1.30% |
- 1.47 |
- 0.92 |
- 1 |
- Y |
-
-
- | 129 |
- R975E.2 |
- BXD70 |
- R975E.2.CEL |
- 1.841 |
- 137.97 |
- 58.00% |
- 40.50% |
- 1.40% |
- 1.36 |
- 0.79 |
- 2 |
- |
-
-
- | 130 |
- R2537E2.1 |
- BXD70 |
- R2537E2.1.CEL |
- 2.93 |
- 99 |
- 58.00% |
- 40.50% |
- 1.60% |
- 1.29 |
- 0.75 |
- 1 |
- |
-
-
- | 131 |
- R4531E |
- BXD71 |
- R4531E.CEL |
- 4.77 |
- 43.48 |
- 62.40% |
- 36.30% |
- 1.40% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 132 |
- R4532E |
- BXD71 |
- R4532E.CEL |
- 5.89 |
- 40.68 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.24 |
- 0.79 |
- 4 |
- Y |
-
-
- | 133 |
- R2779E.2 |
- BXD73 |
- R2779E.2.CEL |
- 1.746 |
- 121.11 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 134 |
- R3024E.3 |
- BXD73 |
- R3024E.3.CEL |
- 1 |
- 78.05 |
- 51.70% |
- 46.60% |
- 1.70% |
- 2.3 |
- 0.94 |
- 3 |
- |
-
-
- | 135 |
- R2565E.1 |
- BXD75 |
- R2565E.1.CEL |
- 1.79 |
- 102 |
- 58.00% |
- 40.50% |
- 1.50% |
- 2.31 |
- 3.47 |
- 1 |
- |
-
-
- | 136 |
- R1397E-re.2 |
- BXD75 |
- R1397E-re.2.CEL |
- 1.449 |
- 189.71 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 137 |
- R2687E.3 |
- BXD77 |
- R2687E.3.CEL |
- 1 |
- 80 |
- 58.00% |
- 40.60% |
- 1.40% |
- 1.57 |
- 0.8 |
- 3 |
- Y |
-
-
- | 138 |
- R2717E.2 |
- BXD77 |
- R2717E.2.CEL |
- 1.797 |
- 84.43 |
- 61.60% |
- 36.90% |
- 1.40% |
- 1.49 |
- 0.76 |
- 2 |
- |
-
-
- | 139 |
- R1421E.3 |
- BXD77 |
- R1421E.3.CEL |
- 1 |
- 94 |
- 52.40% |
- 46.20% |
- 1.40% |
- 2.29 |
- 0.82 |
- 3 |
- |
-
-
- | 140 |
- R2579E.1 |
- BXD80 |
- R2579E.1.CEL |
- 2.42 |
- 72 |
- 59.20% |
- 39.40% |
- 1.50% |
- 1.73 |
- 0.82 |
- 1 |
- |
-
-
- | 141 |
- R2686E.2 |
- BXD80 |
- R2686E.2.CEL |
- 2.342 |
- 119.63 |
- 56.00% |
- 42.60% |
- 1.50% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 142 |
- R2956E.3 |
- BXD83 |
- R2956E.3.CEL |
- 1 |
- 84 |
- 55.40% |
- 43.20% |
- 1.40% |
- 1.39 |
- 0.84 |
- 3 |
- |
-
-
- | 143 |
- R2960E.3 |
- BXD83 |
- R2960E.3.CEL |
- 1 |
- 80 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.5 |
- 0.82 |
- 3 |
- Y |
-
-
- | 144 |
- R2922E.3 |
- BXD84 |
- R2922E.3.CEL |
- 1 |
- 91 |
- 57.80% |
- 40.80% |
- 1.50% |
- 1.47 |
- 0.83 |
- 3 |
- Y |
-
-
- | 145 |
- R2895E.3 |
- BXD84 |
- R2895E.3.CEL |
- 1 |
- 75 |
- 58.30% |
- 40.20% |
- 1.50% |
- 1.56 |
- 0.77 |
- 3 |
- Y |
-
-
- | 146 |
- R2692E.2 |
- BXD85 |
- R2692E.2.CEL |
- 1.423 |
- 160.87 |
- 60.20% |
- 38.30% |
- 1.40% |
- 1.46 |
- 0.79 |
- 2 |
- |
-
-
- | 147 |
- R2715E.2 |
- BXD85 |
- R2715E.2.CEL |
- 1.488 |
- 142.6 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.5 |
- 0.78 |
- 2 |
- |
-
-
- | 148 |
- R1405E.2 |
- BXD86 |
- R1405E.2.CEL |
- 2.351 |
- 119.34 |
- 56.40% |
- 42.20% |
- 1.40% |
- 1.64 |
- 0.81 |
- 2 |
- |
-
-
- | 149 |
- R1225E.3 |
- BXD86 |
- R1225E.3.CEL |
- 1 |
- 71 |
- 53.90% |
- 44.60% |
- 1.40% |
- 3.2 |
- 1.61 |
- 3 |
- |
-
-
- | 150 |
- R2724E.2 |
- BXD87 |
- R2724E.2.CEL |
- 1.906 |
- 113.71 |
- 60.70% |
- 37.90% |
- 1.40% |
- 1.45 |
- 0.79 |
- 2 |
- |
-
-
- | 151 |
- R2540E.1 |
- BXD87 |
- R2540E.1.CEL |
- 2.33 |
- 93 |
- 61.10% |
- 37.40% |
- 1.40% |
- 1.22 |
- 0.81 |
- 1 |
- Y |
-
-
- | 152 |
- R1433E.2 |
- BXD89 |
- R1433E.2.CEL |
- 1 |
- 2.241 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.41 |
- 0.78 |
- 2 |
- |
-
-
- | 153 |
- R2546E.1 |
- BXD89 |
- R2546E.1.CEL |
- 1.99 |
- 96 |
- 58.60% |
- 39.70% |
- 1.70% |
- 1.47 |
- 0.78 |
- 1 |
- |
-
-
- | 154 |
- R2578E2.1 |
- BXD90 |
- R2578E2.1.CEL |
- 2.79 |
- 92 |
- 58.60% |
- 39.80% |
- 1.60% |
- 1.52 |
- 0.77 |
- 1 |
- Y |
-
-
- | 155 |
- R859E.2 |
- BXD90 |
- R859E.2.CEL |
- 1.847 |
- 152.22 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.36 |
- 0.77 |
- 2 |
- |
-
-
- | 156 |
- R2682E.2 |
- BXD92 |
- R2682E.2.CEL |
- 1.547 |
- 156.31 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.37 |
- 0.77 |
- 2 |
- |
-
-
- | 157 |
- R1388E.3 |
- BXD92 |
- R1388E.3.CEL |
- 1 |
- 63 |
- 60.00% |
- 38.60% |
- 1.40% |
- 1.85 |
- 1.03 |
- 3 |
- |
-
-
- | 158 |
- R1322E.3 |
- BXD92 |
- R1322E.3.CEL |
- 1 |
- 80 |
- 55.90% |
- 42.60% |
- 1.50% |
- 1.75 |
- 0.74 |
- 3 |
- |
-
-
- | 159 |
- R2733E.2 |
- BXD96 |
- R2733E.2.CEL |
- 1.7 |
- 113.99 |
- 62.10% |
- 36.60% |
- 1.30% |
- 1.4 |
- 0.78 |
- 2 |
- |
-
-
- | 160 |
- R2554E.1 |
- BXD96 |
- R2554E.1.CEL |
- 2.18 |
- 93 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 161 |
- R2649E.2 |
- BXD97 |
- R2649E.2.CEL |
- 2.343 |
- 119.04 |
- 57.50% |
- 41.20% |
- 1.40% |
- 1.53 |
- 0.8 |
- 2 |
- |
-
-
- | 162 |
- R2577E.1 |
- BXD97 |
- R2577E.1.CEL |
- 2.07 |
- 77 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.87 |
- 1.29 |
- 1 |
- |
-
-
- | 163 |
- R2645E.3 |
- BXD98 |
- R2645E.3.CEL |
- 1 |
- 88 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.59 |
- 0.81 |
- 3 |
- Y |
-
-
- | 164 |
- R2688E.2 |
- BXD98 |
- R2688E.2.CEL |
- 1.772 |
- 145.24 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.48 |
- 0.81 |
- 2 |
- |
-
-
- | 165 |
- R4533E |
- BXD99 |
- R4533E.CEL |
- 1 |
- 37.69 |
- 60.30% |
- 38.20% |
- 1.40% |
- 1.33 |
- 0.89 |
- 4 |
- Y |
-
-
- | 166 |
- R4534E |
- BXD99 |
- R4534E.CEL |
- 5.69 |
- 36.62 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.16 |
- 0.8 |
- 4 |
- Y |
-
-
- | 167 |
- R2885E.3 |
- BXSB/MpJ |
- R2885E.3.CEL |
- 1 |
- 76 |
- 58.10% |
- 40.60% |
- 1.30% |
- 1.88 |
- 1.06 |
- 3 |
- |
-
-
- | 168 |
- R2883E.3 |
- BXSB/MpJ |
- R2883E.3.CEL |
- 1 |
- 71 |
- 56.40% |
- 42.00% |
- 1.50% |
- 1.59 |
- 0.84 |
- 3 |
- Y |
-
-
- | 169 |
- R1700E.1 |
- C3H/HeJ |
- R1700E.1.CEL |
- 2.98 |
- 69 |
- 60.80% |
- 37.90% |
- 1.40% |
- 1.48 |
- 0.78 |
- 1 |
- |
-
-
- | 170 |
- R1704E.1 |
- C3H/HeJ |
- R1704E.1.CEL |
- 2.58 |
- 88 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.38 |
- 0.84 |
- 1 |
- |
-
-
- | 171 |
- R2605E.1 |
- C57BL/6J |
- R2605E.1.CEL |
- 1.82 |
- 131 |
- 60.50% |
- 38.20% |
- 1.30% |
- 1.32 |
- 0.8 |
- 1 |
- Y |
-
-
- | 172 |
- R0871E |
- C57BL/6J |
- R0871E.CEL |
- 6.24 |
- 37.38 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.41 |
- 0.8 |
- 4 |
- Y |
-
-
- | 173 |
- R0872E.1 |
- C57BL/6J |
- R0872E.1.CEL |
- 3.13 |
- 89 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 174 |
- R0872E |
- C57BL/6J |
- R0872E.CEL |
- 3.128 |
- 88.58 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- |
-
-
- | 175 |
- R4507E |
- C57BL/6J-Nyx |
- R4507E.CEL |
- 8.13 |
- 37.5 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.32 |
- 0.8 |
- 4 |
- Y |
-
-
- | 176 |
- R4508E |
- C57BL/6J-Nyx |
- R4508E.CEL |
- 6.33 |
- 37.26 |
- 60.90% |
- 37.80% |
- 1.30% |
- 1.24 |
- 0.82 |
- 4 |
- Y |
-
-
- | 177 |
- R4505E |
- C57BL/6J-Rpe65 |
- R4505E.CEL |
- 5.98 |
- 37.48 |
- 61.80% |
- 36.80% |
- 1.40% |
- 1.45 |
- 0.85 |
- 4 |
- Y |
-
-
- | 178 |
- R4506E |
- C57BL/6J-Rpe65 |
- R4506E.CEL |
- 6.94 |
- 37.9 |
- 61.10% |
- 37.50% |
- 1.30% |
- 1.5 |
- 0.83 |
- 4 |
- Y |
-
-
- | 179 |
- R4535E |
- C57BLKS/J |
- R4535E.CEL |
- 6.59 |
- 37.28 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.26 |
- 0.83 |
- 4 |
- Y |
-
-
- | 180 |
- R4536E |
- C57BLKS/J |
- R4536E.CEL |
- 1 |
- 40.71 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.25 |
- 0.77 |
- 4 |
- Y |
-
-
- | 181 |
- R2564E.1 |
- CAST/EiJ |
- R2564E.1.CEL |
- 1.94 |
- 89 |
- 58.50% |
- 39.90% |
- 1.60% |
- 1.6 |
- 0.77 |
- 1 |
- |
-
-
- | 182 |
- R2580E.1 |
- CAST/EiJ |
- R2580E.1.CEL |
- 2.09 |
- 95 |
- 58.20% |
- 40.10% |
- 1.70% |
- 1.4 |
- 0.76 |
- 1 |
- |
-
-
- | 183 |
- R4537E |
- CBA/CaJ |
- R4537E.CEL |
- 1 |
- 38.45 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.63 |
- 0.82 |
- 4 |
- Y |
-
-
- | 184 |
- R4538E |
- CBA/CaJ |
- R4538E.CEL |
- 5.89 |
- 39.18 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.45 |
- 0.8 |
- 4 |
- Y |
-
-
- | 185 |
- R4539E |
- CZECHII/EiJ |
- R4539E.CEL |
- 7.73 |
- 37.1 |
- 58.30% |
- 40.10% |
- 1.50% |
- 1.7 |
- 0.95 |
- 4 |
- Y |
-
-
- | 186 |
- R4540E |
- CZECHII/EiJ |
- R4540E.CEL |
- 11.04 |
- 36.69 |
- 53.00% |
- 45.30% |
- 1.70% |
- 1.83 |
- 1.32 |
- 4 |
- |
-
-
- | 187 |
- R2600E.1 |
- D2B6F1 |
- R2600E.1.CEL |
- 2.47 |
- 95 |
- 58.10% |
- 40.20% |
- 1.70% |
- 1.41 |
- 0.78 |
- 1 |
- Y |
-
-
- | 188 |
- R2604E.1 |
- D2B6F1 |
- R2604E.1.CEL |
- 2.66 |
- 90 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.28 |
- 0.79 |
- 1 |
- Y |
-
-
- | 189 |
- R1002E.3 |
- DBA/2J |
- R1002E.3.CEL |
- 1 |
- 102 |
- 54.80% |
- 43.70% |
- 1.50% |
- 2.84 |
- 0.83 |
- 3 |
- |
-
-
- | 190 |
- R4541E |
- DBA/2J |
- R4541E.CEL |
- 1 |
- 43.4 |
- 61.40% |
- 37.00% |
- 1.50% |
- 1.37 |
- 0.73 |
- 4 |
- Y |
-
-
- | 191 |
- R959E.3 |
- DBA/2J |
- R959E.3.CEL |
- 1 |
- 89.97 |
- 53.20% |
- 45.30% |
- 1.50% |
- 3.66 |
- 1.09 |
- 4 |
- |
-
-
- | 192 |
- R2572E.1 |
- DBA/2J |
- R2572E.1.CEL |
- 2.41 |
- 79 |
- 55.50% |
- 42.90% |
- 1.60% |
- 1.37 |
- 0.79 |
- 1 |
- |
-
-
- | 193 |
- R4542E |
- DBA/2J |
- R4542E.CEL |
- 5.7 |
- 39.95 |
- 61.00% |
- 37.40% |
- 1.50% |
- 1.23 |
- 0.81 |
- 4 |
- Y |
-
-
- | 194 |
- R2771E.3 |
- FVB/NJ |
- R2771E.3.CEL |
- 1 |
- 70 |
- 55.30% |
- 43.20% |
- 1.50% |
- 1.69 |
- 0.83 |
- 3 |
- |
-
-
- | 195 |
- R2772E.3 |
- FVB/NJ |
- R2772E.3.CEL |
- 1 |
- 76 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.13 |
- 1.02 |
- 3 |
- |
-
-
- | 196 |
- R2636E.1 |
- KK/HlJ |
- R2636E.1.CEL |
- 2.61 |
- 93 |
- 58.90% |
- 39.50% |
- 1.50% |
- 1.39 |
- 0.76 |
- 1 |
- Y |
-
-
- | 197 |
- R2637E.1 |
- KK/HlJ |
- R2637E.1.CEL |
- 2.19 |
- 103 |
- 59.40% |
- 39.00% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 198 |
- R0999E.1 |
- LG/J |
- R0999E.1.CEL |
- 2.45 |
- 82 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 199 |
- R1004E.1 |
- LG/J |
- R1004E.1.CEL |
- 2.44 |
- 92 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 200 |
- R4543E |
- LP/J |
- R4543E.CEL |
- 6.57 |
- 41.99 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.28 |
- 0.75 |
- 4 |
- Y |
-
-
- | 201 |
- R4544E |
- LP/J |
- R4544E.CEL |
- 4.56 |
- 39.9 |
- 62.40% |
- 36.10% |
- 1.50% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 202 |
- R2858E.3 |
- MOLF/EiJ |
- R2858E.3.CEL |
- 1 |
- 64 |
- 53.80% |
- 44.70% |
- 1.50% |
- 1.59 |
- 0.95 |
- 3 |
- |
-
-
- | 203 |
- R2919.3 |
- MOLF/EiJ |
- R2919.3.CEL |
- 1 |
- 64 |
- 52.40% |
- 46.00% |
- 1.60% |
- 2.15 |
- 1.07 |
- 3 |
- |
-
-
- | 204 |
- R1688E.1 |
- NOD/LtJ |
- R1688E.1.CEL |
- 2.66 |
- 98 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 205 |
- R2566E-2.1 |
- NOD/LtJ |
- R2566E-2.1.CEL |
- 3.03 |
- 69 |
- 59.80% |
- 38.80% |
- 1.50% |
- 1.38 |
- 0.75 |
- 1 |
- Y |
-
-
- | 206 |
- R4545E |
- NZB/BlNJ |
- R4545E.CEL |
- 4.23 |
- 43.48 |
- 62.10% |
- 36.40% |
- 1.50% |
- 1.33 |
- 0.76 |
- 4 |
- Y |
-
-
- | 207 |
- R4546E |
- NZB/BlNJ |
- R4546E.CEL |
- 6.27 |
- 44.22 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.17 |
- 0.82 |
- 4 |
- Y |
-
-
- | 208 |
- R2535E.1 |
- NZO/HlLtJ |
- R2535E.1.CEL |
- 1.89 |
- 86 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.41 |
- 0.85 |
- 1 |
- |
-
-
- | 209 |
- R2550E.1 |
- NZO/HlLtJ |
- R2550E.1.CEL |
- 1.79 |
- 87 |
- 60.70% |
- 37.80% |
- 1.50% |
- 1.52 |
- 0.82 |
- 1 |
- |
-
-
- | 210 |
- R2817E.3 |
- NZW/LacJ |
- R2817E.3.CEL |
- 1 |
- 59 |
- 50.90% |
- 47.60% |
- 1.50% |
- 3.59 |
- 1.48 |
- 3 |
- |
-
-
- | 211 |
- R2810E |
- NZW/LacJ |
- R2810E.CEL |
- |
- |
- |
- |
- |
- |
- |
- 3 |
- |
-
-
- | 212 |
- R2810E.3 |
- NZW/LacJ |
- R2810E.3.CEL |
- 1 |
- 74 |
- 57.00% |
- 41.70% |
- 1.40% |
- 2.15 |
- 1.03 |
- 4 |
- Y |
-
-
- | 213 |
- R4547E |
- PANCEVO/EiJ |
- R4547E.CEL |
- 5.27 |
- 51.34 |
- 57.20% |
- 41.10% |
- 1.70% |
- 1.7 |
- 0.83 |
- 4 |
- |
-
-
- | 214 |
- R4548E |
- PANCEVO/EiJ |
- R4548E.CEL |
- 10.54 |
- 37.39 |
- 50.30% |
- 48.00% |
- 1.70% |
- 1.68 |
- 1.09 |
- 4 |
- |
-
-
- | 215 |
- R2635E.1 |
- PWD/PhJ |
- R2635E.1.CEL |
- 3.72 |
- 80 |
- 54.20% |
- 44.10% |
- 1.70% |
- 1.53 |
- 0.85 |
- 1 |
- |
-
-
- | 216 |
- R2634E.1 |
- PWD/PhJ |
- R2634E.1.CEL |
- 3.29 |
- 90 |
- 55.90% |
- 42.50% |
- 1.60% |
- 1.57 |
- 0.81 |
- 1 |
- |
-
-
- | 217 |
- R2544E.1 |
- PWK/PhJ |
- R2544E.1.CEL |
- 2.2 |
- 108 |
- 54.90% |
- 43.50% |
- 1.70% |
- 1.36 |
- 0.82 |
- 1 |
- |
-
-
- | 218 |
- R2549E.1 |
- PWK/PhJ |
- R2549E.1.CEL |
- 2.28 |
- 84 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.57 |
- 0.83 |
- 1 |
- |
-
-
- | 219 |
- R4550E |
- SJL/J |
- R4550E.CEL |
- 5.35 |
- 40.44 |
- 62.30% |
- 36.20% |
- 1.40% |
- 1.24 |
- 0.79 |
- 4 |
- |
-
-
- | 220 |
- R2368E.1 |
- WSB/EiJ |
- R2368E.1.CEL |
- 2.57 |
- 86 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.29 |
- 0.74 |
- 1 |
- Y |
-
-
- | 221 |
- R2547E.1 |
- WSB/EiJ |
- R2547E.1.CEL |
- 2.14 |
- 90 |
- 58.20% |
- 40.10% |
- 1.60% |
- 1.32 |
- 0.77 |
- 1 |
- Y |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_R_WT/summary.rtf b/general/datasets/Eye_M2_0908_R_WT/summary.rtf
deleted file mode 100644
index 44b7e23..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/summary.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-FINAL RECOMMENDED EYE DATA SET. The HEIMED September 2008 RMA data release provides estimates of gene expression in whole eyes of 103 lines of young adult mice generated using 221 Affymetrix M430 2.0 arrays. This data set is intended for exploration of the genetics and genomics of the mouse eye, retina, lens, retinal pigment epithelium, cornea, iris and choroid. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
diff --git a/general/datasets/Eye_M2_0908_R_WT/tissue.rtf b/general/datasets/Eye_M2_0908_R_WT/tissue.rtf
deleted file mode 100644
index 9b6ee0f..0000000
--- a/general/datasets/Eye_M2_0908_R_WT/tissue.rtf
+++ /dev/null
@@ -1,2058 +0,0 @@
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.
-
-Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well balanced sample of males and females, in general without within-strain-by-sex replication. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.
-
-Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.
-
-Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.
-
-
- - Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
- - Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
- - Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
- - Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
-
-
-Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Group |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- R2595E.1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- UTHSC RW |
-
-
- | 2 |
- R2533E.1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- UTHSC RW |
-
-
- | 3 |
- R0754E.1 |
- GDP |
- A/J |
- 60 |
- M |
- JAX |
-
-
- | 4 |
- R4521E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 5 |
- R4522E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 6 |
- R4523E |
- KO |
- B6129P2F2N1-Clcn3 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 7 |
- R4526E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- F |
- TChoi_Deltagen |
-
-
- | 8 |
- R4509E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- M |
- TChoi_Deltagen |
-
-
- | 9 |
- R4510E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 10 |
- R4511E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 20 |
- M |
- TChoi_Deltagen |
-
-
- | 11 |
- R4524E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 12 |
- R4525E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 13 |
- R4515E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 14 |
- R4516E |
- KO |
- B6129P2F2N1-Gabra1 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 15 |
- R4517E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 16 |
- R4512E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- F |
- TChoi_Deltagen |
-
-
- | 17 |
- R4513E |
- KO |
- B6129P2F2N1-Gnb5 |
- 25 |
- M |
- TChoi_Deltagen |
-
-
- | 18 |
- R4514E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 19 |
- R4518E |
- KO |
- B6129P2F2N1-Gpr19 |
- 70 |
- M |
- TChoi_Deltagen |
-
-
- | 20 |
- R4519E |
- KO |
- B6129P2F2N1-Gpr19 |
- 68 |
- M |
- TChoi_Deltagen |
-
-
- | 21 |
- R2601E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 22 |
- R2602E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 23 |
- R1676E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- JAX |
-
-
- | 24 |
- R1672E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- JAX |
-
-
- | 25 |
- R4530E |
- GDP |
- BALB/cJ |
- 66 |
- F |
- JAX |
-
-
- | 26 |
- R4529E |
- GDP |
- BALB/cJ |
- 66 |
- M |
- JAX |
-
-
- | 27 |
- R2704E.2 |
- BXD |
- BXD1 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 28 |
- R2707E.3 |
- BXD |
- BXD1 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 29 |
- R1231E.2 |
- BXD |
- BXD2 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 30 |
- R2598E.1 |
- BXD |
- BXD2 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 31 |
- R2591E.1 |
- BXD |
- BXD5 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 32 |
- R2714E.2 |
- BXD |
- BXD5 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 33 |
- R2570E.1 |
- BXD |
- BXD6 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 34 |
- R2694E.2 |
- BXD |
- BXD6 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 35 |
- R2538E.1 |
- BXD |
- BXD8 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 36 |
- R2709E.2 |
- BXD |
- BXD8 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 37 |
- R2708E.2 |
- BXD |
- BXD9 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 38 |
- R2569E.1 |
- BXD |
- BXD9 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 39 |
- R2581E.1 |
- BXD |
- BXD11 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 40 |
- R2612E.2 |
- BXD |
- BXD11 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 41 |
- R2742E.2 |
- BXD |
- BXD12 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 42 |
- R2543E.1 |
- BXD |
- BXD12 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 43 |
- R2586E.1 |
- BXD |
- BXD13 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 44 |
- R877E.2 |
- BXD |
- BXD13 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 45 |
- R2557E.1 |
- BXD |
- BXD14 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 46 |
- R1128E.2 |
- BXD |
- BXD14 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 47 |
- R2701E.3 |
- BXD |
- BXD15 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 48 |
- R2716E.2 |
- BXD |
- BXD15 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 49 |
- R2711E.2 |
- BXD |
- BXD16 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 50 |
- R2567E.1 |
- BXD |
- BXD16 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 51 |
- R2720E.2 |
- BXD |
- BXD18 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 52 |
- R2559E.1 |
- BXD |
- BXD18 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 53 |
- R2560E.1 |
- BXD |
- BXD19 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 54 |
- R2713E.2 |
- BXD |
- BXD19 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 55 |
- R2584E.1 |
- BXD |
- BXD20 |
- 59 |
- F |
- BIDMC GR |
-
-
- | 56 |
- R2731E.2 |
- BXD |
- BXD20 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 57 |
- R2702E.2 |
- BXD |
- BXD21 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 58 |
- R2541E2.1 |
- BXD |
- BXD21 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 59 |
- R2553E.1 |
- BXD |
- BXD22 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 60 |
- R2700E.2 |
- BXD |
- BXD22 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 61 |
- R2558E-2.1 |
- BXD |
- BXD23 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 62 |
- R1086E.2 |
- BXD |
- BXD23 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 63 |
- R2719E.2 |
- BXD |
- BXD24 |
- 123 |
- F |
- UTHSC RW |
-
-
- | 64 |
- R2589E2.1 |
- BXD |
- BXD24 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 65 |
- R2573E-2.1 |
- BXD |
- BXD25 |
- 67 |
- F |
- UAB |
-
-
- | 66 |
- R2683E.2 |
- BXD |
- BXD25 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 67 |
- R2703E.2 |
- BXD |
- BXD27 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 68 |
- R2729E.3 |
- BXD |
- BXD27 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 69 |
- R2562E.3 |
- BXD |
- BXD28 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 70 |
- R2721E.2 |
- BXD |
- BXD28 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 71 |
- R2561E.3 |
- BXD |
- BXD29 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 72 |
- R1258E.2 |
- BXD |
- BXD31 |
- 57 |
- F |
- UTHSC RW |
-
-
- | 73 |
- R2597E.1 |
- BXD |
- BXD31 |
- 61 |
- M |
- BIDMC GR |
-
-
- | 74 |
- R2563E.1 |
- BXD |
- BXD32 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 75 |
- R1216E.2 |
- BXD |
- BXD32 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 76 |
- R2542E.1 |
- BXD |
- BXD33 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- R857E.2 |
- BXD |
- BXD33 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 78 |
- R1451E.2 |
- BXD |
- BXD34 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 79 |
- R2585E.1 |
- BXD |
- BXD34 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 80 |
- R2698E.3 |
- BXD |
- BXD36 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 81 |
- R2705E.3 |
- BXD |
- BXD36 |
- 57 |
- M |
- BIDMC GR |
-
-
- | 82 |
- R2710E.2 |
- BXD |
- BXD38 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 83 |
- R2532E.1 |
- BXD |
- BXD38 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 84 |
- R2574E.1 |
- BXD |
- BXD39 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 85 |
- R2695E.2 |
- BXD |
- BXD39 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 86 |
- R2699E.2 |
- BXD |
- BXD40 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 87 |
- R2590E.1 |
- BXD |
- BXD40 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 88 |
- R2696E.2 |
- BXD |
- BXD42 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 89 |
- R2596E.1 |
- BXD |
- BXD42 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 90 |
- R994E.2 |
- BXD |
- BXD43 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 91 |
- R2607E.1 |
- BXD |
- BXD43 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 92 |
- R2594E.1 |
- BXD |
- BXD44 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 93 |
- R2610E.2 |
- BXD |
- BXD44 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 94 |
- R2732E.2 |
- BXD |
- BXD45 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 95 |
- R2592E.1 |
- BXD |
- BXD45 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- R967E.2 |
- BXD |
- BXD48 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 97 |
- R2606E.1 |
- BXD |
- BXD48 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 98 |
- R2933E.3 |
- BXD |
- BXD50 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 99 |
- R2937E.3 |
- BXD |
- BXD50 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 100 |
- R2603E.1 |
- BXD |
- BXD51 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 101 |
- R1042E.2 |
- BXD |
- BXD51 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 102 |
- R2980E.3 |
- BXD |
- BXD55 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 103 |
- R2690E.2 |
- BXD |
- BXD55 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 104 |
- R4176E |
- BXD |
- BXD56 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 105 |
- R4175E |
- BXD |
- BXD56 |
- 53 |
- M |
- UTHSC RW |
-
-
- | 106 |
- R1006E.3 |
- BXD |
- BXD60 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 107 |
- R2725E.2 |
- BXD |
- BXD60 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 108 |
- R1074E.3 |
- BXD |
- BXD60 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 109 |
- R2534E2.1 |
- BXD |
- BXD61 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 110 |
- R2684E.2 |
- BXD |
- BXD61 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 111 |
- R1107E.3 |
- BXD |
- BXD62 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 112 |
- R2681E.2 |
- BXD |
- BXD62 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 113 |
- R965E.3 |
- BXD |
- BXD62 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 114 |
- R1425E.2 |
- BXD |
- BXD63 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 115 |
- R2576E.3 |
- BXD |
- BXD63 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 116 |
- R943E-2.2 |
- BXD |
- BXD64 |
- 56 |
- F |
- UTHSC RW |
-
-
- | 117 |
- R2611E.1 |
- BXD |
- BXD64 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 118 |
- R2689E.2 |
- BXD |
- BXD65 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 119 |
- R2583E.1 |
- BXD |
- BXD65 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 120 |
- R2728E.2 |
- BXD |
- BXD66 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 121 |
- R2536E2.1 |
- BXD |
- BXD66 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 122 |
- R1207E.2 |
- BXD |
- BXD66 |
- 83 |
- M |
- UTHSC RW |
-
-
- | 123 |
- R1192E.2 |
- BXD |
- BXD67 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 124 |
- R2727E.3 |
- BXD |
- BXD67 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 125 |
- R2691E.3 |
- BXD |
- BXD67 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 126 |
- R2551E.1 |
- BXD |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 127 |
- R2726E.2 |
- BXD |
- BXD68 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 128 |
- R2593E.1 |
- BXD |
- BXD69 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 129 |
- R975E.2 |
- BXD |
- BXD70 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 130 |
- R2537E2.1 |
- BXD |
- BXD70 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 131 |
- R4531E |
- BXD |
- BXD71 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 132 |
- R4532E |
- BXD |
- BXD71 |
- 86 |
- M |
- UTHSC RW |
-
-
- | 133 |
- R2779E.2 |
- BXD |
- BXD73 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 134 |
- R3024E.3 |
- BXD |
- BXD73 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 135 |
- R2565E.1 |
- BXD |
- BXD75 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 136 |
- R1397E-re.2 |
- BXD |
- BXD75 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 137 |
- R2687E.3 |
- BXD |
- BXD77 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 138 |
- R2717E.2 |
- BXD |
- BXD77 |
- 107 |
- M |
- UTHSC RW |
-
-
- | 139 |
- R1421E.3 |
- BXD |
- BXD77 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 140 |
- R2579E.1 |
- BXD |
- BXD80 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 141 |
- R2686E.2 |
- BXD |
- BXD80 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 142 |
- R2956E.3 |
- BXD |
- BXD83 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 143 |
- R2960E.3 |
- BXD |
- BXD83 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 144 |
- R2922E.3 |
- BXD |
- BXD84 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 145 |
- R2895E.3 |
- BXD |
- BXD84 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- R2692E.2 |
- BXD |
- BXD85 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 147 |
- R2715E.2 |
- BXD |
- BXD85 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 148 |
- R1405E.2 |
- BXD |
- BXD86 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 149 |
- R1225E.3 |
- BXD |
- BXD86 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 150 |
- R2724E.2 |
- BXD |
- BXD87 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 151 |
- R2540E.1 |
- BXD |
- BXD87 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 152 |
- R1433E.2 |
- BXD |
- BXD89 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 153 |
- R2546E.1 |
- BXD |
- BXD89 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 154 |
- R2578E2.1 |
- BXD |
- BXD90 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 155 |
- R859E.2 |
- BXD |
- BXD90 |
- 72 |
- M |
- UTHSC RW |
-
-
- | 156 |
- R2682E.2 |
- BXD |
- BXD92 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 157 |
- R1388E.3 |
- BXD |
- BXD92 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 158 |
- R1322E.3 |
- BXD |
- BXD92 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 159 |
- R2733E.2 |
- BXD |
- BXD96 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 160 |
- R2554E.1 |
- BXD |
- BXD96 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 161 |
- R2649E.2 |
- BXD |
- BXD97 |
- 74 |
- F |
- UTHSC RW |
-
-
- | 162 |
- R2577E.1 |
- BXD |
- BXD97 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 163 |
- R2645E.3 |
- BXD |
- BXD98 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 164 |
- R2688E.2 |
- BXD |
- BXD98 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 165 |
- R4533E |
- BXD |
- BXD99 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 166 |
- R4534E |
- BXD |
- BXD99 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 167 |
- R2885E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 168 |
- R2883E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- M |
- BIDMC GR |
-
-
- | 169 |
- R1700E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- UTHSC RW |
-
-
- | 170 |
- R1704E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- UTHSC RW |
-
-
- | 171 |
- R2605E.1 |
- GDP BXD |
- C57BL/6J |
- 79 |
- F |
- UTHSC RW |
-
-
- | 172 |
- R0871E |
- GDP BXD |
- C57BL/6J |
- 65 |
- F |
- UTHSC RW |
-
-
- | 173 |
- R0872E.1 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 174 |
- R0872E |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 175 |
- R4507E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 176 |
- R4508E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 177 |
- R4505E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 178 |
- R4506E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 179 |
- R4535E |
- GDP |
- C57BLKS/J |
- 66 |
- F |
- JAX |
-
-
- | 180 |
- R4536E |
- GDP |
- C57BLKS/J |
- 66 |
- M |
- JAX |
-
-
- | 181 |
- R2564E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- F |
- JAX |
-
-
- | 182 |
- R2580E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- M |
- JAX |
-
-
- | 183 |
- R4537E |
- GDP |
- CBA/CaJ |
- 66 |
- F |
- JAX |
-
-
- | 184 |
- R4538E |
- GDP |
- CBA/CaJ |
- 66 |
- M |
- JAX |
-
-
- | 185 |
- R4539E |
- GDP |
- CZECHII/EiJ |
- 66 |
- F |
- JAX |
-
-
- | 186 |
- R4540E |
- GDP |
- CZECHII/EiJ |
- 66 |
- M |
- JAX |
-
-
- | 187 |
- R2600E.1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- UTHSC RW |
-
-
- | 188 |
- R2604E.1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- UTHSC RW |
-
-
- | 189 |
- R1002E.3 |
- GDP BXD |
- DBA/2J |
- 72 |
- F |
- UTHSC RW |
-
-
- | 190 |
- R4541E |
- GDP BXD |
- DBA/2J |
- 65 |
- F |
- JAX |
-
-
- | 191 |
- R959E.3 |
- GDP BXD |
- DBA/2J |
- 60 |
- M |
- UTHSC RW |
-
-
- | 192 |
- R2572E.1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 193 |
- R4542E |
- GDP BXD |
- DBA/2J |
- 59 |
- M |
- JAX |
-
-
- | 194 |
- R2771E.3 |
- GDP |
- FVB/NJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 195 |
- R2772E.3 |
- GDP |
- FVB/NJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 196 |
- R2636E.1 |
- GDP |
- KK/HlJ |
- 64 |
- F |
- UTHSC RW |
-
-
- | 197 |
- R2637E.1 |
- GDP |
- KK/HlJ |
- 64 |
- M |
- UTHSC RW |
-
-
- | 198 |
- R0999E.1 |
- GDP |
- LG/J |
- 57 |
- F |
- UTHSC RW |
-
-
- | 199 |
- R1004E.1 |
- GDP |
- LG/J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 200 |
- R4543E |
- GDP |
- LP/J |
- 65 |
- F |
- JAX |
-
-
- | 201 |
- R4544E |
- GDP |
- LP/J |
- 65 |
- M |
- JAX |
-
-
- | 202 |
- R2858E.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 203 |
- R2919.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 204 |
- R1688E.1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- JAX |
-
-
- | 205 |
- R2566E-2.1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- UTHSC RW |
-
-
- | 206 |
- R4545E |
- GDP |
- NZB/BlNJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 207 |
- R4546E |
- GDP |
- NZB/BlNJ |
- 58 |
- M |
- BIDMC GR |
-
-
- | 208 |
- R2535E.1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- JAX |
-
-
- | 209 |
- R2550E.1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- JAX |
-
-
- | 210 |
- R2817E.3 |
- GDP |
- NZW/LacJ |
- 65 |
- F |
- BIDMC GR |
-
-
- | 211 |
- R2810E |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 212 |
- R2810E.3 |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 213 |
- R4547E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- F |
- JAX |
-
-
- | 214 |
- R4548E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- M |
- JAX |
-
-
- | 215 |
- R2635E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- JAX |
-
-
- | 216 |
- R2634E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- JAX |
-
-
- | 217 |
- R2544E.1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- JAX |
-
-
- | 218 |
- R2549E.1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- JAX |
-
-
- | 219 |
- R4550E |
- GDP |
- SJL/J |
- 65 |
- M+F |
- JAX |
-
-
- | 220 |
- R2368E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- UTHSC RW |
-
-
- | 221 |
- R2547E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- UTHSC RW |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_WTWT/acknowledgment.rtf b/general/datasets/Eye_M2_0908_WTWT/acknowledgment.rtf
deleted file mode 100644
index 5098d32..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Support for acquisition of microarray data sets was generously provided by Dr. Barrrett Haik, Chair of the Department of Ophthalmology, and director of the Hamilton Eye Institute. Support for the continued development of GeneNetwork was provided by a NIDA/NIMH/NIAAA Human Brain Project grant and from funds from NEI grant to Dr. Eldon Geisert (R01EY017841), an NEI Vision Core grant (EY14080) and an Unrestricted Grant from Research To Prevent Blindness.
-
-We thank Dr. Ted Choi, Chief Scientific Director of Predictive Biology, Inc. (past director of molecular genetics at Deltagen Inc.) for providing us with eye samples from several interesting DeltaGen knockouts.
diff --git a/general/datasets/Eye_M2_0908_WTWT/cases.rtf b/general/datasets/Eye_M2_0908_WTWT/cases.rtf
deleted file mode 100644
index 552d4a5..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/cases.rtf
+++ /dev/null
@@ -1,57 +0,0 @@
-This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:
-
-
- - 68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.
- - 35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common Mus musculus domesticus inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (Mus musculus domesticus, e.g, WSB/EiJ; M. musculus musculus, e.g., CZECHII/EiJ; M. musculus molossinus, e.g., MOLF/EiJ; M. musculus castaneus, e.g., CAST/EiJ); and even one different species of mouse (Mus spicilegus, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the Nyx-nob mutant:
- - 6 knockouts (KO), including a KO of Rpe65, and 5 DeltaGen Inc. knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: Gabra1, Gabbr1, Gnb1, Gpr19, and Clcn3. We also included one spontaneous mutant of the nyctalopin (Nyx no b wave "nob") gene (Pardue et al., 1998) that is on a BALB/cByJ background.
-
-
-Rod photoreceptor degeneration in inbred mice: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the retinal degeneration 1 (rd1) mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (Pde6b). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.
-
-As expected (Dickerson LW et al., 2002) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, Clcn3) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of Gnat2, a gene associated with cones and achromatopsia in mice and humans.
-
-Lines of mice were selected using the following criteria:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - representation of a fairly wide variety of different subspecies of Mus
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - interesting mutations or knockouts affecting genes with high expression in the eye
- - general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.
-
-
-We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see Perlegen's excellent data resources and browser).
-
-
- - 129S1/SvImJ : Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a cone photoreceptor function loss 3 mutant (Cpfl3 allele) of the Gnat2 gene that is a model for achromatopsia (JAX Stock Number: 002448)
- - A/J: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (Tyr c allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: 000646)
- - BALB/cByJ: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Small brain, not aggressive (JAX Stock Number: 001026)
- - BALB/cJ: Phenome Project A list. A tyrosinase (Tyr c allele) albino mutant and also a tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. Large brain and aggressive (JAX Stock Number: 000651)
- - BXSB/MpJ: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the Yaa gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: 000740)
- - C3H/HeJ: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a Pdeb6 rd1 mutant with near total photoreceptor loss at as early as postnatal day 30. Also a Tlr4 mutant that is endotoxin resistant. (JAX Stock Number: 000659)
- - C57BL/6J: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: 000664)
- - C57BLKS/J: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: 000662)
- - CAST/EiJ: A wild-derived inbred Mus musculus castaneus strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: 000928)
- - CBA/CaJ: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: 000654)
- - CZECHII/EiJ: Czech 2 is a wild-derived inbred strain M. musculus musculus strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: 001144).
- - DBA/2J: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (Tyrp1 b) brown allele mutant. A myosin 5a (Myo5a d) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: 000671)
- - FVB/NJ: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. Tyr c locus albino and a Pdeb6 rd1 mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: 001800).
- - KK/HlJ: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: 002106)
- - LG/J: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A Tyr c locus albino strain. (JAX Stock Number: 000675)
- - LP/J: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B Ednrb gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: 000676)
- - MOLF/EiJ: A wild-derived inbred strain derived from M. musculus molossinus samples camputered in Fukuoka, Japan. This strain has the retinal degeneration rd1 allele in Pde6b. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: 000550)
- - NOD/LtJ: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (ahl) allele mutant of the Cdh23 gene. A Tyr c locus albino strain. (JAX Stock Number: 001976)
- - NZO/HlLtJ: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: 002105)
- - NZB/BlNJ: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: 000648)
- - NZW/LacJ: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the Tyr c locus albino mutation, the pink-eye dilution mutation in the Oca2 or p locus, and the brown allele at Tyrp1. (JAX Stock Number: 001058)
- - PANCEVO/EiJ: PANCEVO/EiJ is a wild-derived inbred strain from the Mus spicilegus samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier 10103). M. spicilegus is a colonial mound-building species. No known ocular or retina mutations, but the expression level of Gnat2 is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: 001384)
- - PWD/PhJ: A wild-derived Mus musculus musculus agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: 004660)
- - PWK/PhJ: A wild-derived Mus musculus musculus inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: 003715)
- - SJL/J: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration rd1 allele in Pde6b. It also carries both the Tyr c albino mutation and the pink-eye dilution mutation in the Oca2 or p locus. Highly aggressive males. (JAX Stock Number: 000686)
- - WSB/EiJ: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived Mus musculus domesticus inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: 001145)
- - B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J 100006)
-
-
-Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, 2008 and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (Tyr, or human OCA1), the brown allele of the tyrosinase related protein 1 (Tyrp1), the pink-eye dilution allele of Oca2 (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein Asip, the steel allele of Kitlg, the dilute allele of Myo5a (probe set 1419754), and the piebald allele of Ednrb. In some of these cases, effects of the mutation are easily detected at the transcript level (Tyrp1, Oca2, and Myo5a), but in the other cases (Tyr, Asip, Ednrb, and Kitlg), mutations do not leave a strong imprint on expression.
diff --git a/general/datasets/Eye_M2_0908_WTWT/experiment-design.rtf b/general/datasets/Eye_M2_0908_WTWT/experiment-design.rtf
deleted file mode 100644
index 1ebe0ad..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression profiling by array
diff --git a/general/datasets/Eye_M2_0908_WTWT/notes.rtf b/general/datasets/Eye_M2_0908_WTWT/notes.rtf
deleted file mode 100644
index 7a26eb5..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Eye_M2_0908_WTWT/platform.rtf b/general/datasets/Eye_M2_0908_WTWT/platform.rtf
deleted file mode 100644
index 9024a99..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/platform.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 arrays: The 430 2.0 array consists of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many probes overlap and target the same transcript). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequences as the old M430A and 430B array pair. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the new 430 2.0.
-
-As part of the development of HEIMED, we have manually annotated individual probe sets by sequence alignment to the mouse genome and transcriptome. Approximately 13,000 probe sets that have comparatively high expression in eye and CNS were curated by one of the authors (RWW) and now have specific information on the part of the transcript targeted by each probe set. The other 33,000 transcripts have corresponding data that was generated by Xusheng Wang using computational methods (BLAT analysis combined with annotated genome sequence).
-
-One example may help explain how to exploit this annotation. The four probe sets for rhodopsin include information on the target location. Only the first probe set targets the last two coding exons. The other three probe sets target different parts of the 3’ UTR (mid, distal, and far distal regions). The probe sets can be reordered by from high to low expression using the Sort By function in Search Results pages. In the case of rhodopsin, the probe set that targets that last two coding exons and proximal parts of the 3’ UTR also has the highest expression . Finally, the HEIMED gene descriptions have been customized to help vision researchers. In the case of rhodopsin, the description appended after the gene name reads “rod photoreceptor pigment, retinitis pigmentosa-associated”. For less well known genes this kind of annotation can be extremely useful. For example, the more verbose annotation for Cerkl reads “neuronal survival and apoptosis-related, retinal ganglion cell expressed, retinitis pigmentosa 26); alternative 3' UTR of short form message, intron 2”.
-
-
-
-
-
-Legend: Distribution of expression values for all probe sets in HEIMED.
diff --git a/general/datasets/Eye_M2_0908_WTWT/processing.rtf b/general/datasets/Eye_M2_0908_WTWT/processing.rtf
deleted file mode 100644
index 4349e60..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/processing.rtf
+++ /dev/null
@@ -1,3381 +0,0 @@
-Range of Gene Expression in the Eye. Expression of transcripts in the HEIMED and most other GN data sets is measured on a log2 scale. Each unit corresponding approximately to a 2-fold difference in hybridization signal intensity. To simplify comparisons among different data sets and cases, log2 RMA values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units (variance stabilized). Values of all 45,101 probe sets in this data set range from a low of 4.8 (Tcf15, probe set 1420281_at) to a high of 15.5 (crystallin gamma C, Crygc, probe set 1422674_s_at). This corresponds to 10.7 units or a 1 to 1700 dynamic range of expression (2^10.73).
-
-We used pooled RNA samples of whole eyes, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-We calibrated this log intensity scale using Affymetrix spike-in control probe sets. These 18 control probe sets target exogenous bacterial mRNAs that are added to each sample (a graded dose spike cocktail) during preparation at concentrations of 1.5, 5, 25, and 100 pM. (To find these probe sets, search GN’s ALL search field using the string “AFFX pM”.) A value of 6 or less is equivalent to an mRNA concentration of under 0.4 pM, a value of 8 is equivalent to ~1.5 pM, 9.5 is equivalent to ~5 pM, 11.5 is equivalent to ~25 pM, 13.5 is equivalent to ~100 pM, and a value of 15.5 is equivalent to an mRNA concentration of 400 pM or greater.
-
-This range can be converted to the mRNA molecules per cell in the eye assuming that a value of 8 is equivalent to about 1 mRNA copy per cell (Kanno et al. 2006, see http://www.biomedcentral.com/1471-2164/7/64). Since the expression of rhodopsin mRNA is normally 15 units, we predict that there are 27 or ~128 Rho mRNAs per cell in the whole eye and ~256 in rods themselves (assuming that rods make up about half of all cells in the eye). For this purpose it may be useful to know that a normal mouse eye contains between 6 and 8 million rod photoreceptors (Guo, Lu, and Williams; GN BXD Phenotype ID 11024).
-
-Note that some probe sets with very low expression still provide reliable data. For example, probe set 1440397_at (Cacna2d1) has expression of only 5.5 units (a value that would be declared as "absent" using conventional Affymetrix procedures), but the values for this calcium channel transcript are associated with a very strong cis QTL with an LRS of 79 (LOD = 17). This strong linkage is definitely not due to chance since the probability of the expression data mapping precisely to the location of the parent gene itself is about 10e-16. This indicates a high signal to noise ratio and the detection of significant strain variation of the correct transcript.
-
-The standard error of the mean for the HEIMED data set is computed for 2 to 6 biological replicates. The standard error of such small samples tends to systematically underestimate the population standard error. With n = 2 the underestimate is about 25%, whereas for n = 6 the underestimate is 5%. Gurland and Tripathi (1971) provide a correction and equation for this effect (see Sokal and Rohlf, Biometry, 2nd ed., 1981, p 53 for an equation of the correction factor for small samples of n < 20.) Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. The CEL files were processed using the RMA protocol. We processed the first three batches together. The last batch was processed separately and merged as described below.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of arrays using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: Finally, when appropriate, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
-
-After RMA processing using Biobase affy10 build running under R version 2.7.1, all array data sets were rank-order normalized. This second round of quantile normalization removes much residual non-linearity across arrays and forces every array to have the same distribution of values as the mean of all arrays. Comparative array data quality was then evaluated in DataDesk. Outlier arrays were flagged by visual inspection in DataDesk, usually by means of an analysis of scatter plots and more quantitatively by generating a correlation matrix of all arrays. Those arrays with mean correlation <0.96 versus all other arrays indicates trouble or a biological outlier). In some cases, outliers were expected, such as samples from strains with retinal degeneration (FVB/NJ, NOD/LtJ, MOLF/EiJ, C3H/HeJ and BXD24), samples from wild subspecies such as WSB/EiJ, CAST/EiJ, PWD/PhJ, and PWK/PhJ, and knockouts. However, when arrays were anomolous both within strain and across strains, they were often simply discarded. The assumption is that anomolous data are much more likely due to experimental and technical errors than to informative biological variation. Approximately 10% of arrays were discarded.
-
-After this process, the acceptable set of arrays was renormalized using all step as above, starting with the original RMA procedure, etc.
-
-We reviewed the data set using a new method developed by RW Williams, Jeremy Peirce, and Hongqiang Li. For the full set of arrays that passed standard QC protocols described above, we computed the strain means for the BXD strains, B6, D2, and F1s. Using this set of strain means we then computed LRS scores for all 45101 probe sets and counted the number of transcripts that generated QTLs with LRS values greater than 50. This value (e.g., 1800) represented the QTL harvest for the full data set. We then dropped a single array from the data set, recomputed strain means, and recomputed the number of transcripts with LRS scores great than 50. This value is expected to typically reduce the number of QTLs that reach the criterion level (e.g., 1750 QTLs > 50). This process was repeated for every array to obtain an array-specific difference value--the effect of removing that array on the total QTL count. For example, the loss of a single array might cause a decrease in 50 QTLs. Values ranged from approximately -90 (good arrays) to +40 (bad arrays). This procedure is similar in some ways to a jackknife protocol, although we are not using this procedure to esimate an error term, but rather as a method to polish a data set.
-
-During this process we discovered that nearly 20 arrays in the batch 2 had been mislabeled at some point in processing. We computed the correct strain membership of each array using a large number of Mendelian probe sets (more than 50) and comparing their match to standard SNP and microsatellite markers and the original array data set of November 2005. This allowed us to rescue a large number of arrays that were of high quality.
-
-A third batch of approximately 40 arrays were processed by Yan Jiao and Weikuan Gu in August 2006. These complete data set assembled by Hongqiang Li. This process again included a correction for a batch effect.
-
-For the June 2006 data set Hongqiang Li used a new batch correction method that stabilizes the range of expression in each batch. For each of the three large batches, we extracted the minumum and maximum raw probe expression (CEL file level) value. We then adjusted raw probe values in each batch to have the same range as the first and largest batch (batch 1) using a simple linear interpolation. These procedures generated new correct CEL files which were then used with RMA to generate final probe set estimates.
-
-For the final fourth batch of arrays (Sept 2008) Arthur Centeno and Rob Williams corrected for a systematic difference in probe set expression values between original arrays run in 2005 and 2006 and the new arrays added in 2008 (n = 45 acceptable arrays). This difference is due to unknown technical batch effects that are probably associated with labeling, hybridization, and scanning. We performed a simple correction to normalize values of the new set of arrays to those of the old set (batches 1 through 3). No changes were made to any values of the previous three batches. We corrected only the probe set level (RMA) values and not the CEL files. For this final batch, we corrected for the difference (offset) in probe set expression between the first three batches arrays run in 2005 and 2006 (a total of 174 acceptable arrays) and the new batch (n = 47 acceptable arrays). This difference is due to unknown technical effects that are probably related to various steps in labeling, hybridization, and scanning. The correction was applied as follows: (1) RWW selected 51 high quality arrays with similar expression characteristics (r = 0.97 or better between pairs of arrays) in the old data set (from batches 1, 2, and 3) and 34 high quality arrays in the final batch. RWW used scatterplots of full RMA transcriptome data sets to review many pairs of arrays within these new and old array batches. Strains with retinal degeneration or unusual eye gene expression characteristics were excluded from these selected subsets. The average expression values for each probe set were then computed for both the old and new array subsets. The offset value (old minus new) was added to each probe set across all 47 new arrays. This processes forces the average probe set in the new arrays to be very close to that of the previous arrays.
-
-Table 2: Sample tube ID, strain, original CEL filename, and Affymetrix quality control values. Columns labeled Scale factor, Background Average, Present, Absent, Marginal and 3'/5' ratios for actin and Gapdh were collated from the Affymetrix Report (RPT) files.
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Strain |
- Original CEL |
- Scale factor |
- Background Average |
- Present |
- Absent |
- Marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- Batch Id |
- Used for batch control |
-
-
- | 1 |
- R2595E.1 |
- 129S1/SvImJ |
- R2595E.1.CEL |
- 1.79 |
- 115 |
- 61.00% |
- 37.50% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 2 |
- R2533E.1 |
- 129S1/SvImJ |
- R2533E.1.CEL |
- 2.11 |
- 94 |
- 57.90% |
- 40.50% |
- 1.60% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 3 |
- R0754E.1 |
- A/J |
- R0754E.1.CEL |
- 2.72 |
- 86 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.36 |
- 0.76 |
- 1 |
- Y |
-
-
- | 4 |
- R4521E |
- B6129P2F2N1-Clcn3 |
- R4521E.CEL |
- 4.83 |
- 38.7 |
- 63.30% |
- 35.30% |
- 1.40% |
- 1.25 |
- 0.77 |
- 4 |
- |
-
-
- | 5 |
- R4522E |
- B6129P2F2N1-Clcn3 |
- R4522E.CEL |
- 5.76 |
- 37.36 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.37 |
- 0.83 |
- 4 |
- |
-
-
- | 6 |
- R4523E |
- B6129P2F2N1-Clcn3 |
- R4523E.CEL |
- 4.88 |
- 40.42 |
- 63.90% |
- 34.70% |
- 1.40% |
- 1.27 |
- 0.77 |
- 4 |
- |
-
-
- | 7 |
- R4526E |
- B6129P2F2N1-Gabbr1 |
- R4526E.CEL |
- 3.84 |
- 44.18 |
- 65.00% |
- 33.70% |
- 1.30% |
- 1.34 |
- 0.78 |
- 4 |
- Y |
-
-
- | 8 |
- R4509E |
- B6129P2F2N1-Gabbr1 |
- R4509E.CEL |
- 7.45 |
- 34.76 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.45 |
- 0.83 |
- 4 |
- |
-
-
- | 9 |
- R4510E |
- B6129P2F2N1-Gabbr1 |
- R4510E.CEL |
- 8.44 |
- 37.44 |
- 57.40% |
- 41.10% |
- 1.50% |
- 1.35 |
- 0.83 |
- 4 |
- |
-
-
- | 10 |
- R4511E |
- B6129P2F2N1-Gabbr1 |
- R4511E.CEL |
- 5.91 |
- 42.02 |
- 61.40% |
- 37.20% |
- 1.40% |
- 1.41 |
- 0.83 |
- 4 |
- |
-
-
- | 11 |
- R4524E |
- B6129P2F2N1-Gabbr1 |
- R4524E.CEL |
- 5.49 |
- 42.34 |
- 62.40% |
- 36.20% |
- 1.40% |
- 1.29 |
- 0.78 |
- 4 |
- Y |
-
-
- | 12 |
- R4525E |
- B6129P2F2N1-Gabbr1 |
- R4525E.CEL |
- 4.69 |
- 41.3 |
- 63.10% |
- 35.50% |
- 1.40% |
- 1.27 |
- 0.8 |
- 4 |
- Y |
-
-
- | 13 |
- R4515E |
- B6129P2F2N1-Gabra1 |
- R4515E.CEL |
- 5.75 |
- 41.76 |
- 62.80% |
- 35.80% |
- 1.40% |
- 1.41 |
- 0.81 |
- 4 |
- Y |
-
-
- | 14 |
- R4516E |
- B6129P2F2N1-Gabra1 |
- R4516E.CEL |
- 7.07 |
- 40.73 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.32 |
- 0.87 |
- 4 |
- Y |
-
-
- | 15 |
- R4517E |
- B6129P2F2N1-Gabra1 |
- R4517E.CEL |
- 5.45 |
- 38.09 |
- 62.70% |
- 35.80% |
- 1.40% |
- 1.34 |
- 0.82 |
- 4 |
- Y |
-
-
- | 16 |
- R4512E |
- B6129P2F2N1-Gnb5 |
- R4512E.CEL |
- 6.56 |
- 38.02 |
- 59.90% |
- 38.70% |
- 1.50% |
- 1.33 |
- 0.83 |
- 4 |
- |
-
-
- | 17 |
- R4513E |
- B6129P2F2N1-Gnb5 |
- R4513E.CEL |
- 4.15 |
- 41.6 |
- 63.40% |
- 35.10% |
- 1.50% |
- 1.34 |
- 0.82 |
- 4 |
- |
-
-
- | 18 |
- R4514E |
- B6129P2F2N1-Gnb5 |
- R4514E.CEL |
- 5.86 |
- 39.2 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.34 |
- 0.81 |
- 4 |
- |
-
-
- | 19 |
- R4518E |
- B6129P2F2N1-Gpr19 |
- R4518E.CEL |
- 5.58 |
- 38.9 |
- 62.60% |
- 36.00% |
- 1.30% |
- 1.39 |
- 0.79 |
- 4 |
- Y |
-
-
- | 20 |
- R4519E |
- B6129P2F2N1-Gpr19 |
- R4519E.CEL |
- 5.95 |
- 41.91 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.35 |
- 0.84 |
- 4 |
- Y |
-
-
- | 21 |
- R2601E.1 |
- B6D2F1 |
- R2601E.1.CEL |
- 2.55 |
- 92 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.44 |
- 0.78 |
- 1 |
- Y |
-
-
- | 22 |
- R2602E.1 |
- B6D2F1 |
- R2602E.1.CEL |
- 2.6 |
- 84 |
- 59.70% |
- 38.80% |
- 1.50% |
- 1.37 |
- 0.78 |
- 1 |
- Y |
-
-
- | 23 |
- R1676E.1 |
- BALB/cByJ |
- R1676E.1.CEL |
- 2.69 |
- 98 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.46 |
- 0.74 |
- 1 |
- |
-
-
- | 24 |
- R1672E.1 |
- BALB/cByJ |
- R1672E.1.CEL |
- 2.22 |
- 111 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 25 |
- R4530E |
- BALB/cJ |
- R4530E.CEL |
- 6.37 |
- 37.53 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.3 |
- 0.84 |
- 4 |
- Y |
-
-
- | 26 |
- R4529E |
- BALB/cJ |
- R4529E.CEL |
- 5.71 |
- 41.33 |
- 60.50% |
- 38.00% |
- 1.50% |
- 1.48 |
- 0.8 |
- 4 |
- Y |
-
-
- | 27 |
- R2704E.2 |
- BXD1 |
- R2704E.2.CEL |
- 2.066 |
- 139.61 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 28 |
- R2707E.3 |
- BXD1 |
- R2707E.3.CEL |
- 1 |
- 80 |
- 56.40% |
- 42.10% |
- 1.50% |
- 1.43 |
- 0.79 |
- 3 |
- |
-
-
- | 29 |
- R1231E.2 |
- BXD2 |
- R1231E.2.CEL |
- 2.197 |
- 138.73 |
- 57.30% |
- 41.30% |
- 1.40% |
- 1.41 |
- 0.77 |
- 2 |
- |
-
-
- | 30 |
- R2598E.1 |
- BXD2 |
- R2598E.1.CEL |
- 1.99 |
- 106 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 31 |
- R2591E.1 |
- BXD5 |
- R2591E.1.CEL |
- 1.7 |
- 136 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.33 |
- 0.78 |
- 1 |
- Y |
-
-
- | 32 |
- R2714E.2 |
- BXD5 |
- R2714E.2.CEL |
- 1.404 |
- 144.35 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 33 |
- R2570E.1 |
- BXD6 |
- R2570E.1.CEL |
- 1.99 |
- 87 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.46 |
- 0.76 |
- 1 |
- Y |
-
-
- | 34 |
- R2694E.2 |
- BXD6 |
- R2694E.2.CEL |
- 1.983 |
- 97.23 |
- 61.60% |
- 37.10% |
- 1.30% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 35 |
- R2538E.1 |
- BXD8 |
- R2538E.1.CEL |
- 1.91 |
- 102 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.52 |
- 0.79 |
- 1 |
- Y |
-
-
- | 36 |
- R2709E.2 |
- BXD8 |
- R2709E.2.CEL |
- 1.99 |
- 99.79 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.42 |
- 0.76 |
- 2 |
- |
-
-
- | 37 |
- R2708E.2 |
- BXD9 |
- R2708E.2.CEL |
- 1.966 |
- 126.46 |
- 57.70% |
- 40.70% |
- 1.50% |
- 1.4 |
- 0.84 |
- 2 |
- |
-
-
- | 38 |
- R2569E.1 |
- BXD9 |
- R2569E.1.CEL |
- 1.75 |
- 87 |
- 55.10% |
- 43.40% |
- 1.50% |
- 2.82 |
- 3.14 |
- 1 |
- |
-
-
- | 39 |
- R2581E.1 |
- BXD11 |
- R2581E.1.CEL |
- 1.94 |
- 89 |
- 62.10% |
- 36.40% |
- 1.60% |
- 1.55 |
- 0.81 |
- 1 |
- Y |
-
-
- | 40 |
- R2612E.2 |
- BXD11 |
- R2612E.2.CEL |
- 1.83 |
- 142.03 |
- 58.20% |
- 40.50% |
- 1.40% |
- 1.78 |
- 0.81 |
- 2 |
- |
-
-
- | 41 |
- R2742E.2 |
- BXD12 |
- R2742E.2.CEL |
- 2.127 |
- 134.14 |
- 57.00% |
- 41.60% |
- 1.40% |
- 1.64 |
- 0.78 |
- 2 |
- |
-
-
- | 42 |
- R2543E.1 |
- BXD12 |
- R2543E.1.CEL |
- 1.61 |
- 118 |
- 58.60% |
- 39.90% |
- 1.60% |
- 1.43 |
- 0.77 |
- 1 |
- Y |
-
-
- | 43 |
- R2586E.1 |
- BXD13 |
- R2586E.1.CEL |
- 2.01 |
- 74 |
- 56.40% |
- 42.00% |
- 1.60% |
- 2.85 |
- 3.81 |
- 1 |
- |
-
-
- | 44 |
- R877E.2 |
- BXD13 |
- R877E.2.CEL |
- 1.558 |
- 125.63 |
- 61.20% |
- 37.50% |
- 1.20% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 45 |
- R2557E.1 |
- BXD14 |
- R2557E.1.CEL |
- 1.83 |
- 99 |
- 62.50% |
- 36.10% |
- 1.40% |
- 1.31 |
- 0.78 |
- 1 |
- Y |
-
-
- | 46 |
- R1128E.2 |
- BXD14 |
- R1128E.2.CEL |
- 1.91 |
- 115 |
- 59.90% |
- 38.80% |
- 1.40% |
- 1.2 |
- 0.82 |
- 1 |
- Y |
-
-
- | 47 |
- R2701E.3 |
- BXD15 |
- R2701E.3.CEL |
- 1 |
- 88 |
- 60.60% |
- 37.90% |
- 1.40% |
- 1.5 |
- 0.77 |
- 3 |
- |
-
-
- | 48 |
- R2716E.2 |
- BXD15 |
- R2716E.2.CEL |
- 2.015 |
- 150.83 |
- 56.40% |
- 42.10% |
- 1.60% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 49 |
- R2711E.2 |
- BXD16 |
- R2711E.2.CEL |
- 1.953 |
- 118.53 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 50 |
- R2567E.1 |
- BXD16 |
- R2567E.1.CEL |
- 2.24 |
- 82 |
- 56.70% |
- 41.60% |
- 1.70% |
- 1.37 |
- 0.75 |
- 1 |
- |
-
-
- | 51 |
- R2720E.2 |
- BXD18 |
- R2720E.2.CEL |
- 2.32 |
- 99.93 |
- 59.50% |
- 39.00% |
- 1.50% |
- 1.33 |
- 0.77 |
- 2 |
- |
-
-
- | 52 |
- R2559E.1 |
- BXD18 |
- R2559E.1.CEL |
- 1.65 |
- 104 |
- 60.80% |
- 37.70% |
- 1.50% |
- 1.27 |
- 0.78 |
- 1 |
- Y |
-
-
- | 53 |
- R2560E.1 |
- BXD19 |
- R2560E.1.CEL |
- 1.79 |
- 98 |
- 60.90% |
- 37.50% |
- 1.60% |
- 1.35 |
- 0.8 |
- 1 |
- Y |
-
-
- | 54 |
- R2713E.2 |
- BXD19 |
- R2713E.2.CEL |
- 1.67 |
- 120.82 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.45 |
- 0.8 |
- 2 |
- |
-
-
- | 55 |
- R2584E.1 |
- BXD20 |
- R2584E.1.CEL |
- 2.07 |
- 84 |
- 59.30% |
- 39.10% |
- 1.60% |
- 1.4 |
- 0.76 |
- 1 |
- Y |
-
-
- | 56 |
- R2731E.2 |
- BXD20 |
- R2731E.2.CEL |
- 1.825 |
- 147 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.4 |
- 0.8 |
- 2 |
- |
-
-
- | 57 |
- R2702E.2 |
- BXD21 |
- R2702E.2.CEL |
- 1.811 |
- 128.65 |
- 59.40% |
- 39.10% |
- 1.40% |
- 1.26 |
- 0.8 |
- 2 |
- |
-
-
- | 58 |
- R2541E2.1 |
- BXD21 |
- R2541E2.1.CEL |
- 2.63 |
- 125 |
- 56.00% |
- 42.40% |
- 1.50% |
- 1.29 |
- 0.78 |
- 1 |
- |
-
-
- | 59 |
- R2553E.1 |
- BXD22 |
- R2553E.1.CEL |
- 1.95 |
- 111 |
- 59.90% |
- 38.50% |
- 1.50% |
- 1.28 |
- 0.76 |
- 1 |
- Y |
-
-
- | 60 |
- R2700E.2 |
- BXD22 |
- R2700E.2.CEL |
- 1.858 |
- 102.96 |
- 61.50% |
- 37.10% |
- 1.30% |
- 1.48 |
- 0.79 |
- 2 |
- |
-
-
- | 61 |
- R2558E-2.1 |
- BXD23 |
- R2558E-2.1.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 62 |
- R1086E.2 |
- BXD23 |
- R1086E.2.CEL |
- 2.233 |
- 125.05 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.43 |
- 0.77 |
- 2 |
- |
-
-
- | 63 |
- R2719E.2 |
- BXD24 |
- R2719E.2.CEL |
- 1.47 |
- 140.38 |
- 61.50% |
- 37.20% |
- 1.30% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 64 |
- R2589E2.1 |
- BXD24 |
- R2589E2.1.CEL |
- 2.61 |
- 112 |
- 57.50% |
- 40.90% |
- 1.60% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 65 |
- R2573E-2.1 |
- BXD25 |
- R2573E-2.1.CEL |
- 3.15 |
- 72 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.77 |
- 0.97 |
- 1 |
- |
-
-
- | 66 |
- R2683E.2 |
- BXD25 |
- R2683E.2.CEL |
- 1.777 |
- 115.64 |
- 58.30% |
- 40.30% |
- 1.40% |
- 2.01 |
- 0.79 |
- 2 |
- |
-
-
- | 67 |
- R2703E.2 |
- BXD27 |
- R2703E.2.CEL |
- 1.263 |
- 134.78 |
- 62.60% |
- 36.10% |
- 1.40% |
- 1.44 |
- 0.78 |
- 2 |
- |
-
-
- | 68 |
- R2729E.3 |
- BXD27 |
- R2729E.3.CEL |
- 1 |
- 87 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.56 |
- 0.84 |
- 3 |
- Y |
-
-
- | 69 |
- R2562E.3 |
- BXD28 |
- R2562E.3.CEL |
- 1.65 |
- 116 |
- 59.90% |
- 38.40% |
- 1.70% |
- 1.37 |
- 0.79 |
- 3 |
- Y |
-
-
- | 70 |
- R2721E.2 |
- BXD28 |
- R2721E.2.CEL |
- 2.065 |
- 157.39 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.31 |
- 0.81 |
- 2 |
- |
-
-
- | 71 |
- R2561E.3 |
- BXD29 |
- R2561E.3.CEL |
- 1 |
- 77 |
- 53.30% |
- 45.40% |
- 1.40% |
- 3.36 |
- 19.66 |
- 3 |
- |
-
-
- | 72 |
- R1258E.2 |
- BXD31 |
- R1258E.2.CEL |
- 2.063 |
- 117.09 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.54 |
- 0.78 |
- 2 |
- |
-
-
- | 73 |
- R2597E.1 |
- BXD31 |
- R2597E.1.CEL |
- 2.37 |
- 94 |
- 60.30% |
- 38.30% |
- 1.50% |
- 1.34 |
- 0.77 |
- 1 |
- Y |
-
-
- | 74 |
- R2563E.1 |
- BXD32 |
- R2563E.1.CEL |
- 1.55 |
- 102 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.5 |
- 0.8 |
- 1 |
- |
-
-
- | 75 |
- R1216E.2 |
- BXD32 |
- R1216E.2.CEL |
- 2.23 |
- 111.99 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.35 |
- 0.79 |
- 2 |
- |
-
-
- | 76 |
- R2542E.1 |
- BXD33 |
- R2542E.1.CEL |
- 2.13 |
- 97 |
- 56.50% |
- 41.80% |
- 1.60% |
- 1.91 |
- 0.93 |
- 1 |
- |
-
-
- | 77 |
- R857E.2 |
- BXD33 |
- R857E.2.CEL |
- 1.737 |
- 113.98 |
- 61.90% |
- 36.70% |
- 1.30% |
- 1.6 |
- 0.77 |
- 2 |
- |
-
-
- | 78 |
- R1451E.2 |
- BXD34 |
- R1451E.2.CEL |
- 1.843 |
- 140.05 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.42 |
- 0.81 |
- 2 |
- Y |
-
-
- | 79 |
- R2585E.1 |
- BXD34 |
- R2585E.1.CEL |
- 2.64 |
- 75 |
- 58.30% |
- 40.00% |
- 1.70% |
- 1.25 |
- 0.77 |
- 1 |
- |
-
-
- | 80 |
- R2698E.3 |
- BXD36 |
- R2698E.3.CEL |
- 1 |
- 86 |
- 59.70% |
- 39.00% |
- 1.30% |
- 1.46 |
- 0.78 |
- 3 |
- |
-
-
- | 81 |
- R2705E.3 |
- BXD36 |
- R2705E.3.CEL |
- 1 |
- 86 |
- 60.20% |
- 38.40% |
- 1.40% |
- 1.46 |
- 0.77 |
- 3 |
- |
-
-
- | 82 |
- R2710E.2 |
- BXD38 |
- R2710E.2.CEL |
- 2.112 |
- 122.1 |
- 58.80% |
- 39.80% |
- 1.40% |
- 1.37 |
- 0.78 |
- 2 |
- |
-
-
- | 83 |
- R2532E.1 |
- BXD38 |
- R2532E.1.CEL |
- 2.04 |
- 94 |
- 59.80% |
- 38.70% |
- 1.50% |
- 1.37 |
- 0.8 |
- 1 |
- Y |
-
-
- | 84 |
- R2574E.1 |
- BXD39 |
- R2574E.1.CEL |
- 1.98 |
- 91 |
- 61.20% |
- 37.30% |
- 1.50% |
- 1.39 |
- 0.78 |
- 1 |
- |
-
-
- | 85 |
- R2695E.2 |
- BXD39 |
- R2695E.2.CEL |
- 1.638 |
- 122.7 |
- 60.80% |
- 37.80% |
- 1.50% |
- 1.42 |
- 0.8 |
- 2 |
- |
-
-
- | 86 |
- R2699E.2 |
- BXD40 |
- R2699E.2.CEL |
- 1.827 |
- 105.23 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.42 |
- 0.81 |
- 2 |
- |
-
-
- | 87 |
- R2590E.1 |
- BXD40 |
- R2590E.1.CEL |
- 2.71 |
- 77 |
- 59.10% |
- 39.30% |
- 1.50% |
- 1.4 |
- 0.77 |
- 1 |
- Y |
-
-
- | 88 |
- R2696E.2 |
- BXD42 |
- R2696E.2.CEL |
- 1.622 |
- 118.95 |
- 62.00% |
- 36.60% |
- 1.50% |
- 1.53 |
- 0.79 |
- 2 |
- |
-
-
- | 89 |
- R2596E.1 |
- BXD42 |
- R2596E.1.CEL |
- 2.63 |
- 108 |
- 59.00% |
- 39.60% |
- 1.50% |
- 1.24 |
- 0.8 |
- 1 |
- |
-
-
- | 90 |
- R994E.2 |
- BXD43 |
- R994E.2.CEL |
- 1.966 |
- 113.12 |
- 60.80% |
- 37.80% |
- 1.40% |
- 1.66 |
- 0.8 |
- 2 |
- |
-
-
- | 91 |
- R2607E.1 |
- BXD43 |
- R2607E.1.CEL |
- 2.43 |
- 115 |
- 58.60% |
- 40.00% |
- 1.40% |
- 1.31 |
- 0.76 |
- 1 |
- Y |
-
-
- | 92 |
- R2594E.1 |
- BXD44 |
- R2594E.1.CEL |
- 1.77 |
- 117 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.35 |
- 0.85 |
- 1 |
- |
-
-
- | 93 |
- R2610E.2 |
- BXD44 |
- R2610E.2.CEL |
- 1.814 |
- 142.91 |
- 59.00% |
- 39.50% |
- 1.50% |
- 1.35 |
- 0.8 |
- 2 |
- |
-
-
- | 94 |
- R2732E.2 |
- BXD45 |
- R2732E.2.CEL |
- 2.154 |
- 122.45 |
- 56.50% |
- 42.10% |
- 1.40% |
- 1.8 |
- 0.83 |
- 2 |
- |
-
-
- | 95 |
- R2592E.1 |
- BXD45 |
- R2592E.1.CEL |
- 1.85 |
- 106 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.43 |
- 0.85 |
- 1 |
- Y |
-
-
- | 96 |
- R967E.2 |
- BXD48 |
- R967E.2.CEL |
- 1.948 |
- 130.95 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.63 |
- 0.81 |
- 2 |
- |
-
-
- | 97 |
- R2606E.1 |
- BXD48 |
- R2606E.1.CEL |
- 2.56 |
- 106 |
- 58.90% |
- 39.70% |
- 1.40% |
- 1.35 |
- 0.83 |
- 1 |
- Y |
-
-
- | 98 |
- R2933E.3 |
- BXD50 |
- R2933E.3.CEL |
- 1 |
- 72 |
- 52.90% |
- 45.60% |
- 1.50% |
- 2.45 |
- 0.98 |
- 3 |
- |
-
-
- | 99 |
- R2937E.3 |
- BXD50 |
- R2937E.3.CEL |
- 1 |
- 89 |
- 56.90% |
- 41.60% |
- 1.40% |
- 1.81 |
- 0.82 |
- 3 |
- |
-
-
- | 100 |
- R2603E.1 |
- BXD51 |
- R2603E.1.CEL |
- 2.49 |
- 115 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.24 |
- 0.79 |
- 1 |
- |
-
-
- | 101 |
- R1042E.2 |
- BXD51 |
- R1042E.2.CEL |
- 2.352 |
- 104.12 |
- 58.70% |
- 39.90% |
- 1.40% |
- 1.53 |
- 0.82 |
- 2 |
- |
-
-
- | 102 |
- R2980E.3 |
- BXD55 |
- R2980E.3.CEL |
- 1 |
- 82 |
- 56.90% |
- 41.70% |
- 1.50% |
- 1.77 |
- 0.84 |
- 3 |
- |
-
-
- | 103 |
- R2690E.2 |
- BXD55 |
- R2690E.2.CEL |
- 1.887 |
- 164.01 |
- 56.10% |
- 42.30% |
- 1.60% |
- 1.43 |
- 0.8 |
- 2 |
- |
-
-
- | 104 |
- R4176E |
- BXD56 |
- R4176E.CEL |
- 4.75 |
- 43.08 |
- 63.00% |
- 35.60% |
- 1.30% |
- 1.39 |
- 0.81 |
- 4 |
- Y |
-
-
- | 105 |
- R4175E |
- BXD56 |
- R4175E.CEL |
- 6 |
- 38.49 |
- 61.30% |
- 37.30% |
- 1.40% |
- 1.47 |
- 0.81 |
- 4 |
- Y |
-
-
- | 106 |
- R1006E.3 |
- BXD60 |
- R1006E.3.CEL |
- 1 |
- 98 |
- 54.90% |
- 43.70% |
- 1.50% |
- 2.7 |
- 0.86 |
- 3 |
- |
-
-
- | 107 |
- R2725E.2 |
- BXD60 |
- R2725E.2.CEL |
- 1.551 |
- 148.01 |
- 59.80% |
- 38.80% |
- 1.40% |
- 1.43 |
- 0.79 |
- 2 |
- |
-
-
- | 108 |
- R1074E.3 |
- BXD60 |
- R1074E.3.CEL |
- 1 |
- 118 |
- 55.50% |
- 43.10% |
- 1.40% |
- 1.96 |
- 0.81 |
- 3 |
- |
-
-
- | 109 |
- R2534E2.1 |
- BXD61 |
- R2534E2.1.CEL |
- 2.47 |
- 118 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.42 |
- 0.79 |
- 1 |
- |
-
-
- | 110 |
- R2684E.2 |
- BXD61 |
- R2684E.2.CEL |
- 2.01 |
- 131.03 |
- 57.00% |
- 41.50% |
- 1.50% |
- 1.34 |
- 0.78 |
- 2 |
- |
-
-
- | 111 |
- R1107E.3 |
- BXD62 |
- R1107E.3.CEL |
- 1 |
- 83 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.43 |
- 0.93 |
- 3 |
- |
-
-
- | 112 |
- R2681E.2 |
- BXD62 |
- R2681E.2.CEL |
- 2.086 |
- 148.24 |
- 57.20% |
- 41.30% |
- 1.50% |
- 1.29 |
- 0.81 |
- 2 |
- |
-
-
- | 113 |
- R965E.3 |
- BXD62 |
- R965E.3.CEL |
- 1 |
- 93.55 |
- 53.30% |
- 45.20% |
- 1.50% |
- 3.11 |
- 0.94 |
- 3 |
- |
-
-
- | 114 |
- R1425E.2 |
- BXD63 |
- R1425E.2.CEL |
- 1.7 |
- 136 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.43 |
- 0.82 |
- 2 |
- |
-
-
- | 115 |
- R2576E.3 |
- BXD63 |
- R2576E.3.CEL |
- 1 |
- 84 |
- 61.30% |
- 37.40% |
- 1.40% |
- 1.48 |
- 0.76 |
- 3 |
- |
-
-
- | 116 |
- R943E-2.2 |
- BXD64 |
- R943E-2.2.CEL |
- 1.591 |
- 141.34 |
- 60.10% |
- 38.40% |
- 1.50% |
- 1.32 |
- 0.76 |
- 2 |
- |
-
-
- | 117 |
- R2611E.1 |
- BXD64 |
- R2611E.1.CEL |
- 2.29 |
- 92 |
- 58.00% |
- 40.50% |
- 1.50% |
- 1.57 |
- 1.06 |
- 1 |
- |
-
-
- | 118 |
- R2689E.2 |
- BXD65 |
- R2689E.2.CEL |
- 1.721 |
- 142.44 |
- 59.90% |
- 38.60% |
- 1.50% |
- 1.38 |
- 0.76 |
- 2 |
- |
-
-
- | 119 |
- R2583E.1 |
- BXD65 |
- R2583E.1.CEL |
- 2.49 |
- 70 |
- 56.90% |
- 41.50% |
- 1.60% |
- 1.67 |
- 1.01 |
- 1 |
- |
-
-
- | 120 |
- R2728E.2 |
- BXD66 |
- R2728E.2.CEL |
- 1.714 |
- 137.45 |
- 59.40% |
- 39.00% |
- 1.60% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 121 |
- R2536E2.1 |
- BXD66 |
- R2536E2.1.CEL |
- 2.74 |
- 109 |
- 56.10% |
- 42.30% |
- 1.70% |
- 1.28 |
- 0.79 |
- 1 |
- |
-
-
- | 122 |
- R1207E.2 |
- BXD66 |
- R1207E.2.CEL |
- 1.681 |
- 136.86 |
- 60.40% |
- 38.10% |
- 1.50% |
- 1.45 |
- 0.77 |
- 2 |
- |
-
-
- | 123 |
- R1192E.2 |
- BXD67 |
- R1192E.2.CEL |
- 2.126 |
- 123.37 |
- 57.90% |
- 40.60% |
- 1.50% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 124 |
- R2727E.3 |
- BXD67 |
- R2727E.3.CEL |
- 1 |
- 82.55 |
- 56.10% |
- 42.40% |
- 1.50% |
- 1.97 |
- 0.87 |
- 2 |
- |
-
-
- | 125 |
- R2691E.3 |
- BXD67 |
- R2691E.3.CEL |
- 1 |
- 90 |
- 54.80% |
- 43.80% |
- 1.50% |
- 2.61 |
- 0.81 |
- 3 |
- |
-
-
- | 126 |
- R2551E.1 |
- BXD68 |
- R2551E.1.CEL |
- 2.49 |
- 92 |
- 54.30% |
- 44.10% |
- 1.60% |
- 2.91 |
- 1.55 |
- 1 |
- |
-
-
- | 127 |
- R2726E.2 |
- BXD68 |
- R2726E.2.CEL |
- 1.811 |
- 153.09 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.39 |
- 0.78 |
- 2 |
- |
-
-
- | 128 |
- R2593E.1 |
- BXD69 |
- R2593E.1.CEL |
- 1.67 |
- 128 |
- 59.20% |
- 39.50% |
- 1.30% |
- 1.47 |
- 0.92 |
- 1 |
- Y |
-
-
- | 129 |
- R975E.2 |
- BXD70 |
- R975E.2.CEL |
- 1.841 |
- 137.97 |
- 58.00% |
- 40.50% |
- 1.40% |
- 1.36 |
- 0.79 |
- 2 |
- |
-
-
- | 130 |
- R2537E2.1 |
- BXD70 |
- R2537E2.1.CEL |
- 2.93 |
- 99 |
- 58.00% |
- 40.50% |
- 1.60% |
- 1.29 |
- 0.75 |
- 1 |
- |
-
-
- | 131 |
- R4531E |
- BXD71 |
- R4531E.CEL |
- 4.77 |
- 43.48 |
- 62.40% |
- 36.30% |
- 1.40% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 132 |
- R4532E |
- BXD71 |
- R4532E.CEL |
- 5.89 |
- 40.68 |
- 60.90% |
- 37.60% |
- 1.50% |
- 1.24 |
- 0.79 |
- 4 |
- Y |
-
-
- | 133 |
- R2779E.2 |
- BXD73 |
- R2779E.2.CEL |
- 1.746 |
- 121.11 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.5 |
- 0.8 |
- 2 |
- |
-
-
- | 134 |
- R3024E.3 |
- BXD73 |
- R3024E.3.CEL |
- 1 |
- 78.05 |
- 51.70% |
- 46.60% |
- 1.70% |
- 2.3 |
- 0.94 |
- 3 |
- |
-
-
- | 135 |
- R2565E.1 |
- BXD75 |
- R2565E.1.CEL |
- 1.79 |
- 102 |
- 58.00% |
- 40.50% |
- 1.50% |
- 2.31 |
- 3.47 |
- 1 |
- |
-
-
- | 136 |
- R1397E-re.2 |
- BXD75 |
- R1397E-re.2.CEL |
- 1.449 |
- 189.71 |
- 59.60% |
- 39.00% |
- 1.40% |
- 1.39 |
- 0.82 |
- 2 |
- |
-
-
- | 137 |
- R2687E.3 |
- BXD77 |
- R2687E.3.CEL |
- 1 |
- 80 |
- 58.00% |
- 40.60% |
- 1.40% |
- 1.57 |
- 0.8 |
- 3 |
- Y |
-
-
- | 138 |
- R2717E.2 |
- BXD77 |
- R2717E.2.CEL |
- 1.797 |
- 84.43 |
- 61.60% |
- 36.90% |
- 1.40% |
- 1.49 |
- 0.76 |
- 2 |
- |
-
-
- | 139 |
- R1421E.3 |
- BXD77 |
- R1421E.3.CEL |
- 1 |
- 94 |
- 52.40% |
- 46.20% |
- 1.40% |
- 2.29 |
- 0.82 |
- 3 |
- |
-
-
- | 140 |
- R2579E.1 |
- BXD80 |
- R2579E.1.CEL |
- 2.42 |
- 72 |
- 59.20% |
- 39.40% |
- 1.50% |
- 1.73 |
- 0.82 |
- 1 |
- |
-
-
- | 141 |
- R2686E.2 |
- BXD80 |
- R2686E.2.CEL |
- 2.342 |
- 119.63 |
- 56.00% |
- 42.60% |
- 1.50% |
- 1.38 |
- 0.79 |
- 2 |
- |
-
-
- | 142 |
- R2956E.3 |
- BXD83 |
- R2956E.3.CEL |
- 1 |
- 84 |
- 55.40% |
- 43.20% |
- 1.40% |
- 1.39 |
- 0.84 |
- 3 |
- |
-
-
- | 143 |
- R2960E.3 |
- BXD83 |
- R2960E.3.CEL |
- 1 |
- 80 |
- 56.60% |
- 41.90% |
- 1.50% |
- 1.5 |
- 0.82 |
- 3 |
- Y |
-
-
- | 144 |
- R2922E.3 |
- BXD84 |
- R2922E.3.CEL |
- 1 |
- 91 |
- 57.80% |
- 40.80% |
- 1.50% |
- 1.47 |
- 0.83 |
- 3 |
- Y |
-
-
- | 145 |
- R2895E.3 |
- BXD84 |
- R2895E.3.CEL |
- 1 |
- 75 |
- 58.30% |
- 40.20% |
- 1.50% |
- 1.56 |
- 0.77 |
- 3 |
- Y |
-
-
- | 146 |
- R2692E.2 |
- BXD85 |
- R2692E.2.CEL |
- 1.423 |
- 160.87 |
- 60.20% |
- 38.30% |
- 1.40% |
- 1.46 |
- 0.79 |
- 2 |
- |
-
-
- | 147 |
- R2715E.2 |
- BXD85 |
- R2715E.2.CEL |
- 1.488 |
- 142.6 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.5 |
- 0.78 |
- 2 |
- |
-
-
- | 148 |
- R1405E.2 |
- BXD86 |
- R1405E.2.CEL |
- 2.351 |
- 119.34 |
- 56.40% |
- 42.20% |
- 1.40% |
- 1.64 |
- 0.81 |
- 2 |
- |
-
-
- | 149 |
- R1225E.3 |
- BXD86 |
- R1225E.3.CEL |
- 1 |
- 71 |
- 53.90% |
- 44.60% |
- 1.40% |
- 3.2 |
- 1.61 |
- 3 |
- |
-
-
- | 150 |
- R2724E.2 |
- BXD87 |
- R2724E.2.CEL |
- 1.906 |
- 113.71 |
- 60.70% |
- 37.90% |
- 1.40% |
- 1.45 |
- 0.79 |
- 2 |
- |
-
-
- | 151 |
- R2540E.1 |
- BXD87 |
- R2540E.1.CEL |
- 2.33 |
- 93 |
- 61.10% |
- 37.40% |
- 1.40% |
- 1.22 |
- 0.81 |
- 1 |
- Y |
-
-
- | 152 |
- R1433E.2 |
- BXD89 |
- R1433E.2.CEL |
- 1 |
- 2.241 |
- 57.70% |
- 40.80% |
- 1.50% |
- 1.41 |
- 0.78 |
- 2 |
- |
-
-
- | 153 |
- R2546E.1 |
- BXD89 |
- R2546E.1.CEL |
- 1.99 |
- 96 |
- 58.60% |
- 39.70% |
- 1.70% |
- 1.47 |
- 0.78 |
- 1 |
- |
-
-
- | 154 |
- R2578E2.1 |
- BXD90 |
- R2578E2.1.CEL |
- 2.79 |
- 92 |
- 58.60% |
- 39.80% |
- 1.60% |
- 1.52 |
- 0.77 |
- 1 |
- Y |
-
-
- | 155 |
- R859E.2 |
- BXD90 |
- R859E.2.CEL |
- 1.847 |
- 152.22 |
- 57.90% |
- 40.70% |
- 1.40% |
- 1.36 |
- 0.77 |
- 2 |
- |
-
-
- | 156 |
- R2682E.2 |
- BXD92 |
- R2682E.2.CEL |
- 1.547 |
- 156.31 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.37 |
- 0.77 |
- 2 |
- |
-
-
- | 157 |
- R1388E.3 |
- BXD92 |
- R1388E.3.CEL |
- 1 |
- 63 |
- 60.00% |
- 38.60% |
- 1.40% |
- 1.85 |
- 1.03 |
- 3 |
- |
-
-
- | 158 |
- R1322E.3 |
- BXD92 |
- R1322E.3.CEL |
- 1 |
- 80 |
- 55.90% |
- 42.60% |
- 1.50% |
- 1.75 |
- 0.74 |
- 3 |
- |
-
-
- | 159 |
- R2733E.2 |
- BXD96 |
- R2733E.2.CEL |
- 1.7 |
- 113.99 |
- 62.10% |
- 36.60% |
- 1.30% |
- 1.4 |
- 0.78 |
- 2 |
- |
-
-
- | 160 |
- R2554E.1 |
- BXD96 |
- R2554E.1.CEL |
- 2.18 |
- 93 |
- 60.20% |
- 38.30% |
- 1.50% |
- 1.46 |
- 0.77 |
- 1 |
- Y |
-
-
- | 161 |
- R2649E.2 |
- BXD97 |
- R2649E.2.CEL |
- 2.343 |
- 119.04 |
- 57.50% |
- 41.20% |
- 1.40% |
- 1.53 |
- 0.8 |
- 2 |
- |
-
-
- | 162 |
- R2577E.1 |
- BXD97 |
- R2577E.1.CEL |
- 2.07 |
- 77 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.87 |
- 1.29 |
- 1 |
- |
-
-
- | 163 |
- R2645E.3 |
- BXD98 |
- R2645E.3.CEL |
- 1 |
- 88 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.59 |
- 0.81 |
- 3 |
- Y |
-
-
- | 164 |
- R2688E.2 |
- BXD98 |
- R2688E.2.CEL |
- 1.772 |
- 145.24 |
- 58.50% |
- 40.00% |
- 1.50% |
- 1.48 |
- 0.81 |
- 2 |
- |
-
-
- | 165 |
- R4533E |
- BXD99 |
- R4533E.CEL |
- 1 |
- 37.69 |
- 60.30% |
- 38.20% |
- 1.40% |
- 1.33 |
- 0.89 |
- 4 |
- Y |
-
-
- | 166 |
- R4534E |
- BXD99 |
- R4534E.CEL |
- 5.69 |
- 36.62 |
- 62.90% |
- 35.70% |
- 1.40% |
- 1.16 |
- 0.8 |
- 4 |
- Y |
-
-
- | 167 |
- R2885E.3 |
- BXSB/MpJ |
- R2885E.3.CEL |
- 1 |
- 76 |
- 58.10% |
- 40.60% |
- 1.30% |
- 1.88 |
- 1.06 |
- 3 |
- |
-
-
- | 168 |
- R2883E.3 |
- BXSB/MpJ |
- R2883E.3.CEL |
- 1 |
- 71 |
- 56.40% |
- 42.00% |
- 1.50% |
- 1.59 |
- 0.84 |
- 3 |
- Y |
-
-
- | 169 |
- R1700E.1 |
- C3H/HeJ |
- R1700E.1.CEL |
- 2.98 |
- 69 |
- 60.80% |
- 37.90% |
- 1.40% |
- 1.48 |
- 0.78 |
- 1 |
- |
-
-
- | 170 |
- R1704E.1 |
- C3H/HeJ |
- R1704E.1.CEL |
- 2.58 |
- 88 |
- 60.10% |
- 38.60% |
- 1.30% |
- 1.38 |
- 0.84 |
- 1 |
- |
-
-
- | 171 |
- R2605E.1 |
- C57BL/6J |
- R2605E.1.CEL |
- 1.82 |
- 131 |
- 60.50% |
- 38.20% |
- 1.30% |
- 1.32 |
- 0.8 |
- 1 |
- Y |
-
-
- | 172 |
- R0871E |
- C57BL/6J |
- R0871E.CEL |
- 6.24 |
- 37.38 |
- 61.90% |
- 36.70% |
- 1.40% |
- 1.41 |
- 0.8 |
- 4 |
- Y |
-
-
- | 173 |
- R0872E.1 |
- C57BL/6J |
- R0872E.1.CEL |
- 3.13 |
- 89 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 174 |
- R0872E |
- C57BL/6J |
- R0872E.CEL |
- 3.128 |
- 88.58 |
- 58.90% |
- 39.60% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- |
-
-
- | 175 |
- R4507E |
- C57BL/6J-Nyx |
- R4507E.CEL |
- 8.13 |
- 37.5 |
- 59.30% |
- 39.30% |
- 1.40% |
- 1.32 |
- 0.8 |
- 4 |
- Y |
-
-
- | 176 |
- R4508E |
- C57BL/6J-Nyx |
- R4508E.CEL |
- 6.33 |
- 37.26 |
- 60.90% |
- 37.80% |
- 1.30% |
- 1.24 |
- 0.82 |
- 4 |
- Y |
-
-
- | 177 |
- R4505E |
- C57BL/6J-Rpe65 |
- R4505E.CEL |
- 5.98 |
- 37.48 |
- 61.80% |
- 36.80% |
- 1.40% |
- 1.45 |
- 0.85 |
- 4 |
- Y |
-
-
- | 178 |
- R4506E |
- C57BL/6J-Rpe65 |
- R4506E.CEL |
- 6.94 |
- 37.9 |
- 61.10% |
- 37.50% |
- 1.30% |
- 1.5 |
- 0.83 |
- 4 |
- Y |
-
-
- | 179 |
- R4535E |
- C57BLKS/J |
- R4535E.CEL |
- 6.59 |
- 37.28 |
- 61.20% |
- 37.30% |
- 1.40% |
- 1.26 |
- 0.83 |
- 4 |
- Y |
-
-
- | 180 |
- R4536E |
- C57BLKS/J |
- R4536E.CEL |
- 1 |
- 40.71 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.25 |
- 0.77 |
- 4 |
- Y |
-
-
- | 181 |
- R2564E.1 |
- CAST/EiJ |
- R2564E.1.CEL |
- 1.94 |
- 89 |
- 58.50% |
- 39.90% |
- 1.60% |
- 1.6 |
- 0.77 |
- 1 |
- |
-
-
- | 182 |
- R2580E.1 |
- CAST/EiJ |
- R2580E.1.CEL |
- 2.09 |
- 95 |
- 58.20% |
- 40.10% |
- 1.70% |
- 1.4 |
- 0.76 |
- 1 |
- |
-
-
- | 183 |
- R4537E |
- CBA/CaJ |
- R4537E.CEL |
- 1 |
- 38.45 |
- 60.60% |
- 37.90% |
- 1.50% |
- 1.63 |
- 0.82 |
- 4 |
- Y |
-
-
- | 184 |
- R4538E |
- CBA/CaJ |
- R4538E.CEL |
- 5.89 |
- 39.18 |
- 61.70% |
- 36.90% |
- 1.40% |
- 1.45 |
- 0.8 |
- 4 |
- Y |
-
-
- | 185 |
- R4539E |
- CZECHII/EiJ |
- R4539E.CEL |
- 7.73 |
- 37.1 |
- 58.30% |
- 40.10% |
- 1.50% |
- 1.7 |
- 0.95 |
- 4 |
- Y |
-
-
- | 186 |
- R4540E |
- CZECHII/EiJ |
- R4540E.CEL |
- 11.04 |
- 36.69 |
- 53.00% |
- 45.30% |
- 1.70% |
- 1.83 |
- 1.32 |
- 4 |
- |
-
-
- | 187 |
- R2600E.1 |
- D2B6F1 |
- R2600E.1.CEL |
- 2.47 |
- 95 |
- 58.10% |
- 40.20% |
- 1.70% |
- 1.41 |
- 0.78 |
- 1 |
- Y |
-
-
- | 188 |
- R2604E.1 |
- D2B6F1 |
- R2604E.1.CEL |
- 2.66 |
- 90 |
- 59.40% |
- 39.20% |
- 1.50% |
- 1.28 |
- 0.79 |
- 1 |
- Y |
-
-
- | 189 |
- R1002E.3 |
- DBA/2J |
- R1002E.3.CEL |
- 1 |
- 102 |
- 54.80% |
- 43.70% |
- 1.50% |
- 2.84 |
- 0.83 |
- 3 |
- |
-
-
- | 190 |
- R4541E |
- DBA/2J |
- R4541E.CEL |
- 1 |
- 43.4 |
- 61.40% |
- 37.00% |
- 1.50% |
- 1.37 |
- 0.73 |
- 4 |
- Y |
-
-
- | 191 |
- R959E.3 |
- DBA/2J |
- R959E.3.CEL |
- 1 |
- 89.97 |
- 53.20% |
- 45.30% |
- 1.50% |
- 3.66 |
- 1.09 |
- 4 |
- |
-
-
- | 192 |
- R2572E.1 |
- DBA/2J |
- R2572E.1.CEL |
- 2.41 |
- 79 |
- 55.50% |
- 42.90% |
- 1.60% |
- 1.37 |
- 0.79 |
- 1 |
- |
-
-
- | 193 |
- R4542E |
- DBA/2J |
- R4542E.CEL |
- 5.7 |
- 39.95 |
- 61.00% |
- 37.40% |
- 1.50% |
- 1.23 |
- 0.81 |
- 4 |
- Y |
-
-
- | 194 |
- R2771E.3 |
- FVB/NJ |
- R2771E.3.CEL |
- 1 |
- 70 |
- 55.30% |
- 43.20% |
- 1.50% |
- 1.69 |
- 0.83 |
- 3 |
- |
-
-
- | 195 |
- R2772E.3 |
- FVB/NJ |
- R2772E.3.CEL |
- 1 |
- 76 |
- 55.20% |
- 43.40% |
- 1.40% |
- 2.13 |
- 1.02 |
- 3 |
- |
-
-
- | 196 |
- R2636E.1 |
- KK/HlJ |
- R2636E.1.CEL |
- 2.61 |
- 93 |
- 58.90% |
- 39.50% |
- 1.50% |
- 1.39 |
- 0.76 |
- 1 |
- Y |
-
-
- | 197 |
- R2637E.1 |
- KK/HlJ |
- R2637E.1.CEL |
- 2.19 |
- 103 |
- 59.40% |
- 39.00% |
- 1.50% |
- 1.3 |
- 0.79 |
- 1 |
- Y |
-
-
- | 198 |
- R0999E.1 |
- LG/J |
- R0999E.1.CEL |
- 2.45 |
- 82 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 199 |
- R1004E.1 |
- LG/J |
- R1004E.1.CEL |
- 2.44 |
- 92 |
- 58.70% |
- 39.80% |
- 1.50% |
- 1.38 |
- 0.79 |
- 1 |
- Y |
-
-
- | 200 |
- R4543E |
- LP/J |
- R4543E.CEL |
- 6.57 |
- 41.99 |
- 60.30% |
- 38.20% |
- 1.50% |
- 1.28 |
- 0.75 |
- 4 |
- Y |
-
-
- | 201 |
- R4544E |
- LP/J |
- R4544E.CEL |
- 4.56 |
- 39.9 |
- 62.40% |
- 36.10% |
- 1.50% |
- 1.23 |
- 0.77 |
- 4 |
- Y |
-
-
- | 202 |
- R2858E.3 |
- MOLF/EiJ |
- R2858E.3.CEL |
- 1 |
- 64 |
- 53.80% |
- 44.70% |
- 1.50% |
- 1.59 |
- 0.95 |
- 3 |
- |
-
-
- | 203 |
- R2919.3 |
- MOLF/EiJ |
- R2919.3.CEL |
- 1 |
- 64 |
- 52.40% |
- 46.00% |
- 1.60% |
- 2.15 |
- 1.07 |
- 3 |
- |
-
-
- | 204 |
- R1688E.1 |
- NOD/LtJ |
- R1688E.1.CEL |
- 2.66 |
- 98 |
- 58.60% |
- 39.90% |
- 1.50% |
- 1.26 |
- 0.8 |
- 1 |
- Y |
-
-
- | 205 |
- R2566E-2.1 |
- NOD/LtJ |
- R2566E-2.1.CEL |
- 3.03 |
- 69 |
- 59.80% |
- 38.80% |
- 1.50% |
- 1.38 |
- 0.75 |
- 1 |
- Y |
-
-
- | 206 |
- R4545E |
- NZB/BlNJ |
- R4545E.CEL |
- 4.23 |
- 43.48 |
- 62.10% |
- 36.40% |
- 1.50% |
- 1.33 |
- 0.76 |
- 4 |
- Y |
-
-
- | 207 |
- R4546E |
- NZB/BlNJ |
- R4546E.CEL |
- 6.27 |
- 44.22 |
- 59.40% |
- 39.10% |
- 1.50% |
- 1.17 |
- 0.82 |
- 4 |
- Y |
-
-
- | 208 |
- R2535E.1 |
- NZO/HlLtJ |
- R2535E.1.CEL |
- 1.89 |
- 86 |
- 60.40% |
- 38.20% |
- 1.40% |
- 1.41 |
- 0.85 |
- 1 |
- |
-
-
- | 209 |
- R2550E.1 |
- NZO/HlLtJ |
- R2550E.1.CEL |
- 1.79 |
- 87 |
- 60.70% |
- 37.80% |
- 1.50% |
- 1.52 |
- 0.82 |
- 1 |
- |
-
-
- | 210 |
- R2817E.3 |
- NZW/LacJ |
- R2817E.3.CEL |
- 1 |
- 59 |
- 50.90% |
- 47.60% |
- 1.50% |
- 3.59 |
- 1.48 |
- 3 |
- |
-
-
- | 211 |
- R2810E |
- NZW/LacJ |
- R2810E.CEL |
- |
- |
- |
- |
- |
- |
- |
- 3 |
- |
-
-
- | 212 |
- R2810E.3 |
- NZW/LacJ |
- R2810E.3.CEL |
- 1 |
- 74 |
- 57.00% |
- 41.70% |
- 1.40% |
- 2.15 |
- 1.03 |
- 4 |
- Y |
-
-
- | 213 |
- R4547E |
- PANCEVO/EiJ |
- R4547E.CEL |
- 5.27 |
- 51.34 |
- 57.20% |
- 41.10% |
- 1.70% |
- 1.7 |
- 0.83 |
- 4 |
- |
-
-
- | 214 |
- R4548E |
- PANCEVO/EiJ |
- R4548E.CEL |
- 10.54 |
- 37.39 |
- 50.30% |
- 48.00% |
- 1.70% |
- 1.68 |
- 1.09 |
- 4 |
- |
-
-
- | 215 |
- R2635E.1 |
- PWD/PhJ |
- R2635E.1.CEL |
- 3.72 |
- 80 |
- 54.20% |
- 44.10% |
- 1.70% |
- 1.53 |
- 0.85 |
- 1 |
- |
-
-
- | 216 |
- R2634E.1 |
- PWD/PhJ |
- R2634E.1.CEL |
- 3.29 |
- 90 |
- 55.90% |
- 42.50% |
- 1.60% |
- 1.57 |
- 0.81 |
- 1 |
- |
-
-
- | 217 |
- R2544E.1 |
- PWK/PhJ |
- R2544E.1.CEL |
- 2.2 |
- 108 |
- 54.90% |
- 43.50% |
- 1.70% |
- 1.36 |
- 0.82 |
- 1 |
- |
-
-
- | 218 |
- R2549E.1 |
- PWK/PhJ |
- R2549E.1.CEL |
- 2.28 |
- 84 |
- 57.30% |
- 41.20% |
- 1.50% |
- 1.57 |
- 0.83 |
- 1 |
- |
-
-
- | 219 |
- R4550E |
- SJL/J |
- R4550E.CEL |
- 5.35 |
- 40.44 |
- 62.30% |
- 36.20% |
- 1.40% |
- 1.24 |
- 0.79 |
- 4 |
- |
-
-
- | 220 |
- R2368E.1 |
- WSB/EiJ |
- R2368E.1.CEL |
- 2.57 |
- 86 |
- 59.50% |
- 39.10% |
- 1.40% |
- 1.29 |
- 0.74 |
- 1 |
- Y |
-
-
- | 221 |
- R2547E.1 |
- WSB/EiJ |
- R2547E.1.CEL |
- 2.14 |
- 90 |
- 58.20% |
- 40.10% |
- 1.60% |
- 1.32 |
- 0.77 |
- 1 |
- Y |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Eye_M2_0908_WTWT/summary.rtf b/general/datasets/Eye_M2_0908_WTWT/summary.rtf
deleted file mode 100644
index 44b7e23..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/summary.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-FINAL RECOMMENDED EYE DATA SET. The HEIMED September 2008 RMA data release provides estimates of gene expression in whole eyes of 103 lines of young adult mice generated using 221 Affymetrix M430 2.0 arrays. This data set is intended for exploration of the genetics and genomics of the mouse eye, retina, lens, retinal pigment epithelium, cornea, iris and choroid. Data were generated at UTHSC with support from a grant from Dr. Barrett Haik, Director of the Hamilton Eye Institute (HEI). We used pooled RNA samples, usually two independent pools--one male, one female pool--for most lines of mice. This data set was processed using the RMA protocol. A total of 2223 probes sets are associated with LRS values greater than 46 (LOD >10).
-
-Users of these mouse eye data may also find the following complementary resources extremely useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
diff --git a/general/datasets/Eye_M2_0908_WTWT/tissue.rtf b/general/datasets/Eye_M2_0908_WTWT/tissue.rtf
deleted file mode 100644
index 9b6ee0f..0000000
--- a/general/datasets/Eye_M2_0908_WTWT/tissue.rtf
+++ /dev/null
@@ -1,2058 +0,0 @@
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 4 to 8 eyes from 2 to 4 animals. RNA was extracted at UTHSC by Zhiping Jia. If tissue was saved for RNA extraction at a later time, eyes were placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. If eyes were used for immediate RNA extraction then we proceeded immediately to the next steps.
-
-Dissecting and preparing eyes for RNA extraction
-
-
- - Place eyes for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below).
- - Store RNA in 75% ethanol at –80 deg. C until use.
-
-
-Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
- - homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue)
- - allowed the homogenate to stand for 5 min at room temperature
- - added 0.2 ml of chloroform per 1 ml RNA STAT-60
- - shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min
- - centrifuged at 12,000 G for 15 min
- - transfered the aqueous phase to a fresh tube
- - added 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - vortexed and allowed sample to stand at room temperature for 5-10 min
- - centrifuged at 12,000 G for 10-15 min
- - removed the supernatant and washed the RNA pellet with 75% ethanol
- - stored the pellet in 75% ethanol at -80 deg C until use
-
-
-Sample Processing. All samples were processed in the VA Medical Center, Memphis, Rheumatology Disease Research Core Center led by Dr. Weikuan Gu. All arrays were processed by Dr. Yan Jiao. In brief, samples were purified using a standard sodium acetate in alcohol method (recommended by Affymetrix). The RNA quality was checked using a 1% agarose gel. The 18S and 28S bands had to be clear and the 28S band had to be more prominent. RNA concentation was measured using a spectrophotometer. The 260/280 ratios had to be greater than 1.7, and the majority were 1.8 or higher. We used a total of 8 micrograms of RNA as starting amount for cDNA synthesis using a standard Eberwine T7 polymerase method (Superscript II RT, Invitrogen Inc., Affy Part No 900431, GeneChip Expression 3' Amplification One-Cyle cDNA Synthesis Kit). The Affymetrix IVT labeling kit (Affy 900449) was used to generate labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above were acceptable) and 1% agarose gel inspection of the product (a size range from 200 to 7000 bp is considered suitable for use). We used 45 micrograms of labeled cRNA for fragmentation. Those samples that passed both QC steps (<10% usually fail) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. C until use (roughly one third) or were used immediately for hybridization.
-
-Dealing with ocular pigmentation: Variable ocular pigmentation is a potential confound in a study of the whole eye transcriptome. Even the most careful RNA preparations taken from brown and beige colored mice tend to have faint residual pigmentation that affects hybridization signal. To address this problem, Dr. Yan Jiao purified total RNA using the Qiagen RNeasy MinElute Cleanup Kit (Cat No. 74204) all four batches.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well balanced sample of males and females, in general without within-strain-by-sex replication. Two strains are represented by a single male sample pool (BXD29 and A/J). Four lines are represented by two or three male sample pools (all of the five DeltaGen KO line). The SJL/J may be a single mixed sex sample. Users can study possible sex effects by comparing any results of expression data to that of a surrogate measurement that summarizes the overall sex balance of HEIMED. To do this just compare your data to those of probe sets 1427262_at (Xist, high in females) and probe set 1426438_at (Ddx3y, high in males). These two sex-specific probes are quantitative surrogates for the sex balance in this data set.
-
-Technical duplicates: One sample, highlighted in the tables below, is a technical duplicate. The pair of technical duplicates were both of high quality. For statistical analysis, they should be combined and treated as single biological sample.
-
-Batch structure: This data set consists of four batches (Table 2, far right column). The final September 2008 data set consists of a total of 221 arrays and 220 independent samples.
-
-
- - Batch 1: November 2005, n = 78 arrays original arrays of which 76 were accepted into this final data set.
- - Batch 2: January 2006, n = 62 arrays of which 62 were accepted.
- - Batch 3: August 2006, n = 39 arrays of which 36 were accepted. (These three batches, including some arrays that were eventually dropped from the final 2008 data set, were combined to form the September 2006 data set.)
- - Batch 4: Summer 2008, n = 53 arrays of which 47 were accepted.
-
-
-Table 1: HEIMED case IDs, including sample tube ID, strain, age, sex, and source of mice (see Table 2 for information on array quality control)
-
-
-
-
-
-
-
-
-
-
- | Index |
- TubeID |
- Group |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- R2595E.1 |
- GDP |
- 129S1/SvImJ |
- 59 |
- F |
- UTHSC RW |
-
-
- | 2 |
- R2533E.1 |
- GDP |
- 129S1/SvImJ |
- 60 |
- M |
- UTHSC RW |
-
-
- | 3 |
- R0754E.1 |
- GDP |
- A/J |
- 60 |
- M |
- JAX |
-
-
- | 4 |
- R4521E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 5 |
- R4522E |
- KO |
- B6129P2F2N1-Clcn3 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 6 |
- R4523E |
- KO |
- B6129P2F2N1-Clcn3 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 7 |
- R4526E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- F |
- TChoi_Deltagen |
-
-
- | 8 |
- R4509E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 16 |
- M |
- TChoi_Deltagen |
-
-
- | 9 |
- R4510E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 10 |
- R4511E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 20 |
- M |
- TChoi_Deltagen |
-
-
- | 11 |
- R4524E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 19 |
- M |
- TChoi_Deltagen |
-
-
- | 12 |
- R4525E |
- KO |
- B6129P2F2N1-Gabbr1 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 13 |
- R4515E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 14 |
- R4516E |
- KO |
- B6129P2F2N1-Gabra1 |
- 69 |
- M |
- TChoi_Deltagen |
-
-
- | 15 |
- R4517E |
- KO |
- B6129P2F2N1-Gabra1 |
- 67 |
- M |
- TChoi_Deltagen |
-
-
- | 16 |
- R4512E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- F |
- TChoi_Deltagen |
-
-
- | 17 |
- R4513E |
- KO |
- B6129P2F2N1-Gnb5 |
- 25 |
- M |
- TChoi_Deltagen |
-
-
- | 18 |
- R4514E |
- KO |
- B6129P2F2N1-Gnb5 |
- 22 |
- M |
- TChoi_Deltagen |
-
-
- | 19 |
- R4518E |
- KO |
- B6129P2F2N1-Gpr19 |
- 70 |
- M |
- TChoi_Deltagen |
-
-
- | 20 |
- R4519E |
- KO |
- B6129P2F2N1-Gpr19 |
- 68 |
- M |
- TChoi_Deltagen |
-
-
- | 21 |
- R2601E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 22 |
- R2602E.1 |
- GDP BXD |
- B6D2F1 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 23 |
- R1676E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- F |
- JAX |
-
-
- | 24 |
- R1672E.1 |
- GDP |
- BALB/cByJ |
- 83 |
- M |
- JAX |
-
-
- | 25 |
- R4530E |
- GDP |
- BALB/cJ |
- 66 |
- F |
- JAX |
-
-
- | 26 |
- R4529E |
- GDP |
- BALB/cJ |
- 66 |
- M |
- JAX |
-
-
- | 27 |
- R2704E.2 |
- BXD |
- BXD1 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 28 |
- R2707E.3 |
- BXD |
- BXD1 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 29 |
- R1231E.2 |
- BXD |
- BXD2 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 30 |
- R2598E.1 |
- BXD |
- BXD2 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 31 |
- R2591E.1 |
- BXD |
- BXD5 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 32 |
- R2714E.2 |
- BXD |
- BXD5 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 33 |
- R2570E.1 |
- BXD |
- BXD6 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 34 |
- R2694E.2 |
- BXD |
- BXD6 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 35 |
- R2538E.1 |
- BXD |
- BXD8 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 36 |
- R2709E.2 |
- BXD |
- BXD8 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 37 |
- R2708E.2 |
- BXD |
- BXD9 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 38 |
- R2569E.1 |
- BXD |
- BXD9 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 39 |
- R2581E.1 |
- BXD |
- BXD11 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 40 |
- R2612E.2 |
- BXD |
- BXD11 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 41 |
- R2742E.2 |
- BXD |
- BXD12 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 42 |
- R2543E.1 |
- BXD |
- BXD12 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 43 |
- R2586E.1 |
- BXD |
- BXD13 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 44 |
- R877E.2 |
- BXD |
- BXD13 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 45 |
- R2557E.1 |
- BXD |
- BXD14 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 46 |
- R1128E.2 |
- BXD |
- BXD14 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 47 |
- R2701E.3 |
- BXD |
- BXD15 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 48 |
- R2716E.2 |
- BXD |
- BXD15 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 49 |
- R2711E.2 |
- BXD |
- BXD16 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 50 |
- R2567E.1 |
- BXD |
- BXD16 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 51 |
- R2720E.2 |
- BXD |
- BXD18 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 52 |
- R2559E.1 |
- BXD |
- BXD18 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 53 |
- R2560E.1 |
- BXD |
- BXD19 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 54 |
- R2713E.2 |
- BXD |
- BXD19 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 55 |
- R2584E.1 |
- BXD |
- BXD20 |
- 59 |
- F |
- BIDMC GR |
-
-
- | 56 |
- R2731E.2 |
- BXD |
- BXD20 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 57 |
- R2702E.2 |
- BXD |
- BXD21 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 58 |
- R2541E2.1 |
- BXD |
- BXD21 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 59 |
- R2553E.1 |
- BXD |
- BXD22 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 60 |
- R2700E.2 |
- BXD |
- BXD22 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 61 |
- R2558E-2.1 |
- BXD |
- BXD23 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 62 |
- R1086E.2 |
- BXD |
- BXD23 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 63 |
- R2719E.2 |
- BXD |
- BXD24 |
- 123 |
- F |
- UTHSC RW |
-
-
- | 64 |
- R2589E2.1 |
- BXD |
- BXD24 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 65 |
- R2573E-2.1 |
- BXD |
- BXD25 |
- 67 |
- F |
- UAB |
-
-
- | 66 |
- R2683E.2 |
- BXD |
- BXD25 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 67 |
- R2703E.2 |
- BXD |
- BXD27 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 68 |
- R2729E.3 |
- BXD |
- BXD27 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 69 |
- R2562E.3 |
- BXD |
- BXD28 |
- 60 |
- F |
- BIDMC GR |
-
-
- | 70 |
- R2721E.2 |
- BXD |
- BXD28 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 71 |
- R2561E.3 |
- BXD |
- BXD29 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 72 |
- R1258E.2 |
- BXD |
- BXD31 |
- 57 |
- F |
- UTHSC RW |
-
-
- | 73 |
- R2597E.1 |
- BXD |
- BXD31 |
- 61 |
- M |
- BIDMC GR |
-
-
- | 74 |
- R2563E.1 |
- BXD |
- BXD32 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 75 |
- R1216E.2 |
- BXD |
- BXD32 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 76 |
- R2542E.1 |
- BXD |
- BXD33 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- R857E.2 |
- BXD |
- BXD33 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 78 |
- R1451E.2 |
- BXD |
- BXD34 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 79 |
- R2585E.1 |
- BXD |
- BXD34 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 80 |
- R2698E.3 |
- BXD |
- BXD36 |
- 58 |
- F |
- BIDMC GR |
-
-
- | 81 |
- R2705E.3 |
- BXD |
- BXD36 |
- 57 |
- M |
- BIDMC GR |
-
-
- | 82 |
- R2710E.2 |
- BXD |
- BXD38 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 83 |
- R2532E.1 |
- BXD |
- BXD38 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 84 |
- R2574E.1 |
- BXD |
- BXD39 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 85 |
- R2695E.2 |
- BXD |
- BXD39 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 86 |
- R2699E.2 |
- BXD |
- BXD40 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 87 |
- R2590E.1 |
- BXD |
- BXD40 |
- 60 |
- M |
- BIDMC GR |
-
-
- | 88 |
- R2696E.2 |
- BXD |
- BXD42 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 89 |
- R2596E.1 |
- BXD |
- BXD42 |
- 59 |
- M |
- BIDMC GR |
-
-
- | 90 |
- R994E.2 |
- BXD |
- BXD43 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 91 |
- R2607E.1 |
- BXD |
- BXD43 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 92 |
- R2594E.1 |
- BXD |
- BXD44 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 93 |
- R2610E.2 |
- BXD |
- BXD44 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 94 |
- R2732E.2 |
- BXD |
- BXD45 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 95 |
- R2592E.1 |
- BXD |
- BXD45 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- R967E.2 |
- BXD |
- BXD48 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 97 |
- R2606E.1 |
- BXD |
- BXD48 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 98 |
- R2933E.3 |
- BXD |
- BXD50 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 99 |
- R2937E.3 |
- BXD |
- BXD50 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 100 |
- R2603E.1 |
- BXD |
- BXD51 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 101 |
- R1042E.2 |
- BXD |
- BXD51 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 102 |
- R2980E.3 |
- BXD |
- BXD55 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 103 |
- R2690E.2 |
- BXD |
- BXD55 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 104 |
- R4176E |
- BXD |
- BXD56 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 105 |
- R4175E |
- BXD |
- BXD56 |
- 53 |
- M |
- UTHSC RW |
-
-
- | 106 |
- R1006E.3 |
- BXD |
- BXD60 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 107 |
- R2725E.2 |
- BXD |
- BXD60 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 108 |
- R1074E.3 |
- BXD |
- BXD60 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 109 |
- R2534E2.1 |
- BXD |
- BXD61 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 110 |
- R2684E.2 |
- BXD |
- BXD61 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 111 |
- R1107E.3 |
- BXD |
- BXD62 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 112 |
- R2681E.2 |
- BXD |
- BXD62 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 113 |
- R965E.3 |
- BXD |
- BXD62 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 114 |
- R1425E.2 |
- BXD |
- BXD63 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 115 |
- R2576E.3 |
- BXD |
- BXD63 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 116 |
- R943E-2.2 |
- BXD |
- BXD64 |
- 56 |
- F |
- UTHSC RW |
-
-
- | 117 |
- R2611E.1 |
- BXD |
- BXD64 |
- 68 |
- M |
- UTHSC RW |
-
-
- | 118 |
- R2689E.2 |
- BXD |
- BXD65 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 119 |
- R2583E.1 |
- BXD |
- BXD65 |
- 60 |
- M |
- UTHSC RW |
-
-
- | 120 |
- R2728E.2 |
- BXD |
- BXD66 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 121 |
- R2536E2.1 |
- BXD |
- BXD66 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 122 |
- R1207E.2 |
- BXD |
- BXD66 |
- 83 |
- M |
- UTHSC RW |
-
-
- | 123 |
- R1192E.2 |
- BXD |
- BXD67 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 124 |
- R2727E.3 |
- BXD |
- BXD67 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 125 |
- R2691E.3 |
- BXD |
- BXD67 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 126 |
- R2551E.1 |
- BXD |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 127 |
- R2726E.2 |
- BXD |
- BXD68 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 128 |
- R2593E.1 |
- BXD |
- BXD69 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 129 |
- R975E.2 |
- BXD |
- BXD70 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 130 |
- R2537E2.1 |
- BXD |
- BXD70 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 131 |
- R4531E |
- BXD |
- BXD71 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 132 |
- R4532E |
- BXD |
- BXD71 |
- 86 |
- M |
- UTHSC RW |
-
-
- | 133 |
- R2779E.2 |
- BXD |
- BXD73 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 134 |
- R3024E.3 |
- BXD |
- BXD73 |
- 54 |
- M |
- UTHSC RW |
-
-
- | 135 |
- R2565E.1 |
- BXD |
- BXD75 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 136 |
- R1397E-re.2 |
- BXD |
- BXD75 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 137 |
- R2687E.3 |
- BXD |
- BXD77 |
- 60 |
- F |
- UTHSC RW |
-
-
- | 138 |
- R2717E.2 |
- BXD |
- BXD77 |
- 107 |
- M |
- UTHSC RW |
-
-
- | 139 |
- R1421E.3 |
- BXD |
- BXD77 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 140 |
- R2579E.1 |
- BXD |
- BXD80 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 141 |
- R2686E.2 |
- BXD |
- BXD80 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 142 |
- R2956E.3 |
- BXD |
- BXD83 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 143 |
- R2960E.3 |
- BXD |
- BXD83 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 144 |
- R2922E.3 |
- BXD |
- BXD84 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 145 |
- R2895E.3 |
- BXD |
- BXD84 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- R2692E.2 |
- BXD |
- BXD85 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 147 |
- R2715E.2 |
- BXD |
- BXD85 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 148 |
- R1405E.2 |
- BXD |
- BXD86 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 149 |
- R1225E.3 |
- BXD |
- BXD86 |
- 58 |
- M |
- UTHSC RW |
-
-
- | 150 |
- R2724E.2 |
- BXD |
- BXD87 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 151 |
- R2540E.1 |
- BXD |
- BXD87 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 152 |
- R1433E.2 |
- BXD |
- BXD89 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 153 |
- R2546E.1 |
- BXD |
- BXD89 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 154 |
- R2578E2.1 |
- BXD |
- BXD90 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 155 |
- R859E.2 |
- BXD |
- BXD90 |
- 72 |
- M |
- UTHSC RW |
-
-
- | 156 |
- R2682E.2 |
- BXD |
- BXD92 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 157 |
- R1388E.3 |
- BXD |
- BXD92 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 158 |
- R1322E.3 |
- BXD |
- BXD92 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 159 |
- R2733E.2 |
- BXD |
- BXD96 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 160 |
- R2554E.1 |
- BXD |
- BXD96 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 161 |
- R2649E.2 |
- BXD |
- BXD97 |
- 74 |
- F |
- UTHSC RW |
-
-
- | 162 |
- R2577E.1 |
- BXD |
- BXD97 |
- 55 |
- M |
- UTHSC RW |
-
-
- | 163 |
- R2645E.3 |
- BXD |
- BXD98 |
- 66 |
- F |
- UTHSC RW |
-
-
- | 164 |
- R2688E.2 |
- BXD |
- BXD98 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 165 |
- R4533E |
- BXD |
- BXD99 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 166 |
- R4534E |
- BXD |
- BXD99 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 167 |
- R2885E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 168 |
- R2883E.3 |
- GDP |
- BXSB/MpJ |
- 61 |
- M |
- BIDMC GR |
-
-
- | 169 |
- R1700E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- F |
- UTHSC RW |
-
-
- | 170 |
- R1704E.1 |
- GDP |
- C3H/HeJ |
- 83 |
- M |
- UTHSC RW |
-
-
- | 171 |
- R2605E.1 |
- GDP BXD |
- C57BL/6J |
- 79 |
- F |
- UTHSC RW |
-
-
- | 172 |
- R0871E |
- GDP BXD |
- C57BL/6J |
- 65 |
- F |
- UTHSC RW |
-
-
- | 173 |
- R0872E.1 |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 174 |
- R0872E |
- GDP BXD |
- C57BL/6J |
- 66 |
- M |
- UTHSC RW |
-
-
- | 175 |
- R4507E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 176 |
- R4508E |
- KO |
- C57BL/6J-Nyx |
- 57 |
- M |
- Geisert |
-
-
- | 177 |
- R4505E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 178 |
- R4506E |
- KO |
- C57BL/6J-Rpe65 |
- 57 |
- F |
- Geisert |
-
-
- | 179 |
- R4535E |
- GDP |
- C57BLKS/J |
- 66 |
- F |
- JAX |
-
-
- | 180 |
- R4536E |
- GDP |
- C57BLKS/J |
- 66 |
- M |
- JAX |
-
-
- | 181 |
- R2564E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- F |
- JAX |
-
-
- | 182 |
- R2580E.1 |
- GDP |
- CAST/EiJ |
- 64 |
- M |
- JAX |
-
-
- | 183 |
- R4537E |
- GDP |
- CBA/CaJ |
- 66 |
- F |
- JAX |
-
-
- | 184 |
- R4538E |
- GDP |
- CBA/CaJ |
- 66 |
- M |
- JAX |
-
-
- | 185 |
- R4539E |
- GDP |
- CZECHII/EiJ |
- 66 |
- F |
- JAX |
-
-
- | 186 |
- R4540E |
- GDP |
- CZECHII/EiJ |
- 66 |
- M |
- JAX |
-
-
- | 187 |
- R2600E.1 |
- GDP BXD |
- D2B6F1 |
- 72 |
- F |
- UTHSC RW |
-
-
- | 188 |
- R2604E.1 |
- GDP BXD |
- D2B6F1 |
- 69 |
- M |
- UTHSC RW |
-
-
- | 189 |
- R1002E.3 |
- GDP BXD |
- DBA/2J |
- 72 |
- F |
- UTHSC RW |
-
-
- | 190 |
- R4541E |
- GDP BXD |
- DBA/2J |
- 65 |
- F |
- JAX |
-
-
- | 191 |
- R959E.3 |
- GDP BXD |
- DBA/2J |
- 60 |
- M |
- UTHSC RW |
-
-
- | 192 |
- R2572E.1 |
- GDP BXD |
- DBA/2J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 193 |
- R4542E |
- GDP BXD |
- DBA/2J |
- 59 |
- M |
- JAX |
-
-
- | 194 |
- R2771E.3 |
- GDP |
- FVB/NJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 195 |
- R2772E.3 |
- GDP |
- FVB/NJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 196 |
- R2636E.1 |
- GDP |
- KK/HlJ |
- 64 |
- F |
- UTHSC RW |
-
-
- | 197 |
- R2637E.1 |
- GDP |
- KK/HlJ |
- 64 |
- M |
- UTHSC RW |
-
-
- | 198 |
- R0999E.1 |
- GDP |
- LG/J |
- 57 |
- F |
- UTHSC RW |
-
-
- | 199 |
- R1004E.1 |
- GDP |
- LG/J |
- 65 |
- M |
- UTHSC RW |
-
-
- | 200 |
- R4543E |
- GDP |
- LP/J |
- 65 |
- F |
- JAX |
-
-
- | 201 |
- R4544E |
- GDP |
- LP/J |
- 65 |
- M |
- JAX |
-
-
- | 202 |
- R2858E.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- F |
- BIDMC GR |
-
-
- | 203 |
- R2919.3 |
- GDP |
- MOLF/EiJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 204 |
- R1688E.1 |
- GDP |
- NOD/LtJ |
- 66 |
- F |
- JAX |
-
-
- | 205 |
- R2566E-2.1 |
- GDP |
- NOD/LtJ |
- 76 |
- M |
- UTHSC RW |
-
-
- | 206 |
- R4545E |
- GDP |
- NZB/BlNJ |
- 61 |
- F |
- BIDMC GR |
-
-
- | 207 |
- R4546E |
- GDP |
- NZB/BlNJ |
- 58 |
- M |
- BIDMC GR |
-
-
- | 208 |
- R2535E.1 |
- GDP |
- NZO/HlLtJ |
- 62 |
- F |
- JAX |
-
-
- | 209 |
- R2550E.1 |
- GDP |
- NZO/HlLtJ |
- 96 |
- M |
- JAX |
-
-
- | 210 |
- R2817E.3 |
- GDP |
- NZW/LacJ |
- 65 |
- F |
- BIDMC GR |
-
-
- | 211 |
- R2810E |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 212 |
- R2810E.3 |
- GDP |
- NZW/LacJ |
- 60 |
- M |
- BIDMC GR |
-
-
- | 213 |
- R4547E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- F |
- JAX |
-
-
- | 214 |
- R4548E |
- GDP |
- PANCEVO/EiJ |
- 68 |
- M |
- JAX |
-
-
- | 215 |
- R2635E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- F |
- JAX |
-
-
- | 216 |
- R2634E.1 |
- GDP |
- PWD/PhJ |
- 62 |
- M |
- JAX |
-
-
- | 217 |
- R2544E.1 |
- GDP |
- PWK/PhJ |
- 63 |
- F |
- JAX |
-
-
- | 218 |
- R2549E.1 |
- GDP |
- PWK/PhJ |
- 83 |
- M |
- JAX |
-
-
- | 219 |
- R4550E |
- GDP |
- SJL/J |
- 65 |
- M+F |
- JAX |
-
-
- | 220 |
- R2368E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- F |
- UTHSC RW |
-
-
- | 221 |
- R2547E.1 |
- GDP |
- WSB/EiJ |
- 67 |
- M |
- UTHSC RW |
-
-
-
- |
-
-
-
diff --git a/general/datasets/FT_2A_0605_Rz/acknowledgment.rtf b/general/datasets/FT_2A_0605_Rz/acknowledgment.rtf
deleted file mode 100644
index f6b54b6..0000000
--- a/general/datasets/FT_2A_0605_Rz/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Intiative; to NH from the German Ministry for Science and Education (National Genome Research Network, NGFN); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. MP is an International Research Scholar of the Howard Hughes Medical Institute.
diff --git a/general/datasets/FT_2A_0605_Rz/cases.rtf b/general/datasets/FT_2A_0605_Rz/cases.rtf
deleted file mode 100644
index f953b8d..0000000
--- a/general/datasets/FT_2A_0605_Rz/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv or HSR = H) and Brown Norway (BN.Lx/Cub= B). These parental strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-The HXB strains were generated by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were generated by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 60th generation of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of kidney and fat (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commercial rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 degrees C. Rats were sexually naive. All males used in the initial transcriptome studies (Hubner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protection Law of the Czech Republic (311/1997).
-
diff --git a/general/datasets/FT_2A_0605_Rz/notes.rtf b/general/datasets/FT_2A_0605_Rz/notes.rtf
deleted file mode 100644
index 815c6d4..0000000
--- a/general/datasets/FT_2A_0605_Rz/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This approved text file originally generated by Robert Williams, Norbert Hubner, Michal Pravenec, Timothy Aitman, April 19, 2005. Updated by RWW, April 20, 2005; April 28, 2005. June 15, 2005 by RWW and SY; June 20 by RWW and NH.
-
-
diff --git a/general/datasets/FT_2A_0605_Rz/platform.rtf b/general/datasets/FT_2A_0605_Rz/platform.rtf
deleted file mode 100644
index 238952f..0000000
--- a/general/datasets/FT_2A_0605_Rz/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 230A GeneChip: Expression data were generated using 230A array. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
diff --git a/general/datasets/FT_2A_0605_Rz/processing.rtf b/general/datasets/FT_2A_0605_Rz/processing.rtf
deleted file mode 100644
index e119fda..0000000
--- a/general/datasets/FT_2A_0605_Rz/processing.rtf
+++ /dev/null
@@ -1,25 +0,0 @@
-Probe and Probe set data: The original cell-level files (in text format) were downloaded from Array Express. These files were then converted to a standard Affymetrix CEL file (old MAS5 style) format using a Perl script written by Senhua Yu. These files were then processed as a large batch (either all 130 arrays or the final 124 arrays) using a custom quantile normalization program written by KF Manly. The output of this program automatically performs the log normalization and variance stabilization at the probe level. We then computed the mean and standard error for each strain using these normalized probe data.
-
-Probe set data were generated starting with the raw Affymetrix CEL file described above (prior to any normalization) and were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003).
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized variance of 2 units within each array). Data were further transformed as follows:
-
-
- - Step 1: RMA values were generated as described above.
- - Step 2: We computed the Z scores for each probe set value for each array.
- - Step 3: We multiplied all Z scores by 2.
- - Step 4: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 5: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for background beyond the background correction implemented by Affymetrix.
-
-
-All transformation steps were carried out by Senhua Yu at UTHSC.
-
-About Quality Control Procedures:
-
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. Fat samples were processed using the Enzo Diagnostics Bioarray High Yield RNA Transcript labeling kit. See Hubner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control assays.
-
-Probe level QC: All 130 CEL files were collected into a single DataDesk 6.2 analysis file. Probe data from pairs of arrays were plotted and compared after quantile normalization. Six arrays were considered potential outliers (despite having passed RNA quality control) and in the interest of minimizing technical variance, a decision was made to withhold them from the calculation of strain means. The remaining 124 arrays were then quantile normalized again and reexamined in DataDesk to ensure reasonable colinearity of all final array data sets.
-
-Strain assignment check: To confirm strain assignment we exploit a set of transcripts with near-Mendelian segregation patterns (search for "test Mendelian"). Strain means with both intermediate expression values AND unusually high error terms often indicate at a misassignment of a case to a particular strain. This error checking has identified 4 strains with possible errors in this data set.
-
-
diff --git a/general/datasets/FT_2A_0605_Rz/summary.rtf b/general/datasets/FT_2A_0605_Rz/summary.rtf
deleted file mode 100644
index f522e76..0000000
--- a/general/datasets/FT_2A_0605_Rz/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-This June 2005 data set provides estimates of mRNA expression in normal peritoneal fat of 32 strains of rats. The set includes the hypertensive SHR strain, the normotensive BN strain, and 30 HXB/BXH recombinant inbred strains. Each strain was sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin-Buch, by Norbert Hubner and colleagues. Transcriptome mapping was carried out by Norbert Hubner, Timothy Aitman and colleagues at the MDC and the MRC Clinicial Sciences Centre, Imperial College London (ICL). Samples were hybridized individually to a total of 130 Affymetrix RAE230A array. This particular data set includes 124 arrays processed using the RMA protocol. RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units (2ZPlus8). This data set complements the MAS5 data set exploited by Hubner and colleagues 2005. Download the particular transform in an Excel work book with both strain means and SEMs.
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/FT_2A_0605_Rz/tissue.rtf b/general/datasets/FT_2A_0605_Rz/tissue.rtf
deleted file mode 100644
index 85eb931..0000000
--- a/general/datasets/FT_2A_0605_Rz/tissue.rtf
+++ /dev/null
@@ -1,542 +0,0 @@
-All tissues were collected at the age of 6 weeks. Peritoneal fat pads were rapidly dissected and cleaned extraneous tissue, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction.
-
-The table below lists 130 arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat. Six arrays marked with asterisks were eventually excluded.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN5 |
-
-
- | BN |
- BN6 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH10 |
- RI 10c-5 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH2 |
- RI 02c-5 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- *RI 05c-3 |
-
-
- | BXH5 |
- RI 05c-5 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-4 |
-
-
- | BXH6 |
- RI 06c-5 |
-
-
- | BXH6 |
- RI 06c-6 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH8 |
- RI 08c-5 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH9 |
- RI 09c-5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB1 |
- RI 01-5 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB10 |
- RI 10-5 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-5 |
-
-
- | HXB15 |
- RI 15-6 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- *RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- *RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- RI 02-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- *RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- *RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- RI 24-5 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- RI 25-4 |
-
-
- | HXB25 |
- RI 25-5 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- *RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-4 |
-
-
- | HXB29 |
- RI 29-5 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR6 |
-
-
- | HSR |
- HSR7 |
-
-
- | HSR |
- HSR8 |
-
-
-
- |
-
-
-
-
-*: These six arrays were excluded in the final strain summary data. See section of Quality Control for further explanation.
diff --git a/general/datasets/FT_2A_0805_M/acknowledgment.rtf b/general/datasets/FT_2A_0805_M/acknowledgment.rtf
deleted file mode 100644
index f6b54b6..0000000
--- a/general/datasets/FT_2A_0805_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Intiative; to NH from the German Ministry for Science and Education (National Genome Research Network, NGFN); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. MP is an International Research Scholar of the Howard Hughes Medical Institute.
diff --git a/general/datasets/FT_2A_0805_M/cases.rtf b/general/datasets/FT_2A_0805_M/cases.rtf
deleted file mode 100644
index f953b8d..0000000
--- a/general/datasets/FT_2A_0805_M/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-We have exploited a set of HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv or HSR = H) and Brown Norway (BN.Lx/Cub= B). These parental strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-The HXB strains were generated by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were generated by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 60th generation of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of kidney and fat (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commercial rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 degrees C. Rats were sexually naive. All males used in the initial transcriptome studies (Hubner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protection Law of the Czech Republic (311/1997).
-
diff --git a/general/datasets/FT_2A_0805_M/notes.rtf b/general/datasets/FT_2A_0805_M/notes.rtf
deleted file mode 100644
index 815c6d4..0000000
--- a/general/datasets/FT_2A_0805_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This approved text file originally generated by Robert Williams, Norbert Hubner, Michal Pravenec, Timothy Aitman, April 19, 2005. Updated by RWW, April 20, 2005; April 28, 2005. June 15, 2005 by RWW and SY; June 20 by RWW and NH.
-
-
diff --git a/general/datasets/FT_2A_0805_M/platform.rtf b/general/datasets/FT_2A_0805_M/platform.rtf
deleted file mode 100644
index 238952f..0000000
--- a/general/datasets/FT_2A_0805_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 230A GeneChip: Expression data were generated using 230A array. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
diff --git a/general/datasets/FT_2A_0805_M/processing.rtf b/general/datasets/FT_2A_0805_M/processing.rtf
deleted file mode 100644
index e119fda..0000000
--- a/general/datasets/FT_2A_0805_M/processing.rtf
+++ /dev/null
@@ -1,25 +0,0 @@
-Probe and Probe set data: The original cell-level files (in text format) were downloaded from Array Express. These files were then converted to a standard Affymetrix CEL file (old MAS5 style) format using a Perl script written by Senhua Yu. These files were then processed as a large batch (either all 130 arrays or the final 124 arrays) using a custom quantile normalization program written by KF Manly. The output of this program automatically performs the log normalization and variance stabilization at the probe level. We then computed the mean and standard error for each strain using these normalized probe data.
-
-Probe set data were generated starting with the raw Affymetrix CEL file described above (prior to any normalization) and were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003).
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized variance of 2 units within each array). Data were further transformed as follows:
-
-
- - Step 1: RMA values were generated as described above.
- - Step 2: We computed the Z scores for each probe set value for each array.
- - Step 3: We multiplied all Z scores by 2.
- - Step 4: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 5: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for background beyond the background correction implemented by Affymetrix.
-
-
-All transformation steps were carried out by Senhua Yu at UTHSC.
-
-About Quality Control Procedures:
-
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. Fat samples were processed using the Enzo Diagnostics Bioarray High Yield RNA Transcript labeling kit. See Hubner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control assays.
-
-Probe level QC: All 130 CEL files were collected into a single DataDesk 6.2 analysis file. Probe data from pairs of arrays were plotted and compared after quantile normalization. Six arrays were considered potential outliers (despite having passed RNA quality control) and in the interest of minimizing technical variance, a decision was made to withhold them from the calculation of strain means. The remaining 124 arrays were then quantile normalized again and reexamined in DataDesk to ensure reasonable colinearity of all final array data sets.
-
-Strain assignment check: To confirm strain assignment we exploit a set of transcripts with near-Mendelian segregation patterns (search for "test Mendelian"). Strain means with both intermediate expression values AND unusually high error terms often indicate at a misassignment of a case to a particular strain. This error checking has identified 4 strains with possible errors in this data set.
-
-
diff --git a/general/datasets/FT_2A_0805_M/summary.rtf b/general/datasets/FT_2A_0805_M/summary.rtf
deleted file mode 100644
index f522e76..0000000
--- a/general/datasets/FT_2A_0805_M/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-This June 2005 data set provides estimates of mRNA expression in normal peritoneal fat of 32 strains of rats. The set includes the hypertensive SHR strain, the normotensive BN strain, and 30 HXB/BXH recombinant inbred strains. Each strain was sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin-Buch, by Norbert Hubner and colleagues. Transcriptome mapping was carried out by Norbert Hubner, Timothy Aitman and colleagues at the MDC and the MRC Clinicial Sciences Centre, Imperial College London (ICL). Samples were hybridized individually to a total of 130 Affymetrix RAE230A array. This particular data set includes 124 arrays processed using the RMA protocol. RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units (2ZPlus8). This data set complements the MAS5 data set exploited by Hubner and colleagues 2005. Download the particular transform in an Excel work book with both strain means and SEMs.
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/FT_2A_0805_M/tissue.rtf b/general/datasets/FT_2A_0805_M/tissue.rtf
deleted file mode 100644
index 85eb931..0000000
--- a/general/datasets/FT_2A_0805_M/tissue.rtf
+++ /dev/null
@@ -1,542 +0,0 @@
-All tissues were collected at the age of 6 weeks. Peritoneal fat pads were rapidly dissected and cleaned extraneous tissue, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction.
-
-The table below lists 130 arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat. Six arrays marked with asterisks were eventually excluded.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN5 |
-
-
- | BN |
- BN6 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH10 |
- RI 10c-5 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH2 |
- RI 02c-5 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- *RI 05c-3 |
-
-
- | BXH5 |
- RI 05c-5 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-4 |
-
-
- | BXH6 |
- RI 06c-5 |
-
-
- | BXH6 |
- RI 06c-6 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH8 |
- RI 08c-5 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH9 |
- RI 09c-5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB1 |
- RI 01-5 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB10 |
- RI 10-5 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-5 |
-
-
- | HXB15 |
- RI 15-6 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- *RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- *RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- RI 02-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- *RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- *RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- RI 24-5 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- RI 25-4 |
-
-
- | HXB25 |
- RI 25-5 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- *RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-4 |
-
-
- | HXB29 |
- RI 29-5 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR6 |
-
-
- | HSR |
- HSR7 |
-
-
- | HSR |
- HSR8 |
-
-
-
- |
-
-
-
-
-*: These six arrays were excluded in the final strain summary data. See section of Quality Control for further explanation.
diff --git a/general/datasets/G2HEIONCRetILM6_0911/acknowledgment.rtf b/general/datasets/G2HEIONCRetILM6_0911/acknowledgment.rtf
deleted file mode 100644
index a41ff76..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/acknowledgment.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The HEI Retinal Database is supported by National Eye Institute Grants:
-
-
-
-
- - R01EY017841 (Dr. Eldon E. Geisert, PI)
-
-
- - P030EY13080 (NEI Vision Core Grant), and
-
-
- - A Unrestricted Grand from Research to Prevent Blindness (Dr. Barrett Haik, PI)
-
diff --git a/general/datasets/G2HEIONCRetILM6_0911/cases.rtf b/general/datasets/G2HEIONCRetILM6_0911/cases.rtf
deleted file mode 100644
index b37d700..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/cases.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 48 and maximum age is 118 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J.
-
-BXD strains:
-
-
- - The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s.
- - In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset.
- - The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set.
-
-
-
-
-What Makes the G2 HEI Retina Database different from the HEI Retina Database Examination of Gfap expression across all of the strains in the HEI Retinal Dataset, reveals that some strains express very high levels of Gfap relative to others. For example, BXD24 expresses Gfap at a 9-fold higher level, than BXD22. It has been established that BXD24 acquired a mutation in Cep290 that results in early onset photoreceptor degeneration (Chang et al., 2006). This degeneration results in reactive gliosis throughout the retina. In addition to BXD24, other BXD strains expressed very high levels of Gfap including: BXD32, BXD49, BXD70, BXD83 and BXD89. For the G2 dataset all of these strains with potential reactive gliosis were removed from the dataset.
diff --git a/general/datasets/G2HEIONCRetILM6_0911/experiment-design.rtf b/general/datasets/G2HEIONCRetILM6_0911/experiment-design.rtf
deleted file mode 100644
index 4fff707..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/experiment-design.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Expression profiling by array
-
-We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.
-
-All normalization was performed by William E. Orr in the HEI Vision Core Facility
-
-
- - Computed the log base 2 of each raw signal value
- - Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
- - Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
diff --git a/general/datasets/G2HEIONCRetILM6_0911/notes.rtf b/general/datasets/G2HEIONCRetILM6_0911/notes.rtf
deleted file mode 100644
index 13ff99a..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/G2HEIONCRetILM6_0911/platform.rtf b/general/datasets/G2HEIONCRetILM6_0911/platform.rtf
deleted file mode 100644
index 2c52707..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina MouseWG-6 v2.0 arrays: The Illumina Sentrix Mouse-6 BeadChip uses 50-nucleotide probes to interrogate approximately 46,000 sequences from the mouse transcriptome. For each array, the RNA was pooled from two retinas.
diff --git a/general/datasets/G2HEIONCRetILM6_0911/processing.rtf b/general/datasets/G2HEIONCRetILM6_0911/processing.rtf
deleted file mode 100644
index 97cc2be..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/processing.rtf
+++ /dev/null
@@ -1,2654 +0,0 @@
-Values of all 45,281 probe sets in this data set range from a low of 6.25 (Rho GTPase activating protein 11A, Arhgap11a, probe ID ILMN_2747167) to a high of 18.08 (Ubiquitin B, Ubb, probe ID ILMN_2516699). This corresponds to 11.83 units or a 1 to 3641 dynamic range of expression (2^11.83). We normalized raw signal values using Beadstudio’s rank invariant normalization algorithm. BXD62 was the strain used as the control group
-
-
-
-Sample Processing: Drs. Natalie E. Freeman-Anderson and Justin P. Templeton extracted the retinas from the mice and Dr. Natalie Freeman-Anderson processed all samples in the HEI Vision Core Facility. The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX) listed above. The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system. The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA. The cRNA for each sample was then hybridized to an Illumina Sentrix® Mouse-6-V2 BeadChip (Illumina, San Diego, CA)
-
-
-
-
-
-Quality control analysis of the raw image data was performed using the Illumina BeadStudio software. MIAME standards were used for all microarray data. Rank invariant normalization with BeadStudio software was used to calculate the data. Once this data was collected, the data was globally normalized across all samples using the formula 2 (z-score of log2 [intensity]) + 8.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.
-
-Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice
-
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain |
- Age |
- Sex |
- Source of Animal |
-
-
- | 1 |
- 121608_11-C57BL/6JcFA |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 2 |
- 121608_12-C57BL/6JcFB |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 3 |
- KA7444-C57BL/6JcMC |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 4 |
- KA7444-C57BL/6JcMD |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 5 |
- 31209.05-DBA2JcFA |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 6 |
- 31209.05-DBA2JcFB |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 7 |
- 121608_13-DBA/2JcMA |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 8 |
- 121608_14-DBA/2JcMB |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 9 |
- KA7446-B6D2F1cFA |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 10 |
- KA7446-B6D2F1cFB |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 11 |
- KA7446-B6D2F1cMC |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 12 |
- KA7446-B6D2F1cMD |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 13 |
- KA7466-D2B6F1cFA |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 14 |
- KA7466-D2B6F1cFB |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 15 |
- KA7466-D2B6F1cMC |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 16 |
- KA7466-D2B6F1cMD |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 17 |
- 82609.13-1cFA |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 18 |
- 82609.14-1cFB |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 19 |
- KA7389-1cFA |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 20 |
- KA7389-1cFB |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 21 |
- KA7389-1cMC |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 22 |
- KA7389-1cMD |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 23 |
- KA7300-2cFA |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 24 |
- KA7300-2cFB |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 25 |
- 100909.01-2cMA |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 26 |
- 100909.02-2cMB |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 27 |
- KA6699-5cFA |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 28 |
- KA6699-5cFB |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 29 |
- KA6699-5cFC |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 30 |
- KA6699-5cFD |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 31 |
- 82609.09-5cMA |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 32 |
- 82609.1-5cMB |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 33 |
- KA6763-6cFA |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 34 |
- KA6763-6cFB |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 35 |
- 81209.06-6cMA |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 36 |
- 81209.07-6cMB |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 37 |
- 82609.07-8cFA |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 38 |
- 82609.08-8cFB |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 39 |
- JAX-8cMA |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 40 |
- JAX-8cMB |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 41 |
- KA7289-9cFA |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 42 |
- KA7289-9cFB |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 43 |
- KA7289-9cMC |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 44 |
- KA7289-9cMD |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 45 |
- JAX-11cFA |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 46 |
- JAX-11cFB |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 47 |
- JAX-11cMC |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 48 |
- JAX-11cMD |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 49 |
- 40209.07-12cFA |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 50 |
- 40209.08-12cFB |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 51 |
- 011309.01-12cMA |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 52 |
- 011309.02-12cMB |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 53 |
- KA7286-13cFA |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 54 |
- KA7286-13cFB |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 55 |
- KA7286-13cMC |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 56 |
- KA7286-13cMD |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 57 |
- KA7302-14cFA |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 58 |
- KA7302-14cFB |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 59 |
- 100909.05-14cMA |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 60 |
- 100909.06-14cMB |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 61 |
- KA7288-15cFA |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 62 |
- KA7288-15cFB |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 63 |
- KA7288-15cMC |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 64 |
- KA7288-15cMD |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 65 |
- 062509.01-16cFA |
- BXD16 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 66 |
- KA7267-16cMA |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 67 |
- KA7267-16cMB |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 68 |
- KA6686-18cFB |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 69 |
- KA6686-18cFC |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 70 |
- KA6686-18cME |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 71 |
- KA6686-18cMF |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 72 |
- KA6676-19cFB |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 73 |
- KA6676-19cFC |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 74 |
- KA6676-19cME |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 75 |
- KA6676-19cMF |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 76 |
- 060409.05-20cFA |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- 060409.06-20cFB |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 78 |
- 021909.03-20cMA |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 79 |
- 021909.04-20cMB |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 80 |
- 82609.02-21cFC |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 81 |
- 82609.03-21cFD |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 82 |
- 121709.01-21cMA |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 83 |
- 121709.02-21cMB |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 84 |
- 121709.03-22cFA |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 85 |
- 121709.04-22cFB |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 86 |
- 092308_03-22cMA |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 87 |
- 092308_04-22cMB |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 88 |
- 80409.01-24AcFA |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 89 |
- 080409_02_24AcFB |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 90 |
- 82609.26-24AcFC |
- BXD24A |
- 64 |
- F |
- UTHSC RW |
-
-
- | 91 |
- 81209.03-24AcMC |
- BXD24A |
- 62 |
- M |
- UTHSC RW |
-
-
- | 92 |
- KA6678-24cFA |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 93 |
- KA6678-24cFB |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 94 |
- KA6678-24cME |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 95 |
- KA6678-24cMF |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- 060409.07-27cFA |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 97 |
- 060409.08-27cFB |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 98 |
- 80409.03-27cMA |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 99 |
- 80409.04-27cMB |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 100 |
- JAX-28cFA |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 101 |
- JAX-28cFB |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 102 |
- JAX-28cMC |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 103 |
- JAX-28cMD |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 104 |
- 82609.11-29cFA |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 105 |
- 82609.12-29cFB |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 106 |
- 82609.04-29cMA |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 107 |
- 82609.05-29cMB |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 108 |
- JAX-31cMB |
- BXD 31 |
- 56 |
- M |
- JAX |
-
-
- | 109 |
- JAX-31cFC |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 110 |
- JAX-31cFD |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 111 |
- 011309.03-32cFA |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 112 |
- 011309.04-32cFB |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 113 |
- KA7318-32cFC |
- BXD32 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 114 |
- KA7319-32cMA |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 115 |
- KA7319-32cMB |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 116 |
- 100909.07-33cFA |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 117 |
- 100909.08-33cFB |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 118 |
- 022609.01-33cMA |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 119 |
- 022609.02-33cMB |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 120 |
- KA7416-34cFA |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 121 |
- KA7416-34cFB |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 122 |
- KA6321-34cMA |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 123 |
- KA6321-34cMB |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 124 |
- 060409.01-36cFA |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 125 |
- 060409.02-36cFB |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 126 |
- 060409.03-36cMC |
- BXD36 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 127 |
- KA6702-38cFA |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 128 |
- KA6702-38cFB |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 129 |
- 82609.24-38cFA |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 130 |
- 82609.25-38cFB |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 131 |
- 100909.03-38cMA |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 132 |
- 100909.04-38cMB |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 133 |
- 022609.05-39cFA |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 134 |
- 022609.06-39cFB |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 135 |
- 31209.01-39cMC |
- BXD39 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 136 |
- 92409.01-40cFA |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 137 |
- 92409.02-40cFB |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 138 |
- KA6173-40cMA |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 139 |
- KA6173-40cMB |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 140 |
- KA6173-40cMC |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 141 |
- 091809.01-42cFA |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 142 |
- 091809.02-42cFB |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 143 |
- 021909.01-42cFA |
- BXD42 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 144 |
- 011309.06-42cMA |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 145 |
- 011309.07-42cMB |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- 110408_02-43cFA |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 147 |
- 110408_03-43cFB |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 148 |
- KA6158-43cMA |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 149 |
- KA6158-43cMB |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 150 |
- 100308_01-44cFA |
- BXD44 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 151 |
- 102208_02-44cMD |
- BXD44 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 152 |
- 103009.03-45cFA |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 153 |
- 103009.04-45cFB |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 154 |
- 022609.03-45cFA |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 155 |
- 022609.04-45cFB |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 156 |
- 40309.05-45cMB |
- BXD45 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 157 |
- 40209.05-48cFB |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 158 |
- 40209.06-48cFC |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 159 |
- 81209.04-48cMA |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 160 |
- 81209.05-48cMB |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 161 |
- 81209.08-49cFA |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 162 |
- 81209.09-49cFB |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 163 |
- 40209.01-49cMA |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 164 |
- 40209.02-49cMB |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 165 |
- 40209.03-49cMC |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 166 |
- KA737850cFA |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 167 |
- KA737850cFB |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 168 |
- 121908_01-50cMA |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 169 |
- 121908_02-50cMB |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 170 |
- 111208_01-51cFA |
- BXD51 |
- 99 |
- F |
- UTHSC RW |
-
-
- | 171 |
- 102208_03-51cMA |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 172 |
- 102208_04-51cMB |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 173 |
- 090208_14-53BcFA |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 174 |
- 090208_15-53BcFB |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 175 |
- 090208_16-53BcMC |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 176 |
- 090208_17-53BcMD |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 177 |
- 111208_05-55cFB |
- BXD55 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 178 |
- KA6183-55cMA |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 179 |
- KA6183-55cMB |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 180 |
- KA7362-56cFB |
- BXD 56 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 181 |
- KA6088-56cMA |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 182 |
- KA6088-56cMB |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 183 |
- KA6088-56cMC |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 184 |
- 21810.01-60RFA |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 185 |
- 21810.02-60RFB |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 186 |
- 21810.02-60RFC |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 187 |
- SQ7325-60cMA |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 188 |
- SQ7325-60cMB |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 189 |
- 092308_10-61cFA |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 190 |
- 092308_11-61cFB |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 191 |
- 31909.01-61cMA |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 192 |
- 31909.02-61cMB |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 193 |
- KA7462-62cFA |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 194 |
- KA7462-62cFB |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 195 |
- KA5996-62cMA |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 196 |
- KA5996-62cMB |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 197 |
- KA5996-62cMC |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 198 |
- 090309.01-63cFA |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 199 |
- 090309.02-63cFB |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 200 |
- 110609.01-63cMA |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 201 |
- 110609.02-63cMB |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 202 |
- 091809.03-65cFA |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 203 |
- 091809.04-65cFB |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 204 |
- 103009.01-65cMA |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 205 |
- 103009.02-65cMB |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 206 |
- 110408_05-66cFB |
- BXD66 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 207 |
- KA7165-66cMA |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 208 |
- KA7165-66cMB |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 209 |
- 90809.01-67cMA |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 210 |
- 90809.02-67cMB |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 211 |
- 110609.03-67cFA |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 212 |
- 110609.04-67cFB |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 213 |
- 120408_01-68cFA |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 214 |
- 120408_02-68cFB |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 215 |
- SQ7205-68cMA |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 216 |
- SQ7205-68cMB |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 217 |
- KA6316-68cMA |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 218 |
- KA6316-68cMB |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 219 |
- KA6316-68cMC |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 220 |
- KA76-69cFA |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 221 |
- KA76-69cFB |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 222 |
- KA6074-69cMA |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 223 |
- KA6074-69cMB |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 224 |
- 121608_01-70cFA |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 225 |
- 121608_02-70cFB |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 226 |
- KA7394-70cMA |
- BXD70 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 227 |
- 81209.08-70cMA |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 228 |
- 81209.09-70cMB |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 229 |
- 052809.01-71cFA |
- BXD71 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 230 |
- 060409.09-71cMA |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 231 |
- 060409.10-71cMB |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 232 |
- 40809.01-73cFA |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 233 |
- 40809.02-73cFB |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 234 |
- 111708_01-73cFA |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 235 |
- 111708_01-73cFB |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 236 |
- KA6164-73cMB |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 237 |
- KA6164-73cMC |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 238 |
- 82609.22-74cFA |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 239 |
- 82609.23-74cFB |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 240 |
- 82609.20-74cMA |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 241 |
- 82609.21-74cMB |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 242 |
- KA733675cFA |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 243 |
- KA733675cFB |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 244 |
- KA38-75cMB |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 245 |
- KA38-75cMC |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 246 |
- 41509.01-77cFA |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 247 |
- 41509.02-77cFB |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 248 |
- 41509.03-77cMC |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 249 |
- 41509.04-77cMD |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 250 |
- 121608_03-80cFA |
- BXD80 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 251 |
- 121608_05-80cMC |
- BXD80 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 252 |
- KA23-80cMC |
- BXD80 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 253 |
- KA7305-81cFA |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 254 |
- KA7305-81cFB |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 255 |
- KA7305-81cMD |
- BXD81 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 256 |
- 060409.11-83cFA |
- BXD83 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 257 |
- KA24-83cFA |
- BXD83 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 258 |
- 121608_07-83cMA |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 259 |
- 121608_08-83cMB |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 260 |
- KA24-83cMD |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 261 |
- 090409.05-84cFA |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 262 |
- 090409.06-84cFB |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 263 |
- KA6203-84cMA |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 264 |
- KA6203-84cMB |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 265 |
- 40309.02-85cFD |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 266 |
- 40309.03-85cFE |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 267 |
- 32609.01-85cMA |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 268 |
- 32609.02-85cMB |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 269 |
- 41509.05-86cFA |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 270 |
- 41509.06-86cFB |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 271 |
- KA6101-86cMA |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 272 |
- KA6101-86cMC |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 273 |
- 070909.02-87cFA |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 274 |
- 070909.03-87cFB |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 275 |
- KA7407-87cMA |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 276 |
- KA7407-87cMB |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 277 |
- 102208_05-89cFA |
- BXD89 |
- 82 |
- F |
- UTHSC RW |
-
-
- | 278 |
- KA5974-89cMA |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 279 |
- KA5974-89cMB |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 280 |
- 102208_06-89cMC |
- BXD89 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 281 |
- 72309.01-90cFA |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 282 |
- 72309.02-90cFB |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 283 |
- 090409.03-90cMA |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 284 |
- 090409.04-90cMB |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 285 |
- KA6094-92cMA |
- BXD92 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 286 |
- 020609.01-95cFA |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 287 |
- 020609.02-95cFB |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 288 |
- KA6181-95cMA |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 289 |
- KA6181-95cMB |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 290 |
- 31209.03-96cFA |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 291 |
- 31209.04-96cFB |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 292 |
- KA7246-96cMA |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 293 |
- KA7246-96cMB |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 294 |
- 81209.10-97cFA |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 295 |
- 81209.11-97cFB |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 296 |
- 81209.1-97cMA |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 297 |
- 81209.11-97cMB |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 298 |
- SQ7520-98cFA |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 299 |
- SQ7520-98cFB |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 300 |
- SQ7520-98cMC |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 301 |
- SQ7520-98cMD |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 302 |
- 82609.17-99cFA |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 303 |
- 82609.18-99cFB |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 304 |
- 81409.01-99cMA |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 305 |
- 81409.02-99cMB |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 306 |
- 121608_09-100cFA |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 307 |
- 121608_10-100cFB |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 308 |
- KA6001-100cMA |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 309 |
- KA6001-100cMB |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 310 |
- 81209.12-101cFA |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 311 |
- 81209.13-101cFB |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 312 |
- KA7296-101cMA |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 313 |
- KA7296-101cMB |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 314 |
- 92409.03-102cFA |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 315 |
- 92409.04-102cFB |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 316 |
- KA7380-102cMA |
- BXD102 |
- 115 |
- M |
- UTHSC RW |
-
-
- | 317 |
- 43009.01-103cFA |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 318 |
- 43009.02-103cFB |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 319 |
- KA79-103cFA |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 320 |
- KA79-103cFB |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 321 |
- KA79-103cMC |
- BXD103 |
- 48 |
- M |
- UTHSC RW |
-
-
- | 322 |
- 82609.15-103cMA |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 323 |
- 82609.16-103cMB |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 324 |
- 102909.01-BALBCcFA |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 325 |
- 102909.02-BALBCcFB |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 326 |
- 102909.03-BALBCcMA |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
- | 327 |
- 102909.04-BALBCcMB |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/G2HEIONCRetILM6_0911/summary.rtf b/general/datasets/G2HEIONCRetILM6_0911/summary.rtf
deleted file mode 100644
index 44e98a7..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/summary.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-
-This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork.
-
-HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified.
-
-COMMENT on FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set.
-
-The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as BXD24/TyJ-Cep290/J, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243).
-
-The data are now open and available for analysis.
-
-Please cite: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text PDF or HTML
-
-This is rank invariant expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.25 to 18.08 (11.83 units), a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.
-
-The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842.
-
-The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.
-
-
-
-
-Other Related Publications
-
-
-
-
-
- - Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (Link)
- - Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674
- - Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (Link)
- - Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90.(Link)
-
-
-
-
-
-
-
-Other Data Sets Users of these mouse retina data may also find the following complementary resources useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
-
diff --git a/general/datasets/G2HEIONCRetILM6_0911/tissue.rtf b/general/datasets/G2HEIONCRetILM6_0911/tissue.rtf
deleted file mode 100644
index 766ab59..0000000
--- a/general/datasets/G2HEIONCRetILM6_0911/tissue.rtf
+++ /dev/null
@@ -1,32 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RNAlater at room temperature. Two retinas from one mouse were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.
-
-
-
-Dissecting and preparing eyes for RNA extraction
-
-
-
-Retinas for RNA extraction were placed in RNA STAT-60 (Tel-Test Inc.) and processed per manufacturer’s instructions (in brief form below). Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
-
-
- - Homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue via syringe)
- - Allow the homogenate to stand for 5-10 min at room temperature
- - Add 0.2 ml of chloroform per 1 ml RNA STAT-60
- - Mix the sample vigorously for 15 sec and let the sample incubate at room temperature for 5-10 min
- - Centrifuge at 12,000 g for 1 hr at 4°C
- - Transfer the aqueous phase to a clean centrifuge tube
- - Add 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - Vortex and incubate the sample at -20°C for 1 hr or overnight
- - Centrifuge at 12,000 g for 1 hr
- - Remove the supernatant and wash the RNA pellet with 75% ethanol
- - Remove ethanol, let air dry (5-10 min)
- - Dissolve the pellet in 50 μl of nuclease free water.
-
-
-
-
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf
deleted file mode 100644
index a41ff76..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/acknowledgment.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The HEI Retinal Database is supported by National Eye Institute Grants:
-
-
-
-
- - R01EY017841 (Dr. Eldon E. Geisert, PI)
-
-
- - P030EY13080 (NEI Vision Core Grant), and
-
-
- - A Unrestricted Grand from Research to Prevent Blindness (Dr. Barrett Haik, PI)
-
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/cases.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/cases.rtf
deleted file mode 100644
index b37d700..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/cases.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 48 and maximum age is 118 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J.
-
-BXD strains:
-
-
- - The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s.
- - In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset.
- - The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set.
-
-
-
-
-What Makes the G2 HEI Retina Database different from the HEI Retina Database Examination of Gfap expression across all of the strains in the HEI Retinal Dataset, reveals that some strains express very high levels of Gfap relative to others. For example, BXD24 expresses Gfap at a 9-fold higher level, than BXD22. It has been established that BXD24 acquired a mutation in Cep290 that results in early onset photoreceptor degeneration (Chang et al., 2006). This degeneration results in reactive gliosis throughout the retina. In addition to BXD24, other BXD strains expressed very high levels of Gfap including: BXD32, BXD49, BXD70, BXD83 and BXD89. For the G2 dataset all of these strains with potential reactive gliosis were removed from the dataset.
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf
deleted file mode 100644
index 4fff707..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/experiment-design.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Expression profiling by array
-
-We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.
-
-All normalization was performed by William E. Orr in the HEI Vision Core Facility
-
-
- - Computed the log base 2 of each raw signal value
- - Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
- - Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf
deleted file mode 100644
index 13ff99a..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf
deleted file mode 100644
index 2c52707..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina MouseWG-6 v2.0 arrays: The Illumina Sentrix Mouse-6 BeadChip uses 50-nucleotide probes to interrogate approximately 46,000 sequences from the mouse transcriptome. For each array, the RNA was pooled from two retinas.
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf
deleted file mode 100644
index 97cc2be..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/processing.rtf
+++ /dev/null
@@ -1,2654 +0,0 @@
-Values of all 45,281 probe sets in this data set range from a low of 6.25 (Rho GTPase activating protein 11A, Arhgap11a, probe ID ILMN_2747167) to a high of 18.08 (Ubiquitin B, Ubb, probe ID ILMN_2516699). This corresponds to 11.83 units or a 1 to 3641 dynamic range of expression (2^11.83). We normalized raw signal values using Beadstudio’s rank invariant normalization algorithm. BXD62 was the strain used as the control group
-
-
-
-Sample Processing: Drs. Natalie E. Freeman-Anderson and Justin P. Templeton extracted the retinas from the mice and Dr. Natalie Freeman-Anderson processed all samples in the HEI Vision Core Facility. The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX) listed above. The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system. The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA. The cRNA for each sample was then hybridized to an Illumina Sentrix® Mouse-6-V2 BeadChip (Illumina, San Diego, CA)
-
-
-
-
-
-Quality control analysis of the raw image data was performed using the Illumina BeadStudio software. MIAME standards were used for all microarray data. Rank invariant normalization with BeadStudio software was used to calculate the data. Once this data was collected, the data was globally normalized across all samples using the formula 2 (z-score of log2 [intensity]) + 8.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.
-
-Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice
-
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain |
- Age |
- Sex |
- Source of Animal |
-
-
- | 1 |
- 121608_11-C57BL/6JcFA |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 2 |
- 121608_12-C57BL/6JcFB |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 3 |
- KA7444-C57BL/6JcMC |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 4 |
- KA7444-C57BL/6JcMD |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 5 |
- 31209.05-DBA2JcFA |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 6 |
- 31209.05-DBA2JcFB |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 7 |
- 121608_13-DBA/2JcMA |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 8 |
- 121608_14-DBA/2JcMB |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 9 |
- KA7446-B6D2F1cFA |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 10 |
- KA7446-B6D2F1cFB |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 11 |
- KA7446-B6D2F1cMC |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 12 |
- KA7446-B6D2F1cMD |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 13 |
- KA7466-D2B6F1cFA |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 14 |
- KA7466-D2B6F1cFB |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 15 |
- KA7466-D2B6F1cMC |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 16 |
- KA7466-D2B6F1cMD |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 17 |
- 82609.13-1cFA |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 18 |
- 82609.14-1cFB |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 19 |
- KA7389-1cFA |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 20 |
- KA7389-1cFB |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 21 |
- KA7389-1cMC |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 22 |
- KA7389-1cMD |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 23 |
- KA7300-2cFA |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 24 |
- KA7300-2cFB |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 25 |
- 100909.01-2cMA |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 26 |
- 100909.02-2cMB |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 27 |
- KA6699-5cFA |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 28 |
- KA6699-5cFB |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 29 |
- KA6699-5cFC |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 30 |
- KA6699-5cFD |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 31 |
- 82609.09-5cMA |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 32 |
- 82609.1-5cMB |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 33 |
- KA6763-6cFA |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 34 |
- KA6763-6cFB |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 35 |
- 81209.06-6cMA |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 36 |
- 81209.07-6cMB |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 37 |
- 82609.07-8cFA |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 38 |
- 82609.08-8cFB |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 39 |
- JAX-8cMA |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 40 |
- JAX-8cMB |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 41 |
- KA7289-9cFA |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 42 |
- KA7289-9cFB |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 43 |
- KA7289-9cMC |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 44 |
- KA7289-9cMD |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 45 |
- JAX-11cFA |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 46 |
- JAX-11cFB |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 47 |
- JAX-11cMC |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 48 |
- JAX-11cMD |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 49 |
- 40209.07-12cFA |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 50 |
- 40209.08-12cFB |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 51 |
- 011309.01-12cMA |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 52 |
- 011309.02-12cMB |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 53 |
- KA7286-13cFA |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 54 |
- KA7286-13cFB |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 55 |
- KA7286-13cMC |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 56 |
- KA7286-13cMD |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 57 |
- KA7302-14cFA |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 58 |
- KA7302-14cFB |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 59 |
- 100909.05-14cMA |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 60 |
- 100909.06-14cMB |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 61 |
- KA7288-15cFA |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 62 |
- KA7288-15cFB |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 63 |
- KA7288-15cMC |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 64 |
- KA7288-15cMD |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 65 |
- 062509.01-16cFA |
- BXD16 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 66 |
- KA7267-16cMA |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 67 |
- KA7267-16cMB |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 68 |
- KA6686-18cFB |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 69 |
- KA6686-18cFC |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 70 |
- KA6686-18cME |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 71 |
- KA6686-18cMF |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 72 |
- KA6676-19cFB |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 73 |
- KA6676-19cFC |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 74 |
- KA6676-19cME |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 75 |
- KA6676-19cMF |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 76 |
- 060409.05-20cFA |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- 060409.06-20cFB |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 78 |
- 021909.03-20cMA |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 79 |
- 021909.04-20cMB |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 80 |
- 82609.02-21cFC |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 81 |
- 82609.03-21cFD |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 82 |
- 121709.01-21cMA |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 83 |
- 121709.02-21cMB |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 84 |
- 121709.03-22cFA |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 85 |
- 121709.04-22cFB |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 86 |
- 092308_03-22cMA |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 87 |
- 092308_04-22cMB |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 88 |
- 80409.01-24AcFA |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 89 |
- 080409_02_24AcFB |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 90 |
- 82609.26-24AcFC |
- BXD24A |
- 64 |
- F |
- UTHSC RW |
-
-
- | 91 |
- 81209.03-24AcMC |
- BXD24A |
- 62 |
- M |
- UTHSC RW |
-
-
- | 92 |
- KA6678-24cFA |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 93 |
- KA6678-24cFB |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 94 |
- KA6678-24cME |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 95 |
- KA6678-24cMF |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- 060409.07-27cFA |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 97 |
- 060409.08-27cFB |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 98 |
- 80409.03-27cMA |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 99 |
- 80409.04-27cMB |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 100 |
- JAX-28cFA |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 101 |
- JAX-28cFB |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 102 |
- JAX-28cMC |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 103 |
- JAX-28cMD |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 104 |
- 82609.11-29cFA |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 105 |
- 82609.12-29cFB |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 106 |
- 82609.04-29cMA |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 107 |
- 82609.05-29cMB |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 108 |
- JAX-31cMB |
- BXD 31 |
- 56 |
- M |
- JAX |
-
-
- | 109 |
- JAX-31cFC |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 110 |
- JAX-31cFD |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 111 |
- 011309.03-32cFA |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 112 |
- 011309.04-32cFB |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 113 |
- KA7318-32cFC |
- BXD32 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 114 |
- KA7319-32cMA |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 115 |
- KA7319-32cMB |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 116 |
- 100909.07-33cFA |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 117 |
- 100909.08-33cFB |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 118 |
- 022609.01-33cMA |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 119 |
- 022609.02-33cMB |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 120 |
- KA7416-34cFA |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 121 |
- KA7416-34cFB |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 122 |
- KA6321-34cMA |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 123 |
- KA6321-34cMB |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 124 |
- 060409.01-36cFA |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 125 |
- 060409.02-36cFB |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 126 |
- 060409.03-36cMC |
- BXD36 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 127 |
- KA6702-38cFA |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 128 |
- KA6702-38cFB |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 129 |
- 82609.24-38cFA |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 130 |
- 82609.25-38cFB |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 131 |
- 100909.03-38cMA |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 132 |
- 100909.04-38cMB |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 133 |
- 022609.05-39cFA |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 134 |
- 022609.06-39cFB |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 135 |
- 31209.01-39cMC |
- BXD39 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 136 |
- 92409.01-40cFA |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 137 |
- 92409.02-40cFB |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 138 |
- KA6173-40cMA |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 139 |
- KA6173-40cMB |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 140 |
- KA6173-40cMC |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 141 |
- 091809.01-42cFA |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 142 |
- 091809.02-42cFB |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 143 |
- 021909.01-42cFA |
- BXD42 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 144 |
- 011309.06-42cMA |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 145 |
- 011309.07-42cMB |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- 110408_02-43cFA |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 147 |
- 110408_03-43cFB |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 148 |
- KA6158-43cMA |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 149 |
- KA6158-43cMB |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 150 |
- 100308_01-44cFA |
- BXD44 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 151 |
- 102208_02-44cMD |
- BXD44 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 152 |
- 103009.03-45cFA |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 153 |
- 103009.04-45cFB |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 154 |
- 022609.03-45cFA |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 155 |
- 022609.04-45cFB |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 156 |
- 40309.05-45cMB |
- BXD45 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 157 |
- 40209.05-48cFB |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 158 |
- 40209.06-48cFC |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 159 |
- 81209.04-48cMA |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 160 |
- 81209.05-48cMB |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 161 |
- 81209.08-49cFA |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 162 |
- 81209.09-49cFB |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 163 |
- 40209.01-49cMA |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 164 |
- 40209.02-49cMB |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 165 |
- 40209.03-49cMC |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 166 |
- KA737850cFA |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 167 |
- KA737850cFB |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 168 |
- 121908_01-50cMA |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 169 |
- 121908_02-50cMB |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 170 |
- 111208_01-51cFA |
- BXD51 |
- 99 |
- F |
- UTHSC RW |
-
-
- | 171 |
- 102208_03-51cMA |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 172 |
- 102208_04-51cMB |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 173 |
- 090208_14-53BcFA |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 174 |
- 090208_15-53BcFB |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 175 |
- 090208_16-53BcMC |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 176 |
- 090208_17-53BcMD |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 177 |
- 111208_05-55cFB |
- BXD55 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 178 |
- KA6183-55cMA |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 179 |
- KA6183-55cMB |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 180 |
- KA7362-56cFB |
- BXD 56 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 181 |
- KA6088-56cMA |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 182 |
- KA6088-56cMB |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 183 |
- KA6088-56cMC |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 184 |
- 21810.01-60RFA |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 185 |
- 21810.02-60RFB |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 186 |
- 21810.02-60RFC |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 187 |
- SQ7325-60cMA |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 188 |
- SQ7325-60cMB |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 189 |
- 092308_10-61cFA |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 190 |
- 092308_11-61cFB |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 191 |
- 31909.01-61cMA |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 192 |
- 31909.02-61cMB |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 193 |
- KA7462-62cFA |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 194 |
- KA7462-62cFB |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 195 |
- KA5996-62cMA |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 196 |
- KA5996-62cMB |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 197 |
- KA5996-62cMC |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 198 |
- 090309.01-63cFA |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 199 |
- 090309.02-63cFB |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 200 |
- 110609.01-63cMA |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 201 |
- 110609.02-63cMB |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 202 |
- 091809.03-65cFA |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 203 |
- 091809.04-65cFB |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 204 |
- 103009.01-65cMA |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 205 |
- 103009.02-65cMB |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 206 |
- 110408_05-66cFB |
- BXD66 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 207 |
- KA7165-66cMA |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 208 |
- KA7165-66cMB |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 209 |
- 90809.01-67cMA |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 210 |
- 90809.02-67cMB |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 211 |
- 110609.03-67cFA |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 212 |
- 110609.04-67cFB |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 213 |
- 120408_01-68cFA |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 214 |
- 120408_02-68cFB |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 215 |
- SQ7205-68cMA |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 216 |
- SQ7205-68cMB |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 217 |
- KA6316-68cMA |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 218 |
- KA6316-68cMB |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 219 |
- KA6316-68cMC |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 220 |
- KA76-69cFA |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 221 |
- KA76-69cFB |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 222 |
- KA6074-69cMA |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 223 |
- KA6074-69cMB |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 224 |
- 121608_01-70cFA |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 225 |
- 121608_02-70cFB |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 226 |
- KA7394-70cMA |
- BXD70 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 227 |
- 81209.08-70cMA |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 228 |
- 81209.09-70cMB |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 229 |
- 052809.01-71cFA |
- BXD71 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 230 |
- 060409.09-71cMA |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 231 |
- 060409.10-71cMB |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 232 |
- 40809.01-73cFA |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 233 |
- 40809.02-73cFB |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 234 |
- 111708_01-73cFA |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 235 |
- 111708_01-73cFB |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 236 |
- KA6164-73cMB |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 237 |
- KA6164-73cMC |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 238 |
- 82609.22-74cFA |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 239 |
- 82609.23-74cFB |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 240 |
- 82609.20-74cMA |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 241 |
- 82609.21-74cMB |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 242 |
- KA733675cFA |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 243 |
- KA733675cFB |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 244 |
- KA38-75cMB |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 245 |
- KA38-75cMC |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 246 |
- 41509.01-77cFA |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 247 |
- 41509.02-77cFB |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 248 |
- 41509.03-77cMC |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 249 |
- 41509.04-77cMD |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 250 |
- 121608_03-80cFA |
- BXD80 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 251 |
- 121608_05-80cMC |
- BXD80 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 252 |
- KA23-80cMC |
- BXD80 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 253 |
- KA7305-81cFA |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 254 |
- KA7305-81cFB |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 255 |
- KA7305-81cMD |
- BXD81 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 256 |
- 060409.11-83cFA |
- BXD83 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 257 |
- KA24-83cFA |
- BXD83 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 258 |
- 121608_07-83cMA |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 259 |
- 121608_08-83cMB |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 260 |
- KA24-83cMD |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 261 |
- 090409.05-84cFA |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 262 |
- 090409.06-84cFB |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 263 |
- KA6203-84cMA |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 264 |
- KA6203-84cMB |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 265 |
- 40309.02-85cFD |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 266 |
- 40309.03-85cFE |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 267 |
- 32609.01-85cMA |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 268 |
- 32609.02-85cMB |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 269 |
- 41509.05-86cFA |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 270 |
- 41509.06-86cFB |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 271 |
- KA6101-86cMA |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 272 |
- KA6101-86cMC |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 273 |
- 070909.02-87cFA |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 274 |
- 070909.03-87cFB |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 275 |
- KA7407-87cMA |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 276 |
- KA7407-87cMB |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 277 |
- 102208_05-89cFA |
- BXD89 |
- 82 |
- F |
- UTHSC RW |
-
-
- | 278 |
- KA5974-89cMA |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 279 |
- KA5974-89cMB |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 280 |
- 102208_06-89cMC |
- BXD89 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 281 |
- 72309.01-90cFA |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 282 |
- 72309.02-90cFB |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 283 |
- 090409.03-90cMA |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 284 |
- 090409.04-90cMB |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 285 |
- KA6094-92cMA |
- BXD92 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 286 |
- 020609.01-95cFA |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 287 |
- 020609.02-95cFB |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 288 |
- KA6181-95cMA |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 289 |
- KA6181-95cMB |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 290 |
- 31209.03-96cFA |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 291 |
- 31209.04-96cFB |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 292 |
- KA7246-96cMA |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 293 |
- KA7246-96cMB |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 294 |
- 81209.10-97cFA |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 295 |
- 81209.11-97cFB |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 296 |
- 81209.1-97cMA |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 297 |
- 81209.11-97cMB |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 298 |
- SQ7520-98cFA |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 299 |
- SQ7520-98cFB |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 300 |
- SQ7520-98cMC |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 301 |
- SQ7520-98cMD |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 302 |
- 82609.17-99cFA |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 303 |
- 82609.18-99cFB |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 304 |
- 81409.01-99cMA |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 305 |
- 81409.02-99cMB |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 306 |
- 121608_09-100cFA |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 307 |
- 121608_10-100cFB |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 308 |
- KA6001-100cMA |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 309 |
- KA6001-100cMB |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 310 |
- 81209.12-101cFA |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 311 |
- 81209.13-101cFB |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 312 |
- KA7296-101cMA |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 313 |
- KA7296-101cMB |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 314 |
- 92409.03-102cFA |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 315 |
- 92409.04-102cFB |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 316 |
- KA7380-102cMA |
- BXD102 |
- 115 |
- M |
- UTHSC RW |
-
-
- | 317 |
- 43009.01-103cFA |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 318 |
- 43009.02-103cFB |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 319 |
- KA79-103cFA |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 320 |
- KA79-103cFB |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 321 |
- KA79-103cMC |
- BXD103 |
- 48 |
- M |
- UTHSC RW |
-
-
- | 322 |
- 82609.15-103cMA |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 323 |
- 82609.16-103cMB |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 324 |
- 102909.01-BALBCcFA |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 325 |
- 102909.02-BALBCcFB |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 326 |
- 102909.03-BALBCcMA |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
- | 327 |
- 102909.04-BALBCcMB |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf
deleted file mode 100644
index 44e98a7..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/summary.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-
-This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork.
-
-HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified.
-
-COMMENT on FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set.
-
-The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as BXD24/TyJ-Cep290/J, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243).
-
-The data are now open and available for analysis.
-
-Please cite: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text PDF or HTML
-
-This is rank invariant expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.25 to 18.08 (11.83 units), a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.
-
-The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842.
-
-The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.
-
-
-
-
-Other Related Publications
-
-
-
-
-
- - Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (Link)
- - Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674
- - Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (Link)
- - Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90.(Link)
-
-
-
-
-
-
-
-Other Data Sets Users of these mouse retina data may also find the following complementary resources useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
-
diff --git a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf b/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf
deleted file mode 100644
index 766ab59..0000000
--- a/general/datasets/G2NEI_ILM_Retina_BXD_RI0410/tissue.rtf
+++ /dev/null
@@ -1,32 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RNAlater at room temperature. Two retinas from one mouse were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.
-
-
-
-Dissecting and preparing eyes for RNA extraction
-
-
-
-Retinas for RNA extraction were placed in RNA STAT-60 (Tel-Test Inc.) and processed per manufacturer’s instructions (in brief form below). Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
-
-
- - Homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue via syringe)
- - Allow the homogenate to stand for 5-10 min at room temperature
- - Add 0.2 ml of chloroform per 1 ml RNA STAT-60
- - Mix the sample vigorously for 15 sec and let the sample incubate at room temperature for 5-10 min
- - Centrifuge at 12,000 g for 1 hr at 4°C
- - Transfer the aqueous phase to a clean centrifuge tube
- - Add 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - Vortex and incubate the sample at -20°C for 1 hr or overnight
- - Centrifuge at 12,000 g for 1 hr
- - Remove the supernatant and wash the RNA pellet with 75% ethanol
- - Remove ethanol, let air dry (5-10 min)
- - Dissolve the pellet in 50 μl of nuclease free water.
-
-
-
-
diff --git a/general/datasets/G2heioncretilm6_0911/experiment-type.rtf b/general/datasets/G2heioncretilm6_0911/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/G2heioncretilm6_0911/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/GCB_M2_0505_M/acknowledgment.rtf b/general/datasets/GCB_M2_0505_M/acknowledgment.rtf
deleted file mode 100644
index 9ff420d..0000000
--- a/general/datasets/GCB_M2_0505_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Genome Explorations, Inc., for the NIAAA as part of an SBIR grant to Dr. Divyen Patel. Mouse colony resources and integration of data into GeneNetwork was carried out by Drs. RW Williams and Lu Lu at UTHSC.
diff --git a/general/datasets/GCB_M2_0505_M/cases.rtf b/general/datasets/GCB_M2_0505_M/cases.rtf
deleted file mode 100644
index a843e87..0000000
--- a/general/datasets/GCB_M2_0505_M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We use a set of BXD recombinant inbred strains and standard inbred strains. The BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTL's genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
-
-Most BXD animals were generated in-house at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and Hui-Chen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).
diff --git a/general/datasets/GCB_M2_0505_M/notes.rtf b/general/datasets/GCB_M2_0505_M/notes.rtf
deleted file mode 100644
index 67339ea..0000000
--- a/general/datasets/GCB_M2_0505_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.
diff --git a/general/datasets/GCB_M2_0505_M/platform.rtf b/general/datasets/GCB_M2_0505_M/platform.rtf
deleted file mode 100644
index fdbfe32..0000000
--- a/general/datasets/GCB_M2_0505_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0: The 430 2.0 array consist of approximately 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430A and 430B series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/GCB_M2_0505_M/processing.rtf b/general/datasets/GCB_M2_0505_M/processing.rtf
deleted file mode 100644
index 6c56850..0000000
--- a/general/datasets/GCB_M2_0505_M/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: No correction for potential batch effect was attempted.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/GCB_M2_0505_M/summary.rtf b/general/datasets/GCB_M2_0505_M/summary.rtf
deleted file mode 100644
index ac3d506..0000000
--- a/general/datasets/GCB_M2_0505_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-NOT RECOMMENDED: This May 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 40 lines of mice including 28 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and 10 other common inbred strains of mice. Data were generated by Genome Explorations Inc. (Divyen Patel and colleagues). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the Microarray Suite 5
-
diff --git a/general/datasets/GCB_M2_0505_M/tissue.rtf b/general/datasets/GCB_M2_0505_M/tissue.rtf
deleted file mode 100644
index af10195..0000000
--- a/general/datasets/GCB_M2_0505_M/tissue.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The May 2005 data set consists of a total of 61 array (Affymetrix 430 2.0 arrays) from 40 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. The M430 2.0 arrays were processed in several batches.
-
-Replication and Sample Balance: We obtained data independent biological sample pools from both sexes for half of the strain, including most of the standard inbred strains (129S1/SvImJ is the exception and is represented by two female-only arrays). Most BXD strains are represented by single pooled samples. You can determine the sex of a sample from the table below or by reviewing the expression of the Ddx3y and Xist RNA signal.
-
-
-
-
-
-Legend: Sex balance of the GE-NIAAA data set can be easily evaluated by analysis of this scatterplot of Ddx3y and Xist. Ddx3y (also called Dby) is a transcript with high expression in males whereas Xist is a transcript with high expression in females. Strains that fall in the upper left quadrant are represented only by a single female sample (except in the case of the 129S1/SvImJ data) whereas strains that fall in the lower right quadrant are represented only a a single male sample.
-
-RNA was extracted at Genome Explorations.
-
-All samples were subsequently processed at the Genome Explorations Inc. by Divyen Patel and colleagues.
diff --git a/general/datasets/GCB_M2_0505_P/acknowledgment.rtf b/general/datasets/GCB_M2_0505_P/acknowledgment.rtf
deleted file mode 100644
index 9ff420d..0000000
--- a/general/datasets/GCB_M2_0505_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Genome Explorations, Inc., for the NIAAA as part of an SBIR grant to Dr. Divyen Patel. Mouse colony resources and integration of data into GeneNetwork was carried out by Drs. RW Williams and Lu Lu at UTHSC.
diff --git a/general/datasets/GCB_M2_0505_P/cases.rtf b/general/datasets/GCB_M2_0505_P/cases.rtf
deleted file mode 100644
index a843e87..0000000
--- a/general/datasets/GCB_M2_0505_P/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We use a set of BXD recombinant inbred strains and standard inbred strains. The BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTL's genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
-
-Most BXD animals were generated in-house at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and Hui-Chen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).
diff --git a/general/datasets/GCB_M2_0505_P/notes.rtf b/general/datasets/GCB_M2_0505_P/notes.rtf
deleted file mode 100644
index 67339ea..0000000
--- a/general/datasets/GCB_M2_0505_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.
diff --git a/general/datasets/GCB_M2_0505_P/platform.rtf b/general/datasets/GCB_M2_0505_P/platform.rtf
deleted file mode 100644
index fdbfe32..0000000
--- a/general/datasets/GCB_M2_0505_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0: The 430 2.0 array consist of approximately 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430A and 430B series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/GCB_M2_0505_P/processing.rtf b/general/datasets/GCB_M2_0505_P/processing.rtf
deleted file mode 100644
index 6c56850..0000000
--- a/general/datasets/GCB_M2_0505_P/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: No correction for potential batch effect was attempted.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/GCB_M2_0505_P/summary.rtf b/general/datasets/GCB_M2_0505_P/summary.rtf
deleted file mode 100644
index ac3d506..0000000
--- a/general/datasets/GCB_M2_0505_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-NOT RECOMMENDED: This May 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 40 lines of mice including 28 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and 10 other common inbred strains of mice. Data were generated by Genome Explorations Inc. (Divyen Patel and colleagues). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the Microarray Suite 5
-
diff --git a/general/datasets/GCB_M2_0505_P/tissue.rtf b/general/datasets/GCB_M2_0505_P/tissue.rtf
deleted file mode 100644
index af10195..0000000
--- a/general/datasets/GCB_M2_0505_P/tissue.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The May 2005 data set consists of a total of 61 array (Affymetrix 430 2.0 arrays) from 40 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. The M430 2.0 arrays were processed in several batches.
-
-Replication and Sample Balance: We obtained data independent biological sample pools from both sexes for half of the strain, including most of the standard inbred strains (129S1/SvImJ is the exception and is represented by two female-only arrays). Most BXD strains are represented by single pooled samples. You can determine the sex of a sample from the table below or by reviewing the expression of the Ddx3y and Xist RNA signal.
-
-
-
-
-
-Legend: Sex balance of the GE-NIAAA data set can be easily evaluated by analysis of this scatterplot of Ddx3y and Xist. Ddx3y (also called Dby) is a transcript with high expression in males whereas Xist is a transcript with high expression in females. Strains that fall in the upper left quadrant are represented only by a single female sample (except in the case of the 129S1/SvImJ data) whereas strains that fall in the lower right quadrant are represented only a a single male sample.
-
-RNA was extracted at Genome Explorations.
-
-All samples were subsequently processed at the Genome Explorations Inc. by Divyen Patel and colleagues.
diff --git a/general/datasets/GCB_M2_0505_R/acknowledgment.rtf b/general/datasets/GCB_M2_0505_R/acknowledgment.rtf
deleted file mode 100644
index 9ff420d..0000000
--- a/general/datasets/GCB_M2_0505_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Genome Explorations, Inc., for the NIAAA as part of an SBIR grant to Dr. Divyen Patel. Mouse colony resources and integration of data into GeneNetwork was carried out by Drs. RW Williams and Lu Lu at UTHSC.
diff --git a/general/datasets/GCB_M2_0505_R/cases.rtf b/general/datasets/GCB_M2_0505_R/cases.rtf
deleted file mode 100644
index a843e87..0000000
--- a/general/datasets/GCB_M2_0505_R/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We use a set of BXD recombinant inbred strains and standard inbred strains. The BXD lines are derived crossed between C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D parental strains have been almost fully sequenced (8x coverage for B6 by a public consortium and approximately 1.5x coverage for D by Celera Discovery Systems) and data for 1.75 millioin B vs D SNPs are incorporated into WebQTL's genetic maps for the BXDs. BXD2 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were also produced by Taylor, but they were generated in the 1990s. These strains are all available from The Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004).
-
-Most BXD animals were generated in-house at the University of Tennessee Health Science Center by Lu Lu and Robert Williams using stock obtained from The Jackson Laboratory between 1999 and 2004. All BXD strains with numbers above 42 are new advanced intecross type BXDs (Peirce et al. 2004) that are current available from UTHSC. Additional cases were provided by Glenn Rosen, John Mountz, and Hui-Chen Hsu. These cases were bred either at The Jackson Laboratory (GR) or at the University of Alabama (JM and HCH).
diff --git a/general/datasets/GCB_M2_0505_R/notes.rtf b/general/datasets/GCB_M2_0505_R/notes.rtf
deleted file mode 100644
index 67339ea..0000000
--- a/general/datasets/GCB_M2_0505_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW and YHQ, March 21, 2005. Updated by RWW, March 23, 2005; RWW April 8.
diff --git a/general/datasets/GCB_M2_0505_R/platform.rtf b/general/datasets/GCB_M2_0505_R/platform.rtf
deleted file mode 100644
index fdbfe32..0000000
--- a/general/datasets/GCB_M2_0505_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0: The 430 2.0 array consist of approximately 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430A and 430B series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/GCB_M2_0505_R/processing.rtf b/general/datasets/GCB_M2_0505_R/processing.rtf
deleted file mode 100644
index 6c56850..0000000
--- a/general/datasets/GCB_M2_0505_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization for the log base 2 values for the total set of 104 arrays (all three batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: No correction for potential batch effect was attempted.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replciates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium March 2005 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/GCB_M2_0505_R/summary.rtf b/general/datasets/GCB_M2_0505_R/summary.rtf
deleted file mode 100644
index ac3d506..0000000
--- a/general/datasets/GCB_M2_0505_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-NOT RECOMMENDED: This May 2005 data freeze provides estimates of mRNA expression in adult cerebellum of 40 lines of mice including 28 BXD recombinant inbred strains, C57BL/6J, DBA/2J, and 10 other common inbred strains of mice. Data were generated by Genome Explorations Inc. (Divyen Patel and colleagues). Cerebellar samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the Microarray Suite 5
-
diff --git a/general/datasets/GCB_M2_0505_R/tissue.rtf b/general/datasets/GCB_M2_0505_R/tissue.rtf
deleted file mode 100644
index af10195..0000000
--- a/general/datasets/GCB_M2_0505_R/tissue.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The May 2005 data set consists of a total of 61 array (Affymetrix 430 2.0 arrays) from 40 different genotypes. Each sample consists of whole cerebellum taken from three adult animals of the same age and sex. The M430 2.0 arrays were processed in several batches.
-
-Replication and Sample Balance: We obtained data independent biological sample pools from both sexes for half of the strain, including most of the standard inbred strains (129S1/SvImJ is the exception and is represented by two female-only arrays). Most BXD strains are represented by single pooled samples. You can determine the sex of a sample from the table below or by reviewing the expression of the Ddx3y and Xist RNA signal.
-
-
-
-
-
-Legend: Sex balance of the GE-NIAAA data set can be easily evaluated by analysis of this scatterplot of Ddx3y and Xist. Ddx3y (also called Dby) is a transcript with high expression in males whereas Xist is a transcript with high expression in females. Strains that fall in the upper left quadrant are represented only by a single female sample (except in the case of the 129S1/SvImJ data) whereas strains that fall in the lower right quadrant are represented only a a single male sample.
-
-RNA was extracted at Genome Explorations.
-
-All samples were subsequently processed at the Genome Explorations Inc. by Divyen Patel and colleagues.
diff --git a/general/datasets/GSE15222_F_A_RI_0409/acknowledgment.rtf b/general/datasets/GSE15222_F_A_RI_0409/acknowledgment.rtf
deleted file mode 100644
index c203ed9..0000000
--- a/general/datasets/GSE15222_F_A_RI_0409/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-http://labs.med.miami.edu/myers
diff --git a/general/datasets/GSE15222_F_A_RI_0409/cases.rtf b/general/datasets/GSE15222_F_A_RI_0409/cases.rtf
deleted file mode 100644
index 6933d14..0000000
--- a/general/datasets/GSE15222_F_A_RI_0409/cases.rtf
+++ /dev/null
@@ -1,3290 +0,0 @@
-
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM225652 |
- Temporal Cortex |
- Normal |
- C225652M85N |
- 85 |
- M |
-
-
- | 2 |
- GSM225662 |
- Temporal Cortex |
- Normal |
- C225662M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM225664 |
- Temporal Cortex |
- Normal |
- C225664F79N |
- 79 |
- F |
-
-
- | 4 |
- GSM225665 |
- Temporal Cortex |
- Normal |
- C225665F85N |
- 85 |
- F |
-
-
- | 5 |
- GSM225666 |
- Temporal Cortex |
- Normal |
- C225666F73N |
- 73 |
- F |
-
-
- | 6 |
- GSM225667 |
- Temporal Cortex |
- Normal |
- C225667M81N |
- 81 |
- M |
-
-
- | 7 |
- GSM225668 |
- Temporal Cortex |
- Normal |
- C225668M79N |
- 79 |
- M |
-
-
- | 8 |
- GSM225669 |
- Temporal Cortex |
- Normal |
- C225669M77N |
- 77 |
- M |
-
-
- | 9 |
- GSM225670 |
- Temporal Cortex |
- Normal |
- C225670M69N |
- 69 |
- M |
-
-
- | 10 |
- GSM225671 |
- Temporal Cortex |
- Normal |
- C225671M86N |
- 86 |
- M |
-
-
- | 11 |
- GSM225672 |
- Temporal Cortex |
- Normal |
- C225672F83N |
- 83 |
- F |
-
-
- | 12 |
- GSM225673 |
- Temporal Cortex |
- Normal |
- C225673M78N |
- 78 |
- M |
-
-
- | 13 |
- GSM225674 |
- Temporal Cortex |
- Normal |
- C225674M94N |
- 94 |
- M |
-
-
- | 14 |
- GSM225675 |
- Temporal Cortex |
- Normal |
- C225675F81N |
- 81 |
- F |
-
-
- | 15 |
- GSM225676 |
- Temporal Cortex |
- Normal |
- C225676M76N |
- 76 |
- M |
-
-
- | 16 |
- GSM225677 |
- Temporal Cortex |
- Normal |
- C225677M83N |
- 83 |
- M |
-
-
- | 17 |
- GSM225678 |
- Temporal Cortex |
- Normal |
- C225678M68N |
- 68 |
- M |
-
-
- | 18 |
- GSM225679 |
- Temporal Cortex |
- Normal |
- C225679F82N |
- 82 |
- F |
-
-
- | 19 |
- GSM225680 |
- Temporal Cortex |
- Normal |
- C225680F70N |
- 70 |
- F |
-
-
- | 20 |
- GSM225681 |
- Temporal Cortex |
- Normal |
- C225681M86N |
- 86 |
- M |
-
-
- | 21 |
- GSM225682 |
- Temporal Cortex |
- Normal |
- C225682M78N |
- 78 |
- M |
-
-
- | 22 |
- GSM225683 |
- Temporal Cortex |
- Normal |
- C225683M82N |
- 82 |
- M |
-
-
- | 23 |
- GSM225684 |
- Temporal Cortex |
- Normal |
- C225684F94N |
- 94 |
- F |
-
-
- | 24 |
- GSM225685 |
- Temporal Cortex |
- Normal |
- C225685F87N |
- 87 |
- F |
-
-
- | 25 |
- GSM225686 |
- Temporal Cortex |
- Normal |
- C225686M74N |
- 74 |
- M |
-
-
- | 26 |
- GSM225687 |
- Temporal Cortex |
- Normal |
- C225687M85N |
- 85 |
- M |
-
-
- | 27 |
- GSM225688 |
- Temporal Cortex |
- Normal |
- C225688M75N |
- 75 |
- M |
-
-
- | 28 |
- GSM225689 |
- Temporal Cortex |
- Normal |
- C225689F86N |
- 86 |
- F |
-
-
- | 29 |
- GSM225690 |
- Temporal Cortex |
- Normal |
- C225690M75N |
- 75 |
- M |
-
-
- | 30 |
- GSM225691 |
- Temporal Cortex |
- Normal |
- C225691M81N |
- 81 |
- M |
-
-
- | 31 |
- GSM225692 |
- Temporal Cortex |
- Normal |
- C225692F72N |
- 72 |
- F |
-
-
- | 32 |
- GSM225693 |
- Temporal Cortex |
- Normal |
- C225693F81N |
- 81 |
- F |
-
-
- | 33 |
- GSM225695 |
- Temporal Cortex |
- Normal |
- C225695M81N |
- 81 |
- M |
-
-
- | 34 |
- GSM225696 |
- Temporal Cortex |
- Normal |
- C225696M81N |
- 81 |
- M |
-
-
- | 35 |
- GSM225697 |
- Temporal Cortex |
- Normal |
- C225697M91N |
- 91 |
- M |
-
-
- | 36 |
- GSM225698 |
- Temporal Cortex |
- Normal |
- C225698M84N |
- 84 |
- M |
-
-
- | 37 |
- GSM225699 |
- Temporal Cortex |
- Normal |
- C225699M96N |
- 96 |
- M |
-
-
- | 38 |
- GSM225700 |
- Temporal Cortex |
- Normal |
- C225700F97N |
- 97 |
- F |
-
-
- | 39 |
- GSM225701 |
- Temporal Cortex |
- Normal |
- C225701M90N |
- 90 |
- M |
-
-
- | 40 |
- GSM225702 |
- Temporal Cortex |
- Normal |
- C225702F67N |
- 67 |
- F |
-
-
- | 41 |
- GSM225703 |
- Temporal Cortex |
- Normal |
- C225703F83N |
- 83 |
- F |
-
-
- | 42 |
- GSM225704 |
- Temporal Cortex |
- Normal |
- C225704F82N |
- 82 |
- F |
-
-
- | 43 |
- GSM225705 |
- Temporal Cortex |
- Normal |
- C225705F66N |
- 66 |
- F |
-
-
- | 44 |
- GSM225706 |
- Temporal Cortex |
- Normal |
- C225706F72N |
- 72 |
- F |
-
-
- | 45 |
- GSM225707 |
- Temporal Cortex |
- Normal |
- C225707F65N |
- 65 |
- F |
-
-
- | 46 |
- GSM225708 |
- Temporal Cortex |
- Normal |
- C225708F75N |
- 75 |
- F |
-
-
- | 47 |
- GSM225709 |
- Temporal Cortex |
- Normal |
- C225709F74N |
- 74 |
- F |
-
-
- | 48 |
- GSM225711 |
- Temporal Cortex |
- Normal |
- C225711M68N |
- 68 |
- M |
-
-
- | 49 |
- GSM225713 |
- Temporal Cortex |
- Normal |
- C225713F80N |
- 80 |
- F |
-
-
- | 50 |
- GSM225714 |
- Temporal Cortex |
- Normal |
- C225714M80N |
- 80 |
- M |
-
-
- | 51 |
- GSM225715 |
- Temporal Cortex |
- Normal |
- C225715M66N |
- 66 |
- M |
-
-
- | 52 |
- GSM225717 |
- Temporal Cortex |
- Normal |
- C225717M88N |
- 88 |
- M |
-
-
- | 53 |
- GSM225718 |
- Temporal Cortex |
- Normal |
- C225718F91N |
- 91 |
- F |
-
-
- | 54 |
- GSM225719 |
- Temporal Cortex |
- Normal |
- C225719M73N |
- 73 |
- M |
-
-
- | 55 |
- GSM225720 |
- Temporal Cortex |
- Normal |
- C225720M76N |
- 76 |
- M |
-
-
- | 56 |
- GSM225721 |
- Temporal Cortex |
- Normal |
- C225721M75N |
- 75 |
- M |
-
-
- | 57 |
- GSM225722 |
- Temporal Cortex |
- Normal |
- C225722F86N |
- 86 |
- F |
-
-
- | 58 |
- GSM225723 |
- Temporal Cortex |
- Normal |
- C225723F72N |
- 72 |
- F |
-
-
- | 59 |
- GSM225724 |
- Temporal Cortex |
- Normal |
- C225724M97N |
- 97 |
- M |
-
-
- | 60 |
- GSM225725 |
- Temporal Cortex |
- Normal |
- C225725M86N |
- 86 |
- M |
-
-
- | 61 |
- GSM225726 |
- Temporal Cortex |
- Normal |
- C225726M82N |
- 82 |
- M |
-
-
- | 62 |
- GSM225727 |
- Temporal Cortex |
- Normal |
- C225727F95N |
- 95 |
- F |
-
-
- | 63 |
- GSM225728 |
- Temporal Cortex |
- Normal |
- C225728F76N |
- 76 |
- F |
-
-
- | 64 |
- GSM225729 |
- Temporal Cortex |
- Normal |
- C225729M76N |
- 76 |
- M |
-
-
- | 65 |
- GSM225730 |
- Temporal Cortex |
- Normal |
- C225730M69N |
- 69 |
- M |
-
-
- | 66 |
- GSM225731 |
- Temporal Cortex |
- Normal |
- C225731F80N |
- 80 |
- F |
-
-
- | 67 |
- GSM225732 |
- Temporal Cortex |
- Normal |
- C225732F99N |
- 99 |
- F |
-
-
- | 68 |
- GSM225733 |
- Temporal Cortex |
- Normal |
- C225733M68N |
- 68 |
- M |
-
-
- | 69 |
- GSM225734 |
- Temporal Cortex |
- Normal |
- C225734M70N |
- 70 |
- M |
-
-
- | 70 |
- GSM225735 |
- Temporal Cortex |
- Normal |
- C225735F87N |
- 87 |
- F |
-
-
- | 71 |
- GSM225736 |
- Temporal Cortex |
- Normal |
- C225736F99N |
- 99 |
- F |
-
-
- | 72 |
- GSM225737 |
- Temporal Cortex |
- Normal |
- C225737F88N |
- 88 |
- F |
-
-
- | 73 |
- GSM225739 |
- Temporal Cortex |
- Normal |
- C225739M65N |
- 65 |
- M |
-
-
- | 74 |
- GSM225741 |
- Temporal Cortex |
- Normal |
- C225741M82N |
- 82 |
- M |
-
-
- | 75 |
- GSM225742 |
- Temporal Cortex |
- Normal |
- C225742F78N |
- 78 |
- F |
-
-
- | 76 |
- GSM225743 |
- Temporal Cortex |
- Normal |
- C225743F85N |
- 85 |
- F |
-
-
- | 77 |
- GSM225744 |
- Temporal Cortex |
- Normal |
- C225744F100N |
- 100 |
- F |
-
-
- | 78 |
- GSM225745 |
- Temporal Cortex |
- Normal |
- C225745F87N |
- 87 |
- F |
-
-
- | 79 |
- GSM225746 |
- Temporal Cortex |
- Normal |
- C225746F85N |
- 85 |
- F |
-
-
- | 80 |
- GSM225747 |
- Temporal Cortex |
- Normal |
- C225747F97N |
- 97 |
- F |
-
-
- | 81 |
- GSM225748 |
- Temporal Cortex |
- Normal |
- C225748M65N |
- 65 |
- M |
-
-
- | 82 |
- GSM225749 |
- Temporal Cortex |
- Normal |
- C225749M65N |
- 65 |
- M |
-
-
- | 83 |
- GSM225751 |
- Temporal Cortex |
- Normal |
- C225751F87N |
- 87 |
- F |
-
-
- | 84 |
- GSM225752 |
- Temporal Cortex |
- Normal |
- C225752F85N |
- 85 |
- F |
-
-
- | 85 |
- GSM225753 |
- Temporal Cortex |
- Normal |
- C225753M68N |
- 68 |
- M |
-
-
- | 86 |
- GSM225754 |
- Temporal Cortex |
- Normal |
- C225754M71N |
- 71 |
- M |
-
-
- | 87 |
- GSM225755 |
- Temporal Cortex |
- Normal |
- C225755F83N |
- 83 |
- F |
-
-
- | 88 |
- GSM225756 |
- Temporal Cortex |
- Normal |
- C225756M76N |
- 76 |
- M |
-
-
- | 89 |
- GSM225757 |
- Temporal Cortex |
- Normal |
- C225757M67N |
- 67 |
- M |
-
-
- | 90 |
- GSM225758 |
- Temporal Cortex |
- Normal |
- C225758F100N |
- 100 |
- F |
-
-
- | 91 |
- GSM225759 |
- Temporal Cortex |
- Normal |
- C225759M79N |
- 79 |
- M |
-
-
- | 92 |
- GSM225760 |
- Temporal Cortex |
- Normal |
- C225760M74N |
- 74 |
- M |
-
-
- | 93 |
- GSM225761 |
- Temporal Cortex |
- Normal |
- C225761F88N |
- 88 |
- F |
-
-
- | 94 |
- GSM225762 |
- Temporal Cortex |
- Normal |
- C225762M70N |
- 70 |
- M |
-
-
- | 95 |
- GSM225763 |
- Temporal Cortex |
- Normal |
- C225763F97N |
- 97 |
- F |
-
-
- | 96 |
- GSM225764 |
- Temporal Cortex |
- Normal |
- C225764M69N |
- 69 |
- M |
-
-
- | 97 |
- GSM225915 |
- Temporal Cortex |
- Normal |
- C225915F99N |
- 99 |
- F |
-
-
- | 98 |
- GSM225916 |
- Temporal Cortex |
- Normal |
- C225916M81N |
- 81 |
- M |
-
-
- | 99 |
- GSM225917 |
- Temporal Cortex |
- Normal |
- C225917F85N |
- 85 |
- F |
-
-
- | 100 |
- GSM225918 |
- Temporal Cortex |
- Normal |
- C225918F82N |
- 82 |
- F |
-
-
- | 101 |
- GSM225919 |
- Temporal Cortex |
- Normal |
- C225919M70N |
- 70 |
- M |
-
-
- | 102 |
- GSM225920 |
- Temporal Cortex |
- Normal |
- C225920M73N |
- 73 |
- M |
-
-
- | 103 |
- GSM225921 |
- Temporal Cortex |
- Normal |
- C225921M83N |
- 83 |
- M |
-
-
- | 104 |
- GSM225922 |
- Temporal Cortex |
- Normal |
- C225922M74N |
- 74 |
- M |
-
-
- | 105 |
- GSM225923 |
- Temporal Cortex |
- Normal |
- C225923M77N |
- 77 |
- M |
-
-
- | 106 |
- GSM225924 |
- Temporal Cortex |
- Normal |
- C225924M81N |
- 81 |
- M |
-
-
- | 107 |
- GSM225925 |
- Temporal Cortex |
- Normal |
- C225925M65N |
- 65 |
- M |
-
-
- | 108 |
- GSM225926 |
- Temporal Cortex |
- Normal |
- C225926F73N |
- 73 |
- F |
-
-
- | 109 |
- GSM225927 |
- Temporal Cortex |
- Normal |
- C225927F85N |
- 85 |
- F |
-
-
- | 110 |
- GSM225928 |
- Temporal Cortex |
- Normal |
- C225928M69N |
- 69 |
- M |
-
-
- | 111 |
- GSM225929 |
- Temporal Cortex |
- Normal |
- C225929M72N |
- 72 |
- M |
-
-
- | 112 |
- GSM225930 |
- Temporal Cortex |
- Normal |
- C225930F76N |
- 76 |
- F |
-
-
- | 113 |
- GSM225931 |
- Temporal Cortex |
- Normal |
- C225931M73N |
- 73 |
- M |
-
-
- | 114 |
- GSM225932 |
- Temporal Cortex |
- Normal |
- C225932M66N |
- 66 |
- M |
-
-
- | 115 |
- GSM225933 |
- Temporal Cortex |
- Normal |
- C225933F85N |
- 85 |
- F |
-
-
- | 116 |
- GSM225934 |
- Temporal Cortex |
- Normal |
- C225934M87N |
- 87 |
- M |
-
-
- | 117 |
- GSM225935 |
- Temporal Cortex |
- Normal |
- C225935F86N |
- 86 |
- F |
-
-
- | 118 |
- GSM225936 |
- Temporal Cortex |
- Normal |
- C225936F73N |
- 73 |
- F |
-
-
- | 119 |
- GSM225937 |
- Temporal Cortex |
- Normal |
- C225937M86N |
- 86 |
- M |
-
-
- | 120 |
- GSM225938 |
- Temporal Cortex |
- Normal |
- C225938M72N |
- 72 |
- M |
-
-
- | 121 |
- GSM225939 |
- Temporal Cortex |
- Normal |
- C225939F69N |
- 69 |
- F |
-
-
- | 122 |
- GSM225940 |
- Temporal Cortex |
- Normal |
- C225940F88N |
- 88 |
- F |
-
-
- | 123 |
- GSM225941 |
- Temporal Cortex |
- Normal |
- C225941M77N |
- 77 |
- M |
-
-
- | 124 |
- GSM225942 |
- Temporal Cortex |
- Normal |
- C225942M96N |
- 96 |
- M |
-
-
- | 125 |
- GSM225943 |
- Temporal Cortex |
- Normal |
- C225943F78N |
- 78 |
- F |
-
-
- | 126 |
- GSM225944 |
- Temporal Cortex |
- Normal |
- C225944M77N |
- 77 |
- M |
-
-
- | 127 |
- GSM225945 |
- Temporal Cortex |
- Normal |
- C225945F99N |
- 99 |
- F |
-
-
- | 128 |
- GSM225946 |
- Temporal Cortex |
- Normal |
- C225946M78N |
- 78 |
- M |
-
-
- | 129 |
- GSM225947 |
- Temporal Cortex |
- Normal |
- C225947F76N |
- 76 |
- F |
-
-
- | 130 |
- GSM225948 |
- Temporal Cortex |
- Normal |
- C225948M78N |
- 78 |
- M |
-
-
- | 131 |
- GSM225949 |
- Temporal Cortex |
- Normal |
- C225949F97N |
- 97 |
- F |
-
-
- | 132 |
- GSM225950 |
- Temporal Cortex |
- Normal |
- C225950F86N |
- 86 |
- F |
-
-
- | 133 |
- GSM225951 |
- Temporal Cortex |
- Normal |
- C225951M77N |
- 77 |
- M |
-
-
- | 134 |
- GSM225952 |
- Temporal Cortex |
- Normal |
- C225952M87N |
- 87 |
- M |
-
-
- | 135 |
- GSM225953 |
- Temporal Cortex |
- Normal |
- C225953F72N |
- 72 |
- F |
-
-
- | 136 |
- GSM225954 |
- Temporal Cortex |
- Normal |
- C225954F91N |
- 91 |
- F |
-
-
- | 137 |
- GSM225955 |
- Temporal Cortex |
- Normal |
- C225955F85N |
- 85 |
- F |
-
-
- | 138 |
- GSM225956 |
- Temporal Cortex |
- Normal |
- C225956M88N |
- 88 |
- M |
-
-
- | 139 |
- GSM225957 |
- Temporal Cortex |
- Normal |
- C225957F86N |
- 86 |
- F |
-
-
- | 140 |
- GSM225958 |
- Temporal Cortex |
- Normal |
- C225958F93N |
- 93 |
- F |
-
-
- | 141 |
- GSM225959 |
- Temporal Cortex |
- Normal |
- C225959M82N |
- 82 |
- M |
-
-
- | 142 |
- GSM225961 |
- Temporal Cortex |
- Normal |
- C225961F72N |
- 72 |
- F |
-
-
- | 143 |
- GSM225962 |
- Temporal Cortex |
- Normal |
- C225962F85N |
- 85 |
- F |
-
-
- | 144 |
- GSM225963 |
- Temporal Cortex |
- Normal |
- C225963M70N |
- 70 |
- M |
-
-
- | 145 |
- GSM225964 |
- Temporal Cortex |
- Normal |
- C225964F67N |
- 67 |
- F |
-
-
- | 146 |
- GSM225965 |
- Temporal Cortex |
- Normal |
- C225965F74N |
- 74 |
- F |
-
-
- | 147 |
- GSM226034 |
- Temporal Cortex |
- Normal |
- C226034M69N |
- 69 |
- M |
-
-
- | 148 |
- GSM226035 |
- Temporal Cortex |
- Normal |
- C226035M85N |
- 85 |
- M |
-
-
- | 149 |
- GSM226037 |
- Temporal Cortex |
- Normal |
- C226037M89N |
- 89 |
- M |
-
-
- | 150 |
- GSM226038 |
- Temporal Cortex |
- Normal |
- C226038M86N |
- 86 |
- M |
-
-
- | 151 |
- GSM226039 |
- Temporal Cortex |
- Normal |
- C226039M90N |
- 90 |
- M |
-
-
- | 152 |
- GSM226040 |
- Temporal Cortex |
- Normal |
- C226040F94N |
- 94 |
- F |
-
-
- | 153 |
- GSM226041 |
- Temporal Cortex |
- Normal |
- C226041F91N |
- 91 |
- F |
-
-
- | 154 |
- GSM226042 |
- Temporal Cortex |
- Normal |
- C226042F91N |
- 91 |
- F |
-
-
- | 155 |
- GSM226044 |
- Temporal Cortex |
- Normal |
- C226044F95N |
- 95 |
- F |
-
-
- | 156 |
- GSM226045 |
- Temporal Cortex |
- Normal |
- C226045F95N |
- 95 |
- F |
-
-
- | 157 |
- GSM226046 |
- Temporal Cortex |
- Normal |
- C226046F91N |
- 91 |
- F |
-
-
- | 158 |
- GSM226047 |
- Temporal Cortex |
- Normal |
- C226047M80N |
- 80 |
- M |
-
-
- | 159 |
- GSM226048 |
- Temporal Cortex |
- Normal |
- C226048M83N |
- 83 |
- M |
-
-
- | 160 |
- GSM226049 |
- Temporal Cortex |
- Normal |
- C226049M67N |
- 67 |
- M |
-
-
- | 161 |
- GSM226050 |
- Temporal Cortex |
- Normal |
- C226050M76N |
- 76 |
- M |
-
-
- | 162 |
- GSM226051 |
- Temporal Cortex |
- Normal |
- C226051F86N |
- 86 |
- F |
-
-
- | 163 |
- GSM226052 |
- Temporal Cortex |
- Normal |
- C226052F86N |
- 86 |
- F |
-
-
- | 164 |
- GSM226053 |
- Temporal Cortex |
- Normal |
- C226053M83N |
- 83 |
- M |
-
-
- | 165 |
- GSM226055 |
- Temporal Cortex |
- Normal |
- C226055M84N |
- 84 |
- M |
-
-
- | 166 |
- GSM226056 |
- Temporal Cortex |
- Normal |
- C226056M80N |
- 80 |
- M |
-
-
- | 167 |
- GSM226082 |
- Temporal Cortex |
- Normal |
- C226082M72N |
- 72 |
- M |
-
-
- | 168 |
- GSM226145 |
- Temporal Cortex |
- Normal |
- C226145M67N |
- 67 |
- M |
-
-
- | 169 |
- GSM226146 |
- Temporal Cortex |
- Normal |
- C226146F96N |
- 96 |
- F |
-
-
- | 170 |
- GSM226147 |
- Temporal Cortex |
- Normal |
- C226147F75N |
- 75 |
- F |
-
-
- | 171 |
- GSM226148 |
- Temporal Cortex |
- Normal |
- C226148F89N |
- 89 |
- F |
-
-
- | 172 |
- GSM226149 |
- Temporal Cortex |
- Normal |
- C226149F86N |
- 86 |
- F |
-
-
- | 173 |
- GSM226150 |
- Temporal Cortex |
- Normal |
- C226150M67N |
- 67 |
- M |
-
-
- | 174 |
- GSM226151 |
- Temporal Cortex |
- Normal |
- C226151M77N |
- 77 |
- M |
-
-
- | 175 |
- GSM226154 |
- Temporal Cortex |
- Normal |
- C226154M65N |
- 65 |
- M |
-
-
- | 176 |
- GSM226155 |
- Temporal Cortex |
- Normal |
- C226155M69N |
- 69 |
- M |
-
-
- | 177 |
- GSM226156 |
- Temporal Cortex |
- Normal |
- C226156M84N |
- 84 |
- M |
-
-
- | 178 |
- GSM226157 |
- Temporal Cortex |
- Normal |
- C226157F85N |
- 85 |
- F |
-
-
- | 179 |
- GSM226158 |
- Temporal Cortex |
- Normal |
- C226158M94N |
- 94 |
- M |
-
-
- | 180 |
- GSM226159 |
- Temporal Cortex |
- Normal |
- C226159F89N |
- 89 |
- F |
-
-
- | 181 |
- GSM226160 |
- Temporal Cortex |
- Normal |
- C226160M87N |
- 87 |
- M |
-
-
- | 182 |
- GSM226162 |
- Temporal Cortex |
- Normal |
- C226162M90N |
- 90 |
- M |
-
-
- | 183 |
- GSM226163 |
- Temporal Cortex |
- Normal |
- C226163F88N |
- 88 |
- F |
-
-
- | 184 |
- GSM226164 |
- Temporal Cortex |
- Normal |
- C226164M94N |
- 94 |
- M |
-
-
- | 185 |
- GSM226165 |
- Temporal Cortex |
- Normal |
- C226165F86N |
- 86 |
- F |
-
-
- | 186 |
- GSM226167 |
- Temporal Cortex |
- Normal |
- C226167F93N |
- 93 |
- F |
-
-
- | 187 |
- GSM226168 |
- Temporal Cortex |
- Normal |
- C226168M91N |
- 91 |
- M |
-
-
- | 188 |
- GSM388217 |
- Cortical Tissue |
- Alzheimer's |
- C388217F97A |
- 97 |
- F |
-
-
- | 189 |
- GSM388218 |
- Cortical Tissue |
- Alzheimer's |
- C388218F101A |
- 101 |
- F |
-
-
- | 190 |
- GSM388219 |
- Cortical Tissue |
- Alzheimer's |
- C388219M84A |
- 84 |
- M |
-
-
- | 191 |
- GSM388220 |
- Cortical Tissue |
- Alzheimer's |
- C388220F95A |
- 95 |
- F |
-
-
- | 192 |
- GSM388221 |
- Cortical Tissue |
- Alzheimer's |
- C388221F97A |
- 97 |
- F |
-
-
- | 193 |
- GSM388222 |
- Cortical Tissue |
- Alzheimer's |
- C388222F102A |
- 102 |
- F |
-
-
- | 194 |
- GSM388223 |
- Cortical Tissue |
- Alzheimer's |
- C388223M87A |
- 87 |
- M |
-
-
- | 195 |
- GSM388224 |
- Cortical Tissue |
- Alzheimer's |
- C388224F77A |
- 77 |
- F |
-
-
- | 196 |
- GSM388225 |
- Cortical Tissue |
- Alzheimer's |
- C388225M87A |
- 87 |
- M |
-
-
- | 197 |
- GSM388226 |
- Cortical Tissue |
- Alzheimer's |
- C388226M84A |
- 84 |
- M |
-
-
- | 198 |
- GSM388228 |
- Cortical Tissue |
- Alzheimer's |
- C388228F92A |
- 92 |
- F |
-
-
- | 199 |
- GSM388229 |
- Cortical Tissue |
- Alzheimer's |
- C388229M93A |
- 93 |
- M |
-
-
- | 200 |
- GSM388230 |
- Cortical Tissue |
- Alzheimer's |
- C388230F93A |
- 93 |
- F |
-
-
- | 201 |
- GSM388231 |
- Cortical Tissue |
- Alzheimer's |
- C388231F87A |
- 87 |
- F |
-
-
- | 202 |
- GSM388232 |
- Cortical Tissue |
- Alzheimer's |
- C388232F90A |
- 90 |
- F |
-
-
- | 203 |
- GSM388233 |
- Cortical Tissue |
- Alzheimer's |
- C388233M75A |
- 75 |
- M |
-
-
- | 204 |
- GSM388234 |
- Cortical Tissue |
- Alzheimer's |
- C388234M92A |
- 92 |
- M |
-
-
- | 205 |
- GSM388235 |
- Cortical Tissue |
- Alzheimer's |
- C388235M83A |
- 83 |
- M |
-
-
- | 206 |
- GSM388236 |
- Cortical Tissue |
- Alzheimer's |
- C388236M88A |
- 88 |
- M |
-
-
- | 207 |
- GSM388237 |
- Cortical Tissue |
- Alzheimer's |
- C388237M89A |
- 89 |
- M |
-
-
- | 208 |
- GSM388238 |
- Cortical Tissue |
- Alzheimer's |
- C388238F74A |
- 74 |
- F |
-
-
- | 209 |
- GSM388239 |
- Cortical Tissue |
- Alzheimer's |
- C388239F79A |
- 79 |
- F |
-
-
- | 210 |
- GSM388240 |
- Cortical Tissue |
- Alzheimer's |
- C388240M80A |
- 80 |
- M |
-
-
- | 211 |
- GSM388241 |
- Cortical Tissue |
- Alzheimer's |
- C388241F97A |
- 97 |
- F |
-
-
- | 212 |
- GSM388242 |
- Cortical Tissue |
- Alzheimer's |
- C388242M87A |
- 87 |
- M |
-
-
- | 213 |
- GSM388243 |
- Cortical Tissue |
- Alzheimer's |
- C388243F89A |
- 89 |
- F |
-
-
- | 214 |
- GSM388244 |
- Cortical Tissue |
- Alzheimer's |
- C388244F90A |
- 90 |
- F |
-
-
- | 215 |
- GSM388245 |
- Cortical Tissue |
- Alzheimer's |
- C388245M90A |
- 90 |
- M |
-
-
- | 216 |
- GSM388246 |
- Cortical Tissue |
- Alzheimer's |
- C388246M78A |
- 78 |
- M |
-
-
- | 217 |
- GSM388247 |
- Cortical Tissue |
- Alzheimer's |
- C388247F80A |
- 80 |
- F |
-
-
- | 218 |
- GSM388248 |
- Cortical Tissue |
- Alzheimer's |
- C388248F79A |
- 79 |
- F |
-
-
- | 219 |
- GSM388249 |
- Cortical Tissue |
- Alzheimer's |
- C388249F87A |
- 87 |
- F |
-
-
- | 220 |
- GSM388250 |
- Cortical Tissue |
- Alzheimer's |
- C388250F88A |
- 88 |
- F |
-
-
- | 221 |
- GSM388251 |
- Cortical Tissue |
- Alzheimer's |
- C388251M86A |
- 86 |
- M |
-
-
- | 222 |
- GSM388252 |
- Cortical Tissue |
- Alzheimer's |
- C388252F74A |
- 74 |
- F |
-
-
- | 223 |
- GSM388253 |
- Cortical Tissue |
- Alzheimer's |
- C388253F72A |
- 72 |
- F |
-
-
- | 224 |
- GSM388254 |
- Cortical Tissue |
- Alzheimer's |
- C388254M81A |
- 81 |
- M |
-
-
- | 225 |
- GSM388255 |
- Cortical Tissue |
- Alzheimer's |
- C388255F68A |
- 68 |
- F |
-
-
- | 226 |
- GSM388256 |
- Cortical Tissue |
- Alzheimer's |
- C388256F81A |
- 81 |
- F |
-
-
- | 227 |
- GSM388257 |
- Cortical Tissue |
- Alzheimer's |
- C388257F82A |
- 82 |
- F |
-
-
- | 228 |
- GSM388258 |
- Cortical Tissue |
- Alzheimer's |
- C388258M78A |
- 78 |
- M |
-
-
- | 229 |
- GSM388259 |
- Cortical Tissue |
- Alzheimer's |
- C388259M74A |
- 74 |
- M |
-
-
- | 230 |
- GSM388260 |
- Cortical Tissue |
- Alzheimer's |
- C388260M88A |
- 88 |
- M |
-
-
- | 231 |
- GSM388261 |
- Cortical Tissue |
- Alzheimer's |
- C388261F78A |
- 78 |
- F |
-
-
- | 232 |
- GSM388262 |
- Cortical Tissue |
- Alzheimer's |
- C388262M83A |
- 83 |
- M |
-
-
- | 233 |
- GSM388263 |
- Cortical Tissue |
- Alzheimer's |
- C388263M83A |
- 83 |
- M |
-
-
- | 234 |
- GSM388264 |
- Cortical Tissue |
- Alzheimer's |
- C388264M80A |
- 80 |
- M |
-
-
- | 235 |
- GSM388265 |
- Cortical Tissue |
- Alzheimer's |
- C388265M84A |
- 84 |
- M |
-
-
- | 236 |
- GSM388266 |
- Cortical Tissue |
- Alzheimer's |
- C388266F79A |
- 79 |
- F |
-
-
- | 237 |
- GSM388267 |
- Cortical Tissue |
- Alzheimer's |
- C388267F86A |
- 86 |
- F |
-
-
- | 238 |
- GSM388268 |
- Cortical Tissue |
- Alzheimer's |
- C388268M92A |
- 92 |
- M |
-
-
- | 239 |
- GSM388269 |
- Cortical Tissue |
- Alzheimer's |
- C388269F81A |
- 81 |
- F |
-
-
- | 240 |
- GSM388270 |
- Cortical Tissue |
- Alzheimer's |
- C388270F79A |
- 79 |
- F |
-
-
- | 241 |
- GSM388271 |
- Cortical Tissue |
- Alzheimer's |
- C388271M74A |
- 74 |
- M |
-
-
- | 242 |
- GSM388272 |
- Cortical Tissue |
- Alzheimer's |
- C388272F73A |
- 73 |
- F |
-
-
- | 243 |
- GSM388273 |
- Cortical Tissue |
- Alzheimer's |
- C388273M87A |
- 87 |
- M |
-
-
- | 244 |
- GSM388274 |
- Cortical Tissue |
- Alzheimer's |
- C388274F86A |
- 86 |
- F |
-
-
- | 245 |
- GSM388275 |
- Cortical Tissue |
- Alzheimer's |
- C388275F86A |
- 86 |
- F |
-
-
- | 246 |
- GSM388276 |
- Cortical Tissue |
- Alzheimer's |
- C388276F87A |
- 87 |
- F |
-
-
- | 247 |
- GSM388277 |
- Cortical Tissue |
- Alzheimer's |
- C388277F92A |
- 92 |
- F |
-
-
- | 248 |
- GSM388278 |
- Cortical Tissue |
- Alzheimer's |
- C388278F78A |
- 78 |
- F |
-
-
- | 249 |
- GSM388279 |
- Cortical Tissue |
- Alzheimer's |
- C388279F94A |
- 94 |
- F |
-
-
- | 250 |
- GSM388281 |
- Cortical Tissue |
- Alzheimer's |
- C388281F94A |
- 94 |
- F |
-
-
- | 251 |
- GSM388282 |
- Cortical Tissue |
- Alzheimer's |
- C388282M76A |
- 76 |
- M |
-
-
- | 252 |
- GSM388284 |
- Cortical Tissue |
- Alzheimer's |
- C388284M91A |
- 91 |
- M |
-
-
- | 253 |
- GSM388285 |
- Cortical Tissue |
- Alzheimer's |
- C388285M86A |
- 86 |
- M |
-
-
- | 254 |
- GSM388286 |
- Cortical Tissue |
- Alzheimer's |
- C388286M77A |
- 77 |
- M |
-
-
- | 255 |
- GSM388287 |
- Cortical Tissue |
- Alzheimer's |
- C388287M82A |
- 82 |
- M |
-
-
- | 256 |
- GSM388288 |
- Cortical Tissue |
- Alzheimer's |
- C388288M78A |
- 78 |
- M |
-
-
- | 257 |
- GSM388289 |
- Cortical Tissue |
- Alzheimer's |
- C388289M79A |
- 79 |
- M |
-
-
- | 258 |
- GSM388290 |
- Cortical Tissue |
- Alzheimer's |
- C388290F84A |
- 84 |
- F |
-
-
- | 259 |
- GSM388291 |
- Cortical Tissue |
- Alzheimer's |
- C388291F87A |
- 87 |
- F |
-
-
- | 260 |
- GSM388292 |
- Cortical Tissue |
- Alzheimer's |
- C388292F86A |
- 86 |
- F |
-
-
- | 261 |
- GSM388294 |
- Cortical Tissue |
- Alzheimer's |
- C388294M83A |
- 83 |
- M |
-
-
- | 262 |
- GSM388295 |
- Cortical Tissue |
- Alzheimer's |
- C388295M83A |
- 83 |
- M |
-
-
- | 263 |
- GSM388296 |
- Cortical Tissue |
- Alzheimer's |
- C388296M81A |
- 81 |
- M |
-
-
- | 264 |
- GSM388297 |
- Cortical Tissue |
- Alzheimer's |
- C388297F93A |
- 93 |
- F |
-
-
- | 265 |
- GSM388298 |
- Cortical Tissue |
- Alzheimer's |
- C388298M71A |
- 71 |
- M |
-
-
- | 266 |
- GSM388299 |
- Cortical Tissue |
- Alzheimer's |
- C388299M78A |
- 78 |
- M |
-
-
- | 267 |
- GSM388300 |
- Cortical Tissue |
- Alzheimer's |
- C388300F75A |
- 75 |
- F |
-
-
- | 268 |
- GSM388301 |
- Cortical Tissue |
- Alzheimer's |
- C388301F84A |
- 84 |
- F |
-
-
- | 269 |
- GSM388302 |
- Cortical Tissue |
- Alzheimer's |
- C388302M73A |
- 73 |
- M |
-
-
- | 270 |
- GSM388303 |
- Cortical Tissue |
- Alzheimer's |
- C388303F89A |
- 89 |
- F |
-
-
- | 271 |
- GSM388304 |
- Cortical Tissue |
- Alzheimer's |
- C388304FNAA |
- NA |
- F |
-
-
- | 272 |
- GSM388305 |
- Cortical Tissue |
- Alzheimer's |
- C388305M69A |
- 69 |
- M |
-
-
- | 273 |
- GSM388306 |
- Cortical Tissue |
- Alzheimer's |
- C388306M83A |
- 83 |
- M |
-
-
- | 274 |
- GSM388307 |
- Cortical Tissue |
- Alzheimer's |
- C388307M71A |
- 71 |
- M |
-
-
- | 275 |
- GSM388308 |
- Cortical Tissue |
- Alzheimer's |
- C388308F86A |
- 86 |
- F |
-
-
- | 276 |
- GSM388309 |
- Cortical Tissue |
- Alzheimer's |
- C388309M82A |
- 82 |
- M |
-
-
- | 277 |
- GSM388310 |
- Cortical Tissue |
- Alzheimer's |
- C388310FNAA |
- NA |
- F |
-
-
- | 278 |
- GSM388311 |
- Cortical Tissue |
- Alzheimer's |
- C388311M88A |
- 88 |
- M |
-
-
- | 279 |
- GSM388312 |
- Cortical Tissue |
- Alzheimer's |
- C388312M77A |
- 77 |
- M |
-
-
- | 280 |
- GSM388313 |
- Cortical Tissue |
- Alzheimer's |
- C388313M85A |
- 85 |
- M |
-
-
- | 281 |
- GSM388314 |
- Cortical Tissue |
- Alzheimer's |
- C388314F81A |
- 81 |
- F |
-
-
- | 282 |
- GSM388315 |
- Cortical Tissue |
- Alzheimer's |
- C388315F86A |
- 86 |
- F |
-
-
- | 283 |
- GSM388316 |
- Cortical Tissue |
- Alzheimer's |
- C388316M89A |
- 89 |
- M |
-
-
- | 284 |
- GSM388317 |
- Cortical Tissue |
- Alzheimer's |
- C388317F73A |
- 73 |
- F |
-
-
- | 285 |
- GSM388318 |
- Cortical Tissue |
- Alzheimer's |
- C388318F96A |
- 96 |
- F |
-
-
- | 286 |
- GSM388319 |
- Cortical Tissue |
- Alzheimer's |
- C388319M73A |
- 73 |
- M |
-
-
- | 287 |
- GSM388320 |
- Cortical Tissue |
- Alzheimer's |
- C388320M81A |
- 81 |
- M |
-
-
- | 288 |
- GSM388321 |
- Cortical Tissue |
- Alzheimer's |
- C388321F84A |
- 84 |
- F |
-
-
- | 289 |
- GSM388322 |
- Cortical Tissue |
- Alzheimer's |
- C388322F93A |
- 93 |
- F |
-
-
- | 290 |
- GSM388323 |
- Cortical Tissue |
- Alzheimer's |
- C388323F82A |
- 82 |
- F |
-
-
- | 291 |
- GSM388324 |
- Cortical Tissue |
- Alzheimer's |
- C388324M76A |
- 76 |
- M |
-
-
- | 292 |
- GSM388325 |
- Cortical Tissue |
- Alzheimer's |
- C388325M77A |
- 77 |
- M |
-
-
- | 293 |
- GSM388326 |
- Cortical Tissue |
- Alzheimer's |
- C388326F86A |
- 86 |
- F |
-
-
- | 294 |
- GSM388327 |
- Cortical Tissue |
- Alzheimer's |
- C388327F85A |
- 85 |
- F |
-
-
- | 295 |
- GSM388328 |
- Cortical Tissue |
- Alzheimer's |
- C388328M83A |
- 83 |
- M |
-
-
- | 296 |
- GSM388329 |
- Cortical Tissue |
- Alzheimer's |
- C388329M76A |
- 76 |
- M |
-
-
- | 297 |
- GSM388330 |
- Cortical Tissue |
- Alzheimer's |
- C388330M81A |
- 81 |
- M |
-
-
- | 298 |
- GSM388331 |
- Cortical Tissue |
- Alzheimer's |
- C388331M79A |
- 79 |
- M |
-
-
- | 299 |
- GSM388332 |
- Cortical Tissue |
- Alzheimer's |
- C388332M81A |
- 81 |
- M |
-
-
- | 300 |
- GSM388333 |
- Cortical Tissue |
- Alzheimer's |
- C388333F78A |
- 78 |
- F |
-
-
- | 301 |
- GSM388334 |
- Cortical Tissue |
- Alzheimer's |
- C388334M80A |
- 80 |
- M |
-
-
- | 302 |
- GSM388335 |
- Cortical Tissue |
- Alzheimer's |
- C388335M84A |
- 84 |
- M |
-
-
- | 303 |
- GSM388336 |
- Cortical Tissue |
- Alzheimer's |
- C388336F85A |
- 85 |
- F |
-
-
- | 304 |
- GSM388337 |
- Cortical Tissue |
- Alzheimer's |
- C388337M75A |
- 75 |
- M |
-
-
- | 305 |
- GSM388338 |
- Cortical Tissue |
- Alzheimer's |
- C388338F80A |
- 80 |
- F |
-
-
- | 306 |
- GSM388339 |
- Cortical Tissue |
- Alzheimer's |
- C388339F97A |
- 97 |
- F |
-
-
- | 307 |
- GSM388340 |
- Cortical Tissue |
- Alzheimer's |
- C388340F82A |
- 82 |
- F |
-
-
- | 308 |
- GSM388341 |
- Cortical Tissue |
- Alzheimer's |
- C388341M82A |
- 82 |
- M |
-
-
- | 309 |
- GSM388342 |
- Cortical Tissue |
- Alzheimer's |
- C388342M77A |
- 77 |
- M |
-
-
- | 310 |
- GSM388343 |
- Cortical Tissue |
- Alzheimer's |
- C388343M81A |
- 81 |
- M |
-
-
- | 311 |
- GSM388345 |
- Cortical Tissue |
- Alzheimer's |
- C388345F96A |
- 96 |
- F |
-
-
- | 312 |
- GSM388346 |
- Cortical Tissue |
- Alzheimer's |
- C388346F90A |
- 90 |
- F |
-
-
- | 313 |
- GSM388347 |
- Cortical Tissue |
- Alzheimer's |
- C388347M86A |
- 86 |
- M |
-
-
- | 314 |
- GSM388348 |
- Cortical Tissue |
- Alzheimer's |
- C388348M88A |
- 88 |
- M |
-
-
- | 315 |
- GSM388349 |
- Cortical Tissue |
- Alzheimer's |
- C388349F90A |
- 90 |
- F |
-
-
- | 316 |
- GSM388350 |
- Cortical Tissue |
- Alzheimer's |
- C388350F90A |
- 90 |
- F |
-
-
- | 317 |
- GSM388351 |
- Cortical Tissue |
- Alzheimer's |
- C388351F84A |
- 84 |
- F |
-
-
- | 318 |
- GSM388352 |
- Cortical Tissue |
- Alzheimer's |
- C388352M84A |
- 84 |
- M |
-
-
- | 319 |
- GSM388353 |
- Cortical Tissue |
- Alzheimer's |
- C388353F91A |
- 91 |
- F |
-
-
- | 320 |
- GSM388354 |
- Cortical Tissue |
- Alzheimer's |
- C388354F81A |
- 81 |
- F |
-
-
- | 321 |
- GSM388355 |
- Cortical Tissue |
- Alzheimer's |
- C388355F84A |
- 84 |
- F |
-
-
- | 322 |
- GSM388356 |
- Cortical Tissue |
- Alzheimer's |
- C388356M80A |
- 80 |
- M |
-
-
- | 323 |
- GSM388357 |
- Cortical Tissue |
- Alzheimer's |
- C388357M81A |
- 81 |
- M |
-
-
- | 324 |
- GSM388358 |
- Cortical Tissue |
- Alzheimer's |
- C388358F87A |
- 87 |
- F |
-
-
- | 325 |
- GSM388359 |
- Cortical Tissue |
- Alzheimer's |
- C388359M85A |
- 85 |
- M |
-
-
- | 326 |
- GSM388360 |
- Cortical Tissue |
- Alzheimer's |
- C388360F90A |
- 90 |
- F |
-
-
- | 327 |
- GSM388361 |
- Cortical Tissue |
- Alzheimer's |
- C388361M79A |
- 79 |
- M |
-
-
- | 328 |
- GSM388362 |
- Cortical Tissue |
- Alzheimer's |
- C388362F87A |
- 87 |
- F |
-
-
- | 329 |
- GSM388363 |
- Cortical Tissue |
- Alzheimer's |
- C388363M75A |
- 75 |
- M |
-
-
- | 330 |
- GSM388364 |
- Cortical Tissue |
- Alzheimer's |
- C388364F92A |
- 92 |
- F |
-
-
- | 331 |
- GSM388365 |
- Cortical Tissue |
- Alzheimer's |
- C388365F84A |
- 84 |
- F |
-
-
- | 332 |
- GSM388366 |
- Cortical Tissue |
- Alzheimer's |
- C388366M75A |
- 75 |
- M |
-
-
- | 333 |
- GSM388367 |
- Cortical Tissue |
- Alzheimer's |
- C388367F76A |
- 76 |
- F |
-
-
- | 334 |
- GSM388368 |
- Cortical Tissue |
- Alzheimer's |
- C388368F86A |
- 86 |
- F |
-
-
- | 335 |
- GSM388369 |
- Cortical Tissue |
- Alzheimer's |
- C388369M82A |
- 82 |
- M |
-
-
- | 336 |
- GSM388370 |
- Cortical Tissue |
- Alzheimer's |
- C388370M76A |
- 76 |
- M |
-
-
- | 337 |
- GSM388371 |
- Cortical Tissue |
- Alzheimer's |
- C388371F81A |
- 81 |
- F |
-
-
- | 338 |
- GSM388372 |
- Cortical Tissue |
- Alzheimer's |
- C388372F80A |
- 80 |
- F |
-
-
- | 339 |
- GSM388373 |
- Cortical Tissue |
- Alzheimer's |
- C388373M83A |
- 83 |
- M |
-
-
- | 340 |
- GSM388374 |
- Cortical Tissue |
- Alzheimer's |
- C388374F83A |
- 83 |
- F |
-
-
- | 341 |
- GSM388375 |
- Cortical Tissue |
- Alzheimer's |
- C388375F84A |
- 84 |
- F |
-
-
- | 342 |
- GSM388376 |
- Cortical Tissue |
- Alzheimer's |
- C388376M93A |
- 93 |
- M |
-
-
- | 343 |
- GSM388377 |
- Cortical Tissue |
- Alzheimer's |
- C388377F92A |
- 92 |
- F |
-
-
- | 344 |
- GSM388378 |
- Cortical Tissue |
- Alzheimer's |
- C388378M78A |
- 78 |
- M |
-
-
- | 345 |
- GSM388379 |
- Cortical Tissue |
- Alzheimer's |
- C388379M90A |
- 90 |
- M |
-
-
- | 346 |
- GSM388380 |
- Cortical Tissue |
- Alzheimer's |
- C388380M83A |
- 83 |
- M |
-
-
- | 347 |
- GSM388381 |
- Cortical Tissue |
- Alzheimer's |
- C388381M79A |
- 79 |
- M |
-
-
- | 348 |
- GSM388382 |
- Cortical Tissue |
- Alzheimer's |
- C388382M84A |
- 84 |
- M |
-
-
- | 349 |
- GSM388383 |
- Cortical Tissue |
- Alzheimer's |
- C388383F90A |
- 90 |
- F |
-
-
- | 350 |
- GSM388384 |
- Cortical Tissue |
- Alzheimer's |
- C388384F88A |
- 88 |
- F |
-
-
- | 351 |
- GSM388385 |
- Cortical Tissue |
- Alzheimer's |
- C388385M77A |
- 77 |
- M |
-
-
- | 352 |
- GSM388386 |
- Cortical Tissue |
- Alzheimer's |
- C388386F80A |
- 80 |
- F |
-
-
- | 353 |
- GSM388387 |
- Cortical Tissue |
- Alzheimer's |
- C388387M87A |
- 87 |
- M |
-
-
- | 354 |
- GSM388388 |
- Cortical Tissue |
- Alzheimer's |
- C388388M86A |
- 86 |
- M |
-
-
- | 355 |
- GSM388389 |
- Cortical Tissue |
- Alzheimer's |
- C388389M74A |
- 74 |
- M |
-
-
- | 356 |
- GSM388390 |
- Cortical Tissue |
- Alzheimer's |
- C388390F86A |
- 86 |
- F |
-
-
- | 357 |
- GSM388391 |
- Cortical Tissue |
- Alzheimer's |
- C388391F81A |
- 81 |
- F |
-
-
- | 358 |
- GSM388392 |
- Cortical Tissue |
- Alzheimer's |
- C388392F73A |
- 73 |
- F |
-
-
- | 359 |
- GSM388393 |
- Cortical Tissue |
- Alzheimer's |
- C388393M83A |
- 83 |
- M |
-
-
- | 360 |
- GSM388394 |
- Cortical Tissue |
- Alzheimer's |
- C388394M86A |
- 86 |
- M |
-
-
- | 361 |
- GSM388395 |
- Cortical Tissue |
- Alzheimer's |
- C388395F86A |
- 86 |
- F |
-
-
- | 362 |
- GSM388396 |
- Cortical Tissue |
- Alzheimer's |
- C388396M78A |
- 78 |
- M |
-
-
- | 363 |
- GSM388397 |
- Cortical Tissue |
- Alzheimer's |
- C388397M83A |
- 83 |
- M |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GSE15222_F_A_RI_0409/experiment-design.rtf b/general/datasets/GSE15222_F_A_RI_0409/experiment-design.rtf
deleted file mode 100644
index 07d1b52..0000000
--- a/general/datasets/GSE15222_F_A_RI_0409/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Expression profiling by array
-
-We recently surveyed the relationship between the human brain transcriptome and genome in a series of neuropathologically normal postmortem samples. We now have analyzed additional samples with a confirmed pathologic diagnosis of late onset Alzheimer's disease (LOAD, final n=187 controls, 176 cases). Nine percent of the cortical transcripts we analyzed had expression profiles correlated with their genotypes in the combined cohort and approximately 5% of transcripts had SNP-transcript relationships that could distinguish LOAD samples. Two of these transcripts have been previously implicated in LOAD candidate gene SNP-expression screens. This study shows how the relationship between common inherited genetic variants and brain transcript expression can be used in the study of human brain disorders. We suggest that studying the transcriptome as a quantitative endo-phenotype has greater power to find risk SNPs influencing expression than the use of discrete diagnostic categories such as presence or absence of disease. see DOI:10.1016/j.ajhg.2009.03.011 for further details and complete author list.
-
-Expression quantitative trait loci study using human brain from 363 cortical samples. Affymetrix 500K chip for genotyping, Illumina Sentrix Human-ref 8 bead array chip for expression. Genotyping data will be available at dbGAP.
diff --git a/general/datasets/GSE15222_F_A_RI_0409/notes.rtf b/general/datasets/GSE15222_F_A_RI_0409/notes.rtf
deleted file mode 100644
index e7bd85c..0000000
--- a/general/datasets/GSE15222_F_A_RI_0409/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Access to the original data from Dr. Myers' laboratory
-or GEO GSE15222
-PMI = Post Mortem Interval
-Cannot find this record in the GEO website: WGACON-120
-
-This data is based on May 2004 (NCBI35/hg17).
diff --git a/general/datasets/GSE15222_F_A_RI_0409/platform.rtf b/general/datasets/GSE15222_F_A_RI_0409/platform.rtf
deleted file mode 100644
index 5bcda8b..0000000
--- a/general/datasets/GSE15222_F_A_RI_0409/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Illumina Human 50 mer probes. Total of 24357 probes according to Myers et al. A total of 24354 probes included in this GeneNetwork file.
-
-From the Methods section of the paper:
-
-Genotyping and Expression Proï¬ling DNA was hybridized to the Affymetrix GeneChip Human Mapping 500K Array Set (502,627 SNPs) as previously described.11,12 Genotypes were extracted with the use of both SNiPer-HD13 and BRLMM (Affymetrix, Santa Clara, CA) algorithms. Genotypes that exhibited less than 98% concordance between calls were excluded. SNPs with call rates less than 90% were excluded from the analysis. HardyWeinberg equilibrium (HWE) was assessed with exact tests and the PLINK analysis toolset.14 SNPs with HWE exact-test p values less than 0.05, as well as SNPs with minor-allele frequencies less than 1%, were excluded. Allele calls had a mean of 97% and a range of 90%–99%. cRNA was hybridized to Illumina Human Refseq-8 Expression BeadChip (24,357 transcripts) via standard protocols. Expression proï¬les were extracted and rank invariant normalized15–17 with the use of the BeadStudio software available from Illumina, with the Illumina custom error model used. Rankinvariant-normalized expression data were log10 transformed, and missing data were encoded as missing, rather than as a zero level of expression.
diff --git a/general/datasets/GSE15222_F_A_RI_0409/summary.rtf b/general/datasets/GSE15222_F_A_RI_0409/summary.rtf
deleted file mode 100644
index e99fa9e..0000000
--- a/general/datasets/GSE15222_F_A_RI_0409/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Myers and colleagues generated massive neocortical transcriptome data sets for a set of unrelated elderly neurologically and neuropathologically normal humans and from confirmed late onset Alzheimer's disease patients (LOAD, n = 187 normal and 176 LOAD cases, see DOI:10.1016/j.ajhg.2009.03.011 for detail). They used an Illumina Sentrix Bead array (HumanRef-8) that measures expression of approximately 19,730 curated RefSeq sequences (Human Build 34).
-
-Case identifiers: All case identifiers (IDs) in GeneNetwork begin with a capital C followed by a six digit GEO identifier, followed by the sex and age in years. Non-Alzheimer cases are labeled with the suffix letter N: C225652M85N. Alzheimer cases are labeled with the suffix letter A: C388217F97A.
-
-Data were initially downloaded from the NCBI GEO archive under the experiment ID GSE15222. All data were generated using the Illumina HumanRef-8 expression BeadChip (GPL2700) v2 Rev0. This data set in GeneNetwork includes data for 24,354 probes. We have realigned the 50-mer sequences by BLAT to the latest version of the human genome (Feb 2009, hg19) and reannotated the array (August 2009). The annotation in GN will differ from that provided in GEO for this platform. We were unable to obtain 50-mer sequences for several thousand probes (e.g., HTT), and these probes have therefore not been realigned to the human genome.
-
-The GEO data set was processed by Myers and colleagues using Illumina's Rank Invariant transform. We performed a series of QC and renormalization steps to the data to allow more facile comparison to other data sets in GeneNetwork. In brief, data is log2 transformed. We recentered each array to a mean expression of 8 units and a standard deviation of 2 units (2z + 8 transform). The values are therefore modified z scores and each unit represents roughly a two-fold difference in expression. Average expression across all 363 cases range from a low of 6 units (e.g., SYT15) to a high of 19 units for ARSK. APOE has an average expression of 15 units and APP has an average expression of 11.5 units.. The distribution is far from normal with a great excess of measurements of genes with low to moderate expression clustered between 6.5 and 8.5 units.
-
-A small number of arrays (n = 6, GSM226040, GSM226041, GSM226042, GSM226044, GSM226045, GSM226046) had a different distribution from the great majority of other arrays. This was probably due to a batch processing effect. Members of this minority group belonged to both normal and LOAD cases. This putative batch effect has been eliminated in the GeneNetwork rendition of the Myers data. To eliminate the putative batch effect, we simply computed a mean offset for each probe in the "minority set" relative to the remaining "majority set" and added or subtracted this offset to force the mean of each probe in the minority set to conform to mean of the same probe in the majority set.
diff --git a/general/datasets/GSE15222_F_N_RI_0409/acknowledgment.rtf b/general/datasets/GSE15222_F_N_RI_0409/acknowledgment.rtf
deleted file mode 100644
index c203ed9..0000000
--- a/general/datasets/GSE15222_F_N_RI_0409/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-http://labs.med.miami.edu/myers
diff --git a/general/datasets/GSE15222_F_N_RI_0409/cases.rtf b/general/datasets/GSE15222_F_N_RI_0409/cases.rtf
deleted file mode 100644
index 6933d14..0000000
--- a/general/datasets/GSE15222_F_N_RI_0409/cases.rtf
+++ /dev/null
@@ -1,3290 +0,0 @@
-
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM225652 |
- Temporal Cortex |
- Normal |
- C225652M85N |
- 85 |
- M |
-
-
- | 2 |
- GSM225662 |
- Temporal Cortex |
- Normal |
- C225662M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM225664 |
- Temporal Cortex |
- Normal |
- C225664F79N |
- 79 |
- F |
-
-
- | 4 |
- GSM225665 |
- Temporal Cortex |
- Normal |
- C225665F85N |
- 85 |
- F |
-
-
- | 5 |
- GSM225666 |
- Temporal Cortex |
- Normal |
- C225666F73N |
- 73 |
- F |
-
-
- | 6 |
- GSM225667 |
- Temporal Cortex |
- Normal |
- C225667M81N |
- 81 |
- M |
-
-
- | 7 |
- GSM225668 |
- Temporal Cortex |
- Normal |
- C225668M79N |
- 79 |
- M |
-
-
- | 8 |
- GSM225669 |
- Temporal Cortex |
- Normal |
- C225669M77N |
- 77 |
- M |
-
-
- | 9 |
- GSM225670 |
- Temporal Cortex |
- Normal |
- C225670M69N |
- 69 |
- M |
-
-
- | 10 |
- GSM225671 |
- Temporal Cortex |
- Normal |
- C225671M86N |
- 86 |
- M |
-
-
- | 11 |
- GSM225672 |
- Temporal Cortex |
- Normal |
- C225672F83N |
- 83 |
- F |
-
-
- | 12 |
- GSM225673 |
- Temporal Cortex |
- Normal |
- C225673M78N |
- 78 |
- M |
-
-
- | 13 |
- GSM225674 |
- Temporal Cortex |
- Normal |
- C225674M94N |
- 94 |
- M |
-
-
- | 14 |
- GSM225675 |
- Temporal Cortex |
- Normal |
- C225675F81N |
- 81 |
- F |
-
-
- | 15 |
- GSM225676 |
- Temporal Cortex |
- Normal |
- C225676M76N |
- 76 |
- M |
-
-
- | 16 |
- GSM225677 |
- Temporal Cortex |
- Normal |
- C225677M83N |
- 83 |
- M |
-
-
- | 17 |
- GSM225678 |
- Temporal Cortex |
- Normal |
- C225678M68N |
- 68 |
- M |
-
-
- | 18 |
- GSM225679 |
- Temporal Cortex |
- Normal |
- C225679F82N |
- 82 |
- F |
-
-
- | 19 |
- GSM225680 |
- Temporal Cortex |
- Normal |
- C225680F70N |
- 70 |
- F |
-
-
- | 20 |
- GSM225681 |
- Temporal Cortex |
- Normal |
- C225681M86N |
- 86 |
- M |
-
-
- | 21 |
- GSM225682 |
- Temporal Cortex |
- Normal |
- C225682M78N |
- 78 |
- M |
-
-
- | 22 |
- GSM225683 |
- Temporal Cortex |
- Normal |
- C225683M82N |
- 82 |
- M |
-
-
- | 23 |
- GSM225684 |
- Temporal Cortex |
- Normal |
- C225684F94N |
- 94 |
- F |
-
-
- | 24 |
- GSM225685 |
- Temporal Cortex |
- Normal |
- C225685F87N |
- 87 |
- F |
-
-
- | 25 |
- GSM225686 |
- Temporal Cortex |
- Normal |
- C225686M74N |
- 74 |
- M |
-
-
- | 26 |
- GSM225687 |
- Temporal Cortex |
- Normal |
- C225687M85N |
- 85 |
- M |
-
-
- | 27 |
- GSM225688 |
- Temporal Cortex |
- Normal |
- C225688M75N |
- 75 |
- M |
-
-
- | 28 |
- GSM225689 |
- Temporal Cortex |
- Normal |
- C225689F86N |
- 86 |
- F |
-
-
- | 29 |
- GSM225690 |
- Temporal Cortex |
- Normal |
- C225690M75N |
- 75 |
- M |
-
-
- | 30 |
- GSM225691 |
- Temporal Cortex |
- Normal |
- C225691M81N |
- 81 |
- M |
-
-
- | 31 |
- GSM225692 |
- Temporal Cortex |
- Normal |
- C225692F72N |
- 72 |
- F |
-
-
- | 32 |
- GSM225693 |
- Temporal Cortex |
- Normal |
- C225693F81N |
- 81 |
- F |
-
-
- | 33 |
- GSM225695 |
- Temporal Cortex |
- Normal |
- C225695M81N |
- 81 |
- M |
-
-
- | 34 |
- GSM225696 |
- Temporal Cortex |
- Normal |
- C225696M81N |
- 81 |
- M |
-
-
- | 35 |
- GSM225697 |
- Temporal Cortex |
- Normal |
- C225697M91N |
- 91 |
- M |
-
-
- | 36 |
- GSM225698 |
- Temporal Cortex |
- Normal |
- C225698M84N |
- 84 |
- M |
-
-
- | 37 |
- GSM225699 |
- Temporal Cortex |
- Normal |
- C225699M96N |
- 96 |
- M |
-
-
- | 38 |
- GSM225700 |
- Temporal Cortex |
- Normal |
- C225700F97N |
- 97 |
- F |
-
-
- | 39 |
- GSM225701 |
- Temporal Cortex |
- Normal |
- C225701M90N |
- 90 |
- M |
-
-
- | 40 |
- GSM225702 |
- Temporal Cortex |
- Normal |
- C225702F67N |
- 67 |
- F |
-
-
- | 41 |
- GSM225703 |
- Temporal Cortex |
- Normal |
- C225703F83N |
- 83 |
- F |
-
-
- | 42 |
- GSM225704 |
- Temporal Cortex |
- Normal |
- C225704F82N |
- 82 |
- F |
-
-
- | 43 |
- GSM225705 |
- Temporal Cortex |
- Normal |
- C225705F66N |
- 66 |
- F |
-
-
- | 44 |
- GSM225706 |
- Temporal Cortex |
- Normal |
- C225706F72N |
- 72 |
- F |
-
-
- | 45 |
- GSM225707 |
- Temporal Cortex |
- Normal |
- C225707F65N |
- 65 |
- F |
-
-
- | 46 |
- GSM225708 |
- Temporal Cortex |
- Normal |
- C225708F75N |
- 75 |
- F |
-
-
- | 47 |
- GSM225709 |
- Temporal Cortex |
- Normal |
- C225709F74N |
- 74 |
- F |
-
-
- | 48 |
- GSM225711 |
- Temporal Cortex |
- Normal |
- C225711M68N |
- 68 |
- M |
-
-
- | 49 |
- GSM225713 |
- Temporal Cortex |
- Normal |
- C225713F80N |
- 80 |
- F |
-
-
- | 50 |
- GSM225714 |
- Temporal Cortex |
- Normal |
- C225714M80N |
- 80 |
- M |
-
-
- | 51 |
- GSM225715 |
- Temporal Cortex |
- Normal |
- C225715M66N |
- 66 |
- M |
-
-
- | 52 |
- GSM225717 |
- Temporal Cortex |
- Normal |
- C225717M88N |
- 88 |
- M |
-
-
- | 53 |
- GSM225718 |
- Temporal Cortex |
- Normal |
- C225718F91N |
- 91 |
- F |
-
-
- | 54 |
- GSM225719 |
- Temporal Cortex |
- Normal |
- C225719M73N |
- 73 |
- M |
-
-
- | 55 |
- GSM225720 |
- Temporal Cortex |
- Normal |
- C225720M76N |
- 76 |
- M |
-
-
- | 56 |
- GSM225721 |
- Temporal Cortex |
- Normal |
- C225721M75N |
- 75 |
- M |
-
-
- | 57 |
- GSM225722 |
- Temporal Cortex |
- Normal |
- C225722F86N |
- 86 |
- F |
-
-
- | 58 |
- GSM225723 |
- Temporal Cortex |
- Normal |
- C225723F72N |
- 72 |
- F |
-
-
- | 59 |
- GSM225724 |
- Temporal Cortex |
- Normal |
- C225724M97N |
- 97 |
- M |
-
-
- | 60 |
- GSM225725 |
- Temporal Cortex |
- Normal |
- C225725M86N |
- 86 |
- M |
-
-
- | 61 |
- GSM225726 |
- Temporal Cortex |
- Normal |
- C225726M82N |
- 82 |
- M |
-
-
- | 62 |
- GSM225727 |
- Temporal Cortex |
- Normal |
- C225727F95N |
- 95 |
- F |
-
-
- | 63 |
- GSM225728 |
- Temporal Cortex |
- Normal |
- C225728F76N |
- 76 |
- F |
-
-
- | 64 |
- GSM225729 |
- Temporal Cortex |
- Normal |
- C225729M76N |
- 76 |
- M |
-
-
- | 65 |
- GSM225730 |
- Temporal Cortex |
- Normal |
- C225730M69N |
- 69 |
- M |
-
-
- | 66 |
- GSM225731 |
- Temporal Cortex |
- Normal |
- C225731F80N |
- 80 |
- F |
-
-
- | 67 |
- GSM225732 |
- Temporal Cortex |
- Normal |
- C225732F99N |
- 99 |
- F |
-
-
- | 68 |
- GSM225733 |
- Temporal Cortex |
- Normal |
- C225733M68N |
- 68 |
- M |
-
-
- | 69 |
- GSM225734 |
- Temporal Cortex |
- Normal |
- C225734M70N |
- 70 |
- M |
-
-
- | 70 |
- GSM225735 |
- Temporal Cortex |
- Normal |
- C225735F87N |
- 87 |
- F |
-
-
- | 71 |
- GSM225736 |
- Temporal Cortex |
- Normal |
- C225736F99N |
- 99 |
- F |
-
-
- | 72 |
- GSM225737 |
- Temporal Cortex |
- Normal |
- C225737F88N |
- 88 |
- F |
-
-
- | 73 |
- GSM225739 |
- Temporal Cortex |
- Normal |
- C225739M65N |
- 65 |
- M |
-
-
- | 74 |
- GSM225741 |
- Temporal Cortex |
- Normal |
- C225741M82N |
- 82 |
- M |
-
-
- | 75 |
- GSM225742 |
- Temporal Cortex |
- Normal |
- C225742F78N |
- 78 |
- F |
-
-
- | 76 |
- GSM225743 |
- Temporal Cortex |
- Normal |
- C225743F85N |
- 85 |
- F |
-
-
- | 77 |
- GSM225744 |
- Temporal Cortex |
- Normal |
- C225744F100N |
- 100 |
- F |
-
-
- | 78 |
- GSM225745 |
- Temporal Cortex |
- Normal |
- C225745F87N |
- 87 |
- F |
-
-
- | 79 |
- GSM225746 |
- Temporal Cortex |
- Normal |
- C225746F85N |
- 85 |
- F |
-
-
- | 80 |
- GSM225747 |
- Temporal Cortex |
- Normal |
- C225747F97N |
- 97 |
- F |
-
-
- | 81 |
- GSM225748 |
- Temporal Cortex |
- Normal |
- C225748M65N |
- 65 |
- M |
-
-
- | 82 |
- GSM225749 |
- Temporal Cortex |
- Normal |
- C225749M65N |
- 65 |
- M |
-
-
- | 83 |
- GSM225751 |
- Temporal Cortex |
- Normal |
- C225751F87N |
- 87 |
- F |
-
-
- | 84 |
- GSM225752 |
- Temporal Cortex |
- Normal |
- C225752F85N |
- 85 |
- F |
-
-
- | 85 |
- GSM225753 |
- Temporal Cortex |
- Normal |
- C225753M68N |
- 68 |
- M |
-
-
- | 86 |
- GSM225754 |
- Temporal Cortex |
- Normal |
- C225754M71N |
- 71 |
- M |
-
-
- | 87 |
- GSM225755 |
- Temporal Cortex |
- Normal |
- C225755F83N |
- 83 |
- F |
-
-
- | 88 |
- GSM225756 |
- Temporal Cortex |
- Normal |
- C225756M76N |
- 76 |
- M |
-
-
- | 89 |
- GSM225757 |
- Temporal Cortex |
- Normal |
- C225757M67N |
- 67 |
- M |
-
-
- | 90 |
- GSM225758 |
- Temporal Cortex |
- Normal |
- C225758F100N |
- 100 |
- F |
-
-
- | 91 |
- GSM225759 |
- Temporal Cortex |
- Normal |
- C225759M79N |
- 79 |
- M |
-
-
- | 92 |
- GSM225760 |
- Temporal Cortex |
- Normal |
- C225760M74N |
- 74 |
- M |
-
-
- | 93 |
- GSM225761 |
- Temporal Cortex |
- Normal |
- C225761F88N |
- 88 |
- F |
-
-
- | 94 |
- GSM225762 |
- Temporal Cortex |
- Normal |
- C225762M70N |
- 70 |
- M |
-
-
- | 95 |
- GSM225763 |
- Temporal Cortex |
- Normal |
- C225763F97N |
- 97 |
- F |
-
-
- | 96 |
- GSM225764 |
- Temporal Cortex |
- Normal |
- C225764M69N |
- 69 |
- M |
-
-
- | 97 |
- GSM225915 |
- Temporal Cortex |
- Normal |
- C225915F99N |
- 99 |
- F |
-
-
- | 98 |
- GSM225916 |
- Temporal Cortex |
- Normal |
- C225916M81N |
- 81 |
- M |
-
-
- | 99 |
- GSM225917 |
- Temporal Cortex |
- Normal |
- C225917F85N |
- 85 |
- F |
-
-
- | 100 |
- GSM225918 |
- Temporal Cortex |
- Normal |
- C225918F82N |
- 82 |
- F |
-
-
- | 101 |
- GSM225919 |
- Temporal Cortex |
- Normal |
- C225919M70N |
- 70 |
- M |
-
-
- | 102 |
- GSM225920 |
- Temporal Cortex |
- Normal |
- C225920M73N |
- 73 |
- M |
-
-
- | 103 |
- GSM225921 |
- Temporal Cortex |
- Normal |
- C225921M83N |
- 83 |
- M |
-
-
- | 104 |
- GSM225922 |
- Temporal Cortex |
- Normal |
- C225922M74N |
- 74 |
- M |
-
-
- | 105 |
- GSM225923 |
- Temporal Cortex |
- Normal |
- C225923M77N |
- 77 |
- M |
-
-
- | 106 |
- GSM225924 |
- Temporal Cortex |
- Normal |
- C225924M81N |
- 81 |
- M |
-
-
- | 107 |
- GSM225925 |
- Temporal Cortex |
- Normal |
- C225925M65N |
- 65 |
- M |
-
-
- | 108 |
- GSM225926 |
- Temporal Cortex |
- Normal |
- C225926F73N |
- 73 |
- F |
-
-
- | 109 |
- GSM225927 |
- Temporal Cortex |
- Normal |
- C225927F85N |
- 85 |
- F |
-
-
- | 110 |
- GSM225928 |
- Temporal Cortex |
- Normal |
- C225928M69N |
- 69 |
- M |
-
-
- | 111 |
- GSM225929 |
- Temporal Cortex |
- Normal |
- C225929M72N |
- 72 |
- M |
-
-
- | 112 |
- GSM225930 |
- Temporal Cortex |
- Normal |
- C225930F76N |
- 76 |
- F |
-
-
- | 113 |
- GSM225931 |
- Temporal Cortex |
- Normal |
- C225931M73N |
- 73 |
- M |
-
-
- | 114 |
- GSM225932 |
- Temporal Cortex |
- Normal |
- C225932M66N |
- 66 |
- M |
-
-
- | 115 |
- GSM225933 |
- Temporal Cortex |
- Normal |
- C225933F85N |
- 85 |
- F |
-
-
- | 116 |
- GSM225934 |
- Temporal Cortex |
- Normal |
- C225934M87N |
- 87 |
- M |
-
-
- | 117 |
- GSM225935 |
- Temporal Cortex |
- Normal |
- C225935F86N |
- 86 |
- F |
-
-
- | 118 |
- GSM225936 |
- Temporal Cortex |
- Normal |
- C225936F73N |
- 73 |
- F |
-
-
- | 119 |
- GSM225937 |
- Temporal Cortex |
- Normal |
- C225937M86N |
- 86 |
- M |
-
-
- | 120 |
- GSM225938 |
- Temporal Cortex |
- Normal |
- C225938M72N |
- 72 |
- M |
-
-
- | 121 |
- GSM225939 |
- Temporal Cortex |
- Normal |
- C225939F69N |
- 69 |
- F |
-
-
- | 122 |
- GSM225940 |
- Temporal Cortex |
- Normal |
- C225940F88N |
- 88 |
- F |
-
-
- | 123 |
- GSM225941 |
- Temporal Cortex |
- Normal |
- C225941M77N |
- 77 |
- M |
-
-
- | 124 |
- GSM225942 |
- Temporal Cortex |
- Normal |
- C225942M96N |
- 96 |
- M |
-
-
- | 125 |
- GSM225943 |
- Temporal Cortex |
- Normal |
- C225943F78N |
- 78 |
- F |
-
-
- | 126 |
- GSM225944 |
- Temporal Cortex |
- Normal |
- C225944M77N |
- 77 |
- M |
-
-
- | 127 |
- GSM225945 |
- Temporal Cortex |
- Normal |
- C225945F99N |
- 99 |
- F |
-
-
- | 128 |
- GSM225946 |
- Temporal Cortex |
- Normal |
- C225946M78N |
- 78 |
- M |
-
-
- | 129 |
- GSM225947 |
- Temporal Cortex |
- Normal |
- C225947F76N |
- 76 |
- F |
-
-
- | 130 |
- GSM225948 |
- Temporal Cortex |
- Normal |
- C225948M78N |
- 78 |
- M |
-
-
- | 131 |
- GSM225949 |
- Temporal Cortex |
- Normal |
- C225949F97N |
- 97 |
- F |
-
-
- | 132 |
- GSM225950 |
- Temporal Cortex |
- Normal |
- C225950F86N |
- 86 |
- F |
-
-
- | 133 |
- GSM225951 |
- Temporal Cortex |
- Normal |
- C225951M77N |
- 77 |
- M |
-
-
- | 134 |
- GSM225952 |
- Temporal Cortex |
- Normal |
- C225952M87N |
- 87 |
- M |
-
-
- | 135 |
- GSM225953 |
- Temporal Cortex |
- Normal |
- C225953F72N |
- 72 |
- F |
-
-
- | 136 |
- GSM225954 |
- Temporal Cortex |
- Normal |
- C225954F91N |
- 91 |
- F |
-
-
- | 137 |
- GSM225955 |
- Temporal Cortex |
- Normal |
- C225955F85N |
- 85 |
- F |
-
-
- | 138 |
- GSM225956 |
- Temporal Cortex |
- Normal |
- C225956M88N |
- 88 |
- M |
-
-
- | 139 |
- GSM225957 |
- Temporal Cortex |
- Normal |
- C225957F86N |
- 86 |
- F |
-
-
- | 140 |
- GSM225958 |
- Temporal Cortex |
- Normal |
- C225958F93N |
- 93 |
- F |
-
-
- | 141 |
- GSM225959 |
- Temporal Cortex |
- Normal |
- C225959M82N |
- 82 |
- M |
-
-
- | 142 |
- GSM225961 |
- Temporal Cortex |
- Normal |
- C225961F72N |
- 72 |
- F |
-
-
- | 143 |
- GSM225962 |
- Temporal Cortex |
- Normal |
- C225962F85N |
- 85 |
- F |
-
-
- | 144 |
- GSM225963 |
- Temporal Cortex |
- Normal |
- C225963M70N |
- 70 |
- M |
-
-
- | 145 |
- GSM225964 |
- Temporal Cortex |
- Normal |
- C225964F67N |
- 67 |
- F |
-
-
- | 146 |
- GSM225965 |
- Temporal Cortex |
- Normal |
- C225965F74N |
- 74 |
- F |
-
-
- | 147 |
- GSM226034 |
- Temporal Cortex |
- Normal |
- C226034M69N |
- 69 |
- M |
-
-
- | 148 |
- GSM226035 |
- Temporal Cortex |
- Normal |
- C226035M85N |
- 85 |
- M |
-
-
- | 149 |
- GSM226037 |
- Temporal Cortex |
- Normal |
- C226037M89N |
- 89 |
- M |
-
-
- | 150 |
- GSM226038 |
- Temporal Cortex |
- Normal |
- C226038M86N |
- 86 |
- M |
-
-
- | 151 |
- GSM226039 |
- Temporal Cortex |
- Normal |
- C226039M90N |
- 90 |
- M |
-
-
- | 152 |
- GSM226040 |
- Temporal Cortex |
- Normal |
- C226040F94N |
- 94 |
- F |
-
-
- | 153 |
- GSM226041 |
- Temporal Cortex |
- Normal |
- C226041F91N |
- 91 |
- F |
-
-
- | 154 |
- GSM226042 |
- Temporal Cortex |
- Normal |
- C226042F91N |
- 91 |
- F |
-
-
- | 155 |
- GSM226044 |
- Temporal Cortex |
- Normal |
- C226044F95N |
- 95 |
- F |
-
-
- | 156 |
- GSM226045 |
- Temporal Cortex |
- Normal |
- C226045F95N |
- 95 |
- F |
-
-
- | 157 |
- GSM226046 |
- Temporal Cortex |
- Normal |
- C226046F91N |
- 91 |
- F |
-
-
- | 158 |
- GSM226047 |
- Temporal Cortex |
- Normal |
- C226047M80N |
- 80 |
- M |
-
-
- | 159 |
- GSM226048 |
- Temporal Cortex |
- Normal |
- C226048M83N |
- 83 |
- M |
-
-
- | 160 |
- GSM226049 |
- Temporal Cortex |
- Normal |
- C226049M67N |
- 67 |
- M |
-
-
- | 161 |
- GSM226050 |
- Temporal Cortex |
- Normal |
- C226050M76N |
- 76 |
- M |
-
-
- | 162 |
- GSM226051 |
- Temporal Cortex |
- Normal |
- C226051F86N |
- 86 |
- F |
-
-
- | 163 |
- GSM226052 |
- Temporal Cortex |
- Normal |
- C226052F86N |
- 86 |
- F |
-
-
- | 164 |
- GSM226053 |
- Temporal Cortex |
- Normal |
- C226053M83N |
- 83 |
- M |
-
-
- | 165 |
- GSM226055 |
- Temporal Cortex |
- Normal |
- C226055M84N |
- 84 |
- M |
-
-
- | 166 |
- GSM226056 |
- Temporal Cortex |
- Normal |
- C226056M80N |
- 80 |
- M |
-
-
- | 167 |
- GSM226082 |
- Temporal Cortex |
- Normal |
- C226082M72N |
- 72 |
- M |
-
-
- | 168 |
- GSM226145 |
- Temporal Cortex |
- Normal |
- C226145M67N |
- 67 |
- M |
-
-
- | 169 |
- GSM226146 |
- Temporal Cortex |
- Normal |
- C226146F96N |
- 96 |
- F |
-
-
- | 170 |
- GSM226147 |
- Temporal Cortex |
- Normal |
- C226147F75N |
- 75 |
- F |
-
-
- | 171 |
- GSM226148 |
- Temporal Cortex |
- Normal |
- C226148F89N |
- 89 |
- F |
-
-
- | 172 |
- GSM226149 |
- Temporal Cortex |
- Normal |
- C226149F86N |
- 86 |
- F |
-
-
- | 173 |
- GSM226150 |
- Temporal Cortex |
- Normal |
- C226150M67N |
- 67 |
- M |
-
-
- | 174 |
- GSM226151 |
- Temporal Cortex |
- Normal |
- C226151M77N |
- 77 |
- M |
-
-
- | 175 |
- GSM226154 |
- Temporal Cortex |
- Normal |
- C226154M65N |
- 65 |
- M |
-
-
- | 176 |
- GSM226155 |
- Temporal Cortex |
- Normal |
- C226155M69N |
- 69 |
- M |
-
-
- | 177 |
- GSM226156 |
- Temporal Cortex |
- Normal |
- C226156M84N |
- 84 |
- M |
-
-
- | 178 |
- GSM226157 |
- Temporal Cortex |
- Normal |
- C226157F85N |
- 85 |
- F |
-
-
- | 179 |
- GSM226158 |
- Temporal Cortex |
- Normal |
- C226158M94N |
- 94 |
- M |
-
-
- | 180 |
- GSM226159 |
- Temporal Cortex |
- Normal |
- C226159F89N |
- 89 |
- F |
-
-
- | 181 |
- GSM226160 |
- Temporal Cortex |
- Normal |
- C226160M87N |
- 87 |
- M |
-
-
- | 182 |
- GSM226162 |
- Temporal Cortex |
- Normal |
- C226162M90N |
- 90 |
- M |
-
-
- | 183 |
- GSM226163 |
- Temporal Cortex |
- Normal |
- C226163F88N |
- 88 |
- F |
-
-
- | 184 |
- GSM226164 |
- Temporal Cortex |
- Normal |
- C226164M94N |
- 94 |
- M |
-
-
- | 185 |
- GSM226165 |
- Temporal Cortex |
- Normal |
- C226165F86N |
- 86 |
- F |
-
-
- | 186 |
- GSM226167 |
- Temporal Cortex |
- Normal |
- C226167F93N |
- 93 |
- F |
-
-
- | 187 |
- GSM226168 |
- Temporal Cortex |
- Normal |
- C226168M91N |
- 91 |
- M |
-
-
- | 188 |
- GSM388217 |
- Cortical Tissue |
- Alzheimer's |
- C388217F97A |
- 97 |
- F |
-
-
- | 189 |
- GSM388218 |
- Cortical Tissue |
- Alzheimer's |
- C388218F101A |
- 101 |
- F |
-
-
- | 190 |
- GSM388219 |
- Cortical Tissue |
- Alzheimer's |
- C388219M84A |
- 84 |
- M |
-
-
- | 191 |
- GSM388220 |
- Cortical Tissue |
- Alzheimer's |
- C388220F95A |
- 95 |
- F |
-
-
- | 192 |
- GSM388221 |
- Cortical Tissue |
- Alzheimer's |
- C388221F97A |
- 97 |
- F |
-
-
- | 193 |
- GSM388222 |
- Cortical Tissue |
- Alzheimer's |
- C388222F102A |
- 102 |
- F |
-
-
- | 194 |
- GSM388223 |
- Cortical Tissue |
- Alzheimer's |
- C388223M87A |
- 87 |
- M |
-
-
- | 195 |
- GSM388224 |
- Cortical Tissue |
- Alzheimer's |
- C388224F77A |
- 77 |
- F |
-
-
- | 196 |
- GSM388225 |
- Cortical Tissue |
- Alzheimer's |
- C388225M87A |
- 87 |
- M |
-
-
- | 197 |
- GSM388226 |
- Cortical Tissue |
- Alzheimer's |
- C388226M84A |
- 84 |
- M |
-
-
- | 198 |
- GSM388228 |
- Cortical Tissue |
- Alzheimer's |
- C388228F92A |
- 92 |
- F |
-
-
- | 199 |
- GSM388229 |
- Cortical Tissue |
- Alzheimer's |
- C388229M93A |
- 93 |
- M |
-
-
- | 200 |
- GSM388230 |
- Cortical Tissue |
- Alzheimer's |
- C388230F93A |
- 93 |
- F |
-
-
- | 201 |
- GSM388231 |
- Cortical Tissue |
- Alzheimer's |
- C388231F87A |
- 87 |
- F |
-
-
- | 202 |
- GSM388232 |
- Cortical Tissue |
- Alzheimer's |
- C388232F90A |
- 90 |
- F |
-
-
- | 203 |
- GSM388233 |
- Cortical Tissue |
- Alzheimer's |
- C388233M75A |
- 75 |
- M |
-
-
- | 204 |
- GSM388234 |
- Cortical Tissue |
- Alzheimer's |
- C388234M92A |
- 92 |
- M |
-
-
- | 205 |
- GSM388235 |
- Cortical Tissue |
- Alzheimer's |
- C388235M83A |
- 83 |
- M |
-
-
- | 206 |
- GSM388236 |
- Cortical Tissue |
- Alzheimer's |
- C388236M88A |
- 88 |
- M |
-
-
- | 207 |
- GSM388237 |
- Cortical Tissue |
- Alzheimer's |
- C388237M89A |
- 89 |
- M |
-
-
- | 208 |
- GSM388238 |
- Cortical Tissue |
- Alzheimer's |
- C388238F74A |
- 74 |
- F |
-
-
- | 209 |
- GSM388239 |
- Cortical Tissue |
- Alzheimer's |
- C388239F79A |
- 79 |
- F |
-
-
- | 210 |
- GSM388240 |
- Cortical Tissue |
- Alzheimer's |
- C388240M80A |
- 80 |
- M |
-
-
- | 211 |
- GSM388241 |
- Cortical Tissue |
- Alzheimer's |
- C388241F97A |
- 97 |
- F |
-
-
- | 212 |
- GSM388242 |
- Cortical Tissue |
- Alzheimer's |
- C388242M87A |
- 87 |
- M |
-
-
- | 213 |
- GSM388243 |
- Cortical Tissue |
- Alzheimer's |
- C388243F89A |
- 89 |
- F |
-
-
- | 214 |
- GSM388244 |
- Cortical Tissue |
- Alzheimer's |
- C388244F90A |
- 90 |
- F |
-
-
- | 215 |
- GSM388245 |
- Cortical Tissue |
- Alzheimer's |
- C388245M90A |
- 90 |
- M |
-
-
- | 216 |
- GSM388246 |
- Cortical Tissue |
- Alzheimer's |
- C388246M78A |
- 78 |
- M |
-
-
- | 217 |
- GSM388247 |
- Cortical Tissue |
- Alzheimer's |
- C388247F80A |
- 80 |
- F |
-
-
- | 218 |
- GSM388248 |
- Cortical Tissue |
- Alzheimer's |
- C388248F79A |
- 79 |
- F |
-
-
- | 219 |
- GSM388249 |
- Cortical Tissue |
- Alzheimer's |
- C388249F87A |
- 87 |
- F |
-
-
- | 220 |
- GSM388250 |
- Cortical Tissue |
- Alzheimer's |
- C388250F88A |
- 88 |
- F |
-
-
- | 221 |
- GSM388251 |
- Cortical Tissue |
- Alzheimer's |
- C388251M86A |
- 86 |
- M |
-
-
- | 222 |
- GSM388252 |
- Cortical Tissue |
- Alzheimer's |
- C388252F74A |
- 74 |
- F |
-
-
- | 223 |
- GSM388253 |
- Cortical Tissue |
- Alzheimer's |
- C388253F72A |
- 72 |
- F |
-
-
- | 224 |
- GSM388254 |
- Cortical Tissue |
- Alzheimer's |
- C388254M81A |
- 81 |
- M |
-
-
- | 225 |
- GSM388255 |
- Cortical Tissue |
- Alzheimer's |
- C388255F68A |
- 68 |
- F |
-
-
- | 226 |
- GSM388256 |
- Cortical Tissue |
- Alzheimer's |
- C388256F81A |
- 81 |
- F |
-
-
- | 227 |
- GSM388257 |
- Cortical Tissue |
- Alzheimer's |
- C388257F82A |
- 82 |
- F |
-
-
- | 228 |
- GSM388258 |
- Cortical Tissue |
- Alzheimer's |
- C388258M78A |
- 78 |
- M |
-
-
- | 229 |
- GSM388259 |
- Cortical Tissue |
- Alzheimer's |
- C388259M74A |
- 74 |
- M |
-
-
- | 230 |
- GSM388260 |
- Cortical Tissue |
- Alzheimer's |
- C388260M88A |
- 88 |
- M |
-
-
- | 231 |
- GSM388261 |
- Cortical Tissue |
- Alzheimer's |
- C388261F78A |
- 78 |
- F |
-
-
- | 232 |
- GSM388262 |
- Cortical Tissue |
- Alzheimer's |
- C388262M83A |
- 83 |
- M |
-
-
- | 233 |
- GSM388263 |
- Cortical Tissue |
- Alzheimer's |
- C388263M83A |
- 83 |
- M |
-
-
- | 234 |
- GSM388264 |
- Cortical Tissue |
- Alzheimer's |
- C388264M80A |
- 80 |
- M |
-
-
- | 235 |
- GSM388265 |
- Cortical Tissue |
- Alzheimer's |
- C388265M84A |
- 84 |
- M |
-
-
- | 236 |
- GSM388266 |
- Cortical Tissue |
- Alzheimer's |
- C388266F79A |
- 79 |
- F |
-
-
- | 237 |
- GSM388267 |
- Cortical Tissue |
- Alzheimer's |
- C388267F86A |
- 86 |
- F |
-
-
- | 238 |
- GSM388268 |
- Cortical Tissue |
- Alzheimer's |
- C388268M92A |
- 92 |
- M |
-
-
- | 239 |
- GSM388269 |
- Cortical Tissue |
- Alzheimer's |
- C388269F81A |
- 81 |
- F |
-
-
- | 240 |
- GSM388270 |
- Cortical Tissue |
- Alzheimer's |
- C388270F79A |
- 79 |
- F |
-
-
- | 241 |
- GSM388271 |
- Cortical Tissue |
- Alzheimer's |
- C388271M74A |
- 74 |
- M |
-
-
- | 242 |
- GSM388272 |
- Cortical Tissue |
- Alzheimer's |
- C388272F73A |
- 73 |
- F |
-
-
- | 243 |
- GSM388273 |
- Cortical Tissue |
- Alzheimer's |
- C388273M87A |
- 87 |
- M |
-
-
- | 244 |
- GSM388274 |
- Cortical Tissue |
- Alzheimer's |
- C388274F86A |
- 86 |
- F |
-
-
- | 245 |
- GSM388275 |
- Cortical Tissue |
- Alzheimer's |
- C388275F86A |
- 86 |
- F |
-
-
- | 246 |
- GSM388276 |
- Cortical Tissue |
- Alzheimer's |
- C388276F87A |
- 87 |
- F |
-
-
- | 247 |
- GSM388277 |
- Cortical Tissue |
- Alzheimer's |
- C388277F92A |
- 92 |
- F |
-
-
- | 248 |
- GSM388278 |
- Cortical Tissue |
- Alzheimer's |
- C388278F78A |
- 78 |
- F |
-
-
- | 249 |
- GSM388279 |
- Cortical Tissue |
- Alzheimer's |
- C388279F94A |
- 94 |
- F |
-
-
- | 250 |
- GSM388281 |
- Cortical Tissue |
- Alzheimer's |
- C388281F94A |
- 94 |
- F |
-
-
- | 251 |
- GSM388282 |
- Cortical Tissue |
- Alzheimer's |
- C388282M76A |
- 76 |
- M |
-
-
- | 252 |
- GSM388284 |
- Cortical Tissue |
- Alzheimer's |
- C388284M91A |
- 91 |
- M |
-
-
- | 253 |
- GSM388285 |
- Cortical Tissue |
- Alzheimer's |
- C388285M86A |
- 86 |
- M |
-
-
- | 254 |
- GSM388286 |
- Cortical Tissue |
- Alzheimer's |
- C388286M77A |
- 77 |
- M |
-
-
- | 255 |
- GSM388287 |
- Cortical Tissue |
- Alzheimer's |
- C388287M82A |
- 82 |
- M |
-
-
- | 256 |
- GSM388288 |
- Cortical Tissue |
- Alzheimer's |
- C388288M78A |
- 78 |
- M |
-
-
- | 257 |
- GSM388289 |
- Cortical Tissue |
- Alzheimer's |
- C388289M79A |
- 79 |
- M |
-
-
- | 258 |
- GSM388290 |
- Cortical Tissue |
- Alzheimer's |
- C388290F84A |
- 84 |
- F |
-
-
- | 259 |
- GSM388291 |
- Cortical Tissue |
- Alzheimer's |
- C388291F87A |
- 87 |
- F |
-
-
- | 260 |
- GSM388292 |
- Cortical Tissue |
- Alzheimer's |
- C388292F86A |
- 86 |
- F |
-
-
- | 261 |
- GSM388294 |
- Cortical Tissue |
- Alzheimer's |
- C388294M83A |
- 83 |
- M |
-
-
- | 262 |
- GSM388295 |
- Cortical Tissue |
- Alzheimer's |
- C388295M83A |
- 83 |
- M |
-
-
- | 263 |
- GSM388296 |
- Cortical Tissue |
- Alzheimer's |
- C388296M81A |
- 81 |
- M |
-
-
- | 264 |
- GSM388297 |
- Cortical Tissue |
- Alzheimer's |
- C388297F93A |
- 93 |
- F |
-
-
- | 265 |
- GSM388298 |
- Cortical Tissue |
- Alzheimer's |
- C388298M71A |
- 71 |
- M |
-
-
- | 266 |
- GSM388299 |
- Cortical Tissue |
- Alzheimer's |
- C388299M78A |
- 78 |
- M |
-
-
- | 267 |
- GSM388300 |
- Cortical Tissue |
- Alzheimer's |
- C388300F75A |
- 75 |
- F |
-
-
- | 268 |
- GSM388301 |
- Cortical Tissue |
- Alzheimer's |
- C388301F84A |
- 84 |
- F |
-
-
- | 269 |
- GSM388302 |
- Cortical Tissue |
- Alzheimer's |
- C388302M73A |
- 73 |
- M |
-
-
- | 270 |
- GSM388303 |
- Cortical Tissue |
- Alzheimer's |
- C388303F89A |
- 89 |
- F |
-
-
- | 271 |
- GSM388304 |
- Cortical Tissue |
- Alzheimer's |
- C388304FNAA |
- NA |
- F |
-
-
- | 272 |
- GSM388305 |
- Cortical Tissue |
- Alzheimer's |
- C388305M69A |
- 69 |
- M |
-
-
- | 273 |
- GSM388306 |
- Cortical Tissue |
- Alzheimer's |
- C388306M83A |
- 83 |
- M |
-
-
- | 274 |
- GSM388307 |
- Cortical Tissue |
- Alzheimer's |
- C388307M71A |
- 71 |
- M |
-
-
- | 275 |
- GSM388308 |
- Cortical Tissue |
- Alzheimer's |
- C388308F86A |
- 86 |
- F |
-
-
- | 276 |
- GSM388309 |
- Cortical Tissue |
- Alzheimer's |
- C388309M82A |
- 82 |
- M |
-
-
- | 277 |
- GSM388310 |
- Cortical Tissue |
- Alzheimer's |
- C388310FNAA |
- NA |
- F |
-
-
- | 278 |
- GSM388311 |
- Cortical Tissue |
- Alzheimer's |
- C388311M88A |
- 88 |
- M |
-
-
- | 279 |
- GSM388312 |
- Cortical Tissue |
- Alzheimer's |
- C388312M77A |
- 77 |
- M |
-
-
- | 280 |
- GSM388313 |
- Cortical Tissue |
- Alzheimer's |
- C388313M85A |
- 85 |
- M |
-
-
- | 281 |
- GSM388314 |
- Cortical Tissue |
- Alzheimer's |
- C388314F81A |
- 81 |
- F |
-
-
- | 282 |
- GSM388315 |
- Cortical Tissue |
- Alzheimer's |
- C388315F86A |
- 86 |
- F |
-
-
- | 283 |
- GSM388316 |
- Cortical Tissue |
- Alzheimer's |
- C388316M89A |
- 89 |
- M |
-
-
- | 284 |
- GSM388317 |
- Cortical Tissue |
- Alzheimer's |
- C388317F73A |
- 73 |
- F |
-
-
- | 285 |
- GSM388318 |
- Cortical Tissue |
- Alzheimer's |
- C388318F96A |
- 96 |
- F |
-
-
- | 286 |
- GSM388319 |
- Cortical Tissue |
- Alzheimer's |
- C388319M73A |
- 73 |
- M |
-
-
- | 287 |
- GSM388320 |
- Cortical Tissue |
- Alzheimer's |
- C388320M81A |
- 81 |
- M |
-
-
- | 288 |
- GSM388321 |
- Cortical Tissue |
- Alzheimer's |
- C388321F84A |
- 84 |
- F |
-
-
- | 289 |
- GSM388322 |
- Cortical Tissue |
- Alzheimer's |
- C388322F93A |
- 93 |
- F |
-
-
- | 290 |
- GSM388323 |
- Cortical Tissue |
- Alzheimer's |
- C388323F82A |
- 82 |
- F |
-
-
- | 291 |
- GSM388324 |
- Cortical Tissue |
- Alzheimer's |
- C388324M76A |
- 76 |
- M |
-
-
- | 292 |
- GSM388325 |
- Cortical Tissue |
- Alzheimer's |
- C388325M77A |
- 77 |
- M |
-
-
- | 293 |
- GSM388326 |
- Cortical Tissue |
- Alzheimer's |
- C388326F86A |
- 86 |
- F |
-
-
- | 294 |
- GSM388327 |
- Cortical Tissue |
- Alzheimer's |
- C388327F85A |
- 85 |
- F |
-
-
- | 295 |
- GSM388328 |
- Cortical Tissue |
- Alzheimer's |
- C388328M83A |
- 83 |
- M |
-
-
- | 296 |
- GSM388329 |
- Cortical Tissue |
- Alzheimer's |
- C388329M76A |
- 76 |
- M |
-
-
- | 297 |
- GSM388330 |
- Cortical Tissue |
- Alzheimer's |
- C388330M81A |
- 81 |
- M |
-
-
- | 298 |
- GSM388331 |
- Cortical Tissue |
- Alzheimer's |
- C388331M79A |
- 79 |
- M |
-
-
- | 299 |
- GSM388332 |
- Cortical Tissue |
- Alzheimer's |
- C388332M81A |
- 81 |
- M |
-
-
- | 300 |
- GSM388333 |
- Cortical Tissue |
- Alzheimer's |
- C388333F78A |
- 78 |
- F |
-
-
- | 301 |
- GSM388334 |
- Cortical Tissue |
- Alzheimer's |
- C388334M80A |
- 80 |
- M |
-
-
- | 302 |
- GSM388335 |
- Cortical Tissue |
- Alzheimer's |
- C388335M84A |
- 84 |
- M |
-
-
- | 303 |
- GSM388336 |
- Cortical Tissue |
- Alzheimer's |
- C388336F85A |
- 85 |
- F |
-
-
- | 304 |
- GSM388337 |
- Cortical Tissue |
- Alzheimer's |
- C388337M75A |
- 75 |
- M |
-
-
- | 305 |
- GSM388338 |
- Cortical Tissue |
- Alzheimer's |
- C388338F80A |
- 80 |
- F |
-
-
- | 306 |
- GSM388339 |
- Cortical Tissue |
- Alzheimer's |
- C388339F97A |
- 97 |
- F |
-
-
- | 307 |
- GSM388340 |
- Cortical Tissue |
- Alzheimer's |
- C388340F82A |
- 82 |
- F |
-
-
- | 308 |
- GSM388341 |
- Cortical Tissue |
- Alzheimer's |
- C388341M82A |
- 82 |
- M |
-
-
- | 309 |
- GSM388342 |
- Cortical Tissue |
- Alzheimer's |
- C388342M77A |
- 77 |
- M |
-
-
- | 310 |
- GSM388343 |
- Cortical Tissue |
- Alzheimer's |
- C388343M81A |
- 81 |
- M |
-
-
- | 311 |
- GSM388345 |
- Cortical Tissue |
- Alzheimer's |
- C388345F96A |
- 96 |
- F |
-
-
- | 312 |
- GSM388346 |
- Cortical Tissue |
- Alzheimer's |
- C388346F90A |
- 90 |
- F |
-
-
- | 313 |
- GSM388347 |
- Cortical Tissue |
- Alzheimer's |
- C388347M86A |
- 86 |
- M |
-
-
- | 314 |
- GSM388348 |
- Cortical Tissue |
- Alzheimer's |
- C388348M88A |
- 88 |
- M |
-
-
- | 315 |
- GSM388349 |
- Cortical Tissue |
- Alzheimer's |
- C388349F90A |
- 90 |
- F |
-
-
- | 316 |
- GSM388350 |
- Cortical Tissue |
- Alzheimer's |
- C388350F90A |
- 90 |
- F |
-
-
- | 317 |
- GSM388351 |
- Cortical Tissue |
- Alzheimer's |
- C388351F84A |
- 84 |
- F |
-
-
- | 318 |
- GSM388352 |
- Cortical Tissue |
- Alzheimer's |
- C388352M84A |
- 84 |
- M |
-
-
- | 319 |
- GSM388353 |
- Cortical Tissue |
- Alzheimer's |
- C388353F91A |
- 91 |
- F |
-
-
- | 320 |
- GSM388354 |
- Cortical Tissue |
- Alzheimer's |
- C388354F81A |
- 81 |
- F |
-
-
- | 321 |
- GSM388355 |
- Cortical Tissue |
- Alzheimer's |
- C388355F84A |
- 84 |
- F |
-
-
- | 322 |
- GSM388356 |
- Cortical Tissue |
- Alzheimer's |
- C388356M80A |
- 80 |
- M |
-
-
- | 323 |
- GSM388357 |
- Cortical Tissue |
- Alzheimer's |
- C388357M81A |
- 81 |
- M |
-
-
- | 324 |
- GSM388358 |
- Cortical Tissue |
- Alzheimer's |
- C388358F87A |
- 87 |
- F |
-
-
- | 325 |
- GSM388359 |
- Cortical Tissue |
- Alzheimer's |
- C388359M85A |
- 85 |
- M |
-
-
- | 326 |
- GSM388360 |
- Cortical Tissue |
- Alzheimer's |
- C388360F90A |
- 90 |
- F |
-
-
- | 327 |
- GSM388361 |
- Cortical Tissue |
- Alzheimer's |
- C388361M79A |
- 79 |
- M |
-
-
- | 328 |
- GSM388362 |
- Cortical Tissue |
- Alzheimer's |
- C388362F87A |
- 87 |
- F |
-
-
- | 329 |
- GSM388363 |
- Cortical Tissue |
- Alzheimer's |
- C388363M75A |
- 75 |
- M |
-
-
- | 330 |
- GSM388364 |
- Cortical Tissue |
- Alzheimer's |
- C388364F92A |
- 92 |
- F |
-
-
- | 331 |
- GSM388365 |
- Cortical Tissue |
- Alzheimer's |
- C388365F84A |
- 84 |
- F |
-
-
- | 332 |
- GSM388366 |
- Cortical Tissue |
- Alzheimer's |
- C388366M75A |
- 75 |
- M |
-
-
- | 333 |
- GSM388367 |
- Cortical Tissue |
- Alzheimer's |
- C388367F76A |
- 76 |
- F |
-
-
- | 334 |
- GSM388368 |
- Cortical Tissue |
- Alzheimer's |
- C388368F86A |
- 86 |
- F |
-
-
- | 335 |
- GSM388369 |
- Cortical Tissue |
- Alzheimer's |
- C388369M82A |
- 82 |
- M |
-
-
- | 336 |
- GSM388370 |
- Cortical Tissue |
- Alzheimer's |
- C388370M76A |
- 76 |
- M |
-
-
- | 337 |
- GSM388371 |
- Cortical Tissue |
- Alzheimer's |
- C388371F81A |
- 81 |
- F |
-
-
- | 338 |
- GSM388372 |
- Cortical Tissue |
- Alzheimer's |
- C388372F80A |
- 80 |
- F |
-
-
- | 339 |
- GSM388373 |
- Cortical Tissue |
- Alzheimer's |
- C388373M83A |
- 83 |
- M |
-
-
- | 340 |
- GSM388374 |
- Cortical Tissue |
- Alzheimer's |
- C388374F83A |
- 83 |
- F |
-
-
- | 341 |
- GSM388375 |
- Cortical Tissue |
- Alzheimer's |
- C388375F84A |
- 84 |
- F |
-
-
- | 342 |
- GSM388376 |
- Cortical Tissue |
- Alzheimer's |
- C388376M93A |
- 93 |
- M |
-
-
- | 343 |
- GSM388377 |
- Cortical Tissue |
- Alzheimer's |
- C388377F92A |
- 92 |
- F |
-
-
- | 344 |
- GSM388378 |
- Cortical Tissue |
- Alzheimer's |
- C388378M78A |
- 78 |
- M |
-
-
- | 345 |
- GSM388379 |
- Cortical Tissue |
- Alzheimer's |
- C388379M90A |
- 90 |
- M |
-
-
- | 346 |
- GSM388380 |
- Cortical Tissue |
- Alzheimer's |
- C388380M83A |
- 83 |
- M |
-
-
- | 347 |
- GSM388381 |
- Cortical Tissue |
- Alzheimer's |
- C388381M79A |
- 79 |
- M |
-
-
- | 348 |
- GSM388382 |
- Cortical Tissue |
- Alzheimer's |
- C388382M84A |
- 84 |
- M |
-
-
- | 349 |
- GSM388383 |
- Cortical Tissue |
- Alzheimer's |
- C388383F90A |
- 90 |
- F |
-
-
- | 350 |
- GSM388384 |
- Cortical Tissue |
- Alzheimer's |
- C388384F88A |
- 88 |
- F |
-
-
- | 351 |
- GSM388385 |
- Cortical Tissue |
- Alzheimer's |
- C388385M77A |
- 77 |
- M |
-
-
- | 352 |
- GSM388386 |
- Cortical Tissue |
- Alzheimer's |
- C388386F80A |
- 80 |
- F |
-
-
- | 353 |
- GSM388387 |
- Cortical Tissue |
- Alzheimer's |
- C388387M87A |
- 87 |
- M |
-
-
- | 354 |
- GSM388388 |
- Cortical Tissue |
- Alzheimer's |
- C388388M86A |
- 86 |
- M |
-
-
- | 355 |
- GSM388389 |
- Cortical Tissue |
- Alzheimer's |
- C388389M74A |
- 74 |
- M |
-
-
- | 356 |
- GSM388390 |
- Cortical Tissue |
- Alzheimer's |
- C388390F86A |
- 86 |
- F |
-
-
- | 357 |
- GSM388391 |
- Cortical Tissue |
- Alzheimer's |
- C388391F81A |
- 81 |
- F |
-
-
- | 358 |
- GSM388392 |
- Cortical Tissue |
- Alzheimer's |
- C388392F73A |
- 73 |
- F |
-
-
- | 359 |
- GSM388393 |
- Cortical Tissue |
- Alzheimer's |
- C388393M83A |
- 83 |
- M |
-
-
- | 360 |
- GSM388394 |
- Cortical Tissue |
- Alzheimer's |
- C388394M86A |
- 86 |
- M |
-
-
- | 361 |
- GSM388395 |
- Cortical Tissue |
- Alzheimer's |
- C388395F86A |
- 86 |
- F |
-
-
- | 362 |
- GSM388396 |
- Cortical Tissue |
- Alzheimer's |
- C388396M78A |
- 78 |
- M |
-
-
- | 363 |
- GSM388397 |
- Cortical Tissue |
- Alzheimer's |
- C388397M83A |
- 83 |
- M |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GSE15222_F_N_RI_0409/experiment-design.rtf b/general/datasets/GSE15222_F_N_RI_0409/experiment-design.rtf
deleted file mode 100644
index 07d1b52..0000000
--- a/general/datasets/GSE15222_F_N_RI_0409/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Expression profiling by array
-
-We recently surveyed the relationship between the human brain transcriptome and genome in a series of neuropathologically normal postmortem samples. We now have analyzed additional samples with a confirmed pathologic diagnosis of late onset Alzheimer's disease (LOAD, final n=187 controls, 176 cases). Nine percent of the cortical transcripts we analyzed had expression profiles correlated with their genotypes in the combined cohort and approximately 5% of transcripts had SNP-transcript relationships that could distinguish LOAD samples. Two of these transcripts have been previously implicated in LOAD candidate gene SNP-expression screens. This study shows how the relationship between common inherited genetic variants and brain transcript expression can be used in the study of human brain disorders. We suggest that studying the transcriptome as a quantitative endo-phenotype has greater power to find risk SNPs influencing expression than the use of discrete diagnostic categories such as presence or absence of disease. see DOI:10.1016/j.ajhg.2009.03.011 for further details and complete author list.
-
-Expression quantitative trait loci study using human brain from 363 cortical samples. Affymetrix 500K chip for genotyping, Illumina Sentrix Human-ref 8 bead array chip for expression. Genotyping data will be available at dbGAP.
diff --git a/general/datasets/GSE15222_F_N_RI_0409/notes.rtf b/general/datasets/GSE15222_F_N_RI_0409/notes.rtf
deleted file mode 100644
index e7bd85c..0000000
--- a/general/datasets/GSE15222_F_N_RI_0409/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Access to the original data from Dr. Myers' laboratory
-or GEO GSE15222
-PMI = Post Mortem Interval
-Cannot find this record in the GEO website: WGACON-120
-
-This data is based on May 2004 (NCBI35/hg17).
diff --git a/general/datasets/GSE15222_F_N_RI_0409/platform.rtf b/general/datasets/GSE15222_F_N_RI_0409/platform.rtf
deleted file mode 100644
index 5bcda8b..0000000
--- a/general/datasets/GSE15222_F_N_RI_0409/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Illumina Human 50 mer probes. Total of 24357 probes according to Myers et al. A total of 24354 probes included in this GeneNetwork file.
-
-From the Methods section of the paper:
-
-Genotyping and Expression Proï¬ling DNA was hybridized to the Affymetrix GeneChip Human Mapping 500K Array Set (502,627 SNPs) as previously described.11,12 Genotypes were extracted with the use of both SNiPer-HD13 and BRLMM (Affymetrix, Santa Clara, CA) algorithms. Genotypes that exhibited less than 98% concordance between calls were excluded. SNPs with call rates less than 90% were excluded from the analysis. HardyWeinberg equilibrium (HWE) was assessed with exact tests and the PLINK analysis toolset.14 SNPs with HWE exact-test p values less than 0.05, as well as SNPs with minor-allele frequencies less than 1%, were excluded. Allele calls had a mean of 97% and a range of 90%–99%. cRNA was hybridized to Illumina Human Refseq-8 Expression BeadChip (24,357 transcripts) via standard protocols. Expression proï¬les were extracted and rank invariant normalized15–17 with the use of the BeadStudio software available from Illumina, with the Illumina custom error model used. Rankinvariant-normalized expression data were log10 transformed, and missing data were encoded as missing, rather than as a zero level of expression.
diff --git a/general/datasets/GSE15222_F_N_RI_0409/summary.rtf b/general/datasets/GSE15222_F_N_RI_0409/summary.rtf
deleted file mode 100644
index e99fa9e..0000000
--- a/general/datasets/GSE15222_F_N_RI_0409/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Myers and colleagues generated massive neocortical transcriptome data sets for a set of unrelated elderly neurologically and neuropathologically normal humans and from confirmed late onset Alzheimer's disease patients (LOAD, n = 187 normal and 176 LOAD cases, see DOI:10.1016/j.ajhg.2009.03.011 for detail). They used an Illumina Sentrix Bead array (HumanRef-8) that measures expression of approximately 19,730 curated RefSeq sequences (Human Build 34).
-
-Case identifiers: All case identifiers (IDs) in GeneNetwork begin with a capital C followed by a six digit GEO identifier, followed by the sex and age in years. Non-Alzheimer cases are labeled with the suffix letter N: C225652M85N. Alzheimer cases are labeled with the suffix letter A: C388217F97A.
-
-Data were initially downloaded from the NCBI GEO archive under the experiment ID GSE15222. All data were generated using the Illumina HumanRef-8 expression BeadChip (GPL2700) v2 Rev0. This data set in GeneNetwork includes data for 24,354 probes. We have realigned the 50-mer sequences by BLAT to the latest version of the human genome (Feb 2009, hg19) and reannotated the array (August 2009). The annotation in GN will differ from that provided in GEO for this platform. We were unable to obtain 50-mer sequences for several thousand probes (e.g., HTT), and these probes have therefore not been realigned to the human genome.
-
-The GEO data set was processed by Myers and colleagues using Illumina's Rank Invariant transform. We performed a series of QC and renormalization steps to the data to allow more facile comparison to other data sets in GeneNetwork. In brief, data is log2 transformed. We recentered each array to a mean expression of 8 units and a standard deviation of 2 units (2z + 8 transform). The values are therefore modified z scores and each unit represents roughly a two-fold difference in expression. Average expression across all 363 cases range from a low of 6 units (e.g., SYT15) to a high of 19 units for ARSK. APOE has an average expression of 15 units and APP has an average expression of 11.5 units.. The distribution is far from normal with a great excess of measurements of genes with low to moderate expression clustered between 6.5 and 8.5 units.
-
-A small number of arrays (n = 6, GSM226040, GSM226041, GSM226042, GSM226044, GSM226045, GSM226046) had a different distribution from the great majority of other arrays. This was probably due to a batch processing effect. Members of this minority group belonged to both normal and LOAD cases. This putative batch effect has been eliminated in the GeneNetwork rendition of the Myers data. To eliminate the putative batch effect, we simply computed a mean offset for each probe in the "minority set" relative to the remaining "majority set" and added or subtracted this offset to force the mean of each probe in the minority set to conform to mean of the same probe in the majority set.
diff --git a/general/datasets/GSE15222_F_RI_0409/acknowledgment.rtf b/general/datasets/GSE15222_F_RI_0409/acknowledgment.rtf
deleted file mode 100644
index c203ed9..0000000
--- a/general/datasets/GSE15222_F_RI_0409/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-http://labs.med.miami.edu/myers
diff --git a/general/datasets/GSE15222_F_RI_0409/cases.rtf b/general/datasets/GSE15222_F_RI_0409/cases.rtf
deleted file mode 100644
index 6933d14..0000000
--- a/general/datasets/GSE15222_F_RI_0409/cases.rtf
+++ /dev/null
@@ -1,3290 +0,0 @@
-
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM225652 |
- Temporal Cortex |
- Normal |
- C225652M85N |
- 85 |
- M |
-
-
- | 2 |
- GSM225662 |
- Temporal Cortex |
- Normal |
- C225662M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM225664 |
- Temporal Cortex |
- Normal |
- C225664F79N |
- 79 |
- F |
-
-
- | 4 |
- GSM225665 |
- Temporal Cortex |
- Normal |
- C225665F85N |
- 85 |
- F |
-
-
- | 5 |
- GSM225666 |
- Temporal Cortex |
- Normal |
- C225666F73N |
- 73 |
- F |
-
-
- | 6 |
- GSM225667 |
- Temporal Cortex |
- Normal |
- C225667M81N |
- 81 |
- M |
-
-
- | 7 |
- GSM225668 |
- Temporal Cortex |
- Normal |
- C225668M79N |
- 79 |
- M |
-
-
- | 8 |
- GSM225669 |
- Temporal Cortex |
- Normal |
- C225669M77N |
- 77 |
- M |
-
-
- | 9 |
- GSM225670 |
- Temporal Cortex |
- Normal |
- C225670M69N |
- 69 |
- M |
-
-
- | 10 |
- GSM225671 |
- Temporal Cortex |
- Normal |
- C225671M86N |
- 86 |
- M |
-
-
- | 11 |
- GSM225672 |
- Temporal Cortex |
- Normal |
- C225672F83N |
- 83 |
- F |
-
-
- | 12 |
- GSM225673 |
- Temporal Cortex |
- Normal |
- C225673M78N |
- 78 |
- M |
-
-
- | 13 |
- GSM225674 |
- Temporal Cortex |
- Normal |
- C225674M94N |
- 94 |
- M |
-
-
- | 14 |
- GSM225675 |
- Temporal Cortex |
- Normal |
- C225675F81N |
- 81 |
- F |
-
-
- | 15 |
- GSM225676 |
- Temporal Cortex |
- Normal |
- C225676M76N |
- 76 |
- M |
-
-
- | 16 |
- GSM225677 |
- Temporal Cortex |
- Normal |
- C225677M83N |
- 83 |
- M |
-
-
- | 17 |
- GSM225678 |
- Temporal Cortex |
- Normal |
- C225678M68N |
- 68 |
- M |
-
-
- | 18 |
- GSM225679 |
- Temporal Cortex |
- Normal |
- C225679F82N |
- 82 |
- F |
-
-
- | 19 |
- GSM225680 |
- Temporal Cortex |
- Normal |
- C225680F70N |
- 70 |
- F |
-
-
- | 20 |
- GSM225681 |
- Temporal Cortex |
- Normal |
- C225681M86N |
- 86 |
- M |
-
-
- | 21 |
- GSM225682 |
- Temporal Cortex |
- Normal |
- C225682M78N |
- 78 |
- M |
-
-
- | 22 |
- GSM225683 |
- Temporal Cortex |
- Normal |
- C225683M82N |
- 82 |
- M |
-
-
- | 23 |
- GSM225684 |
- Temporal Cortex |
- Normal |
- C225684F94N |
- 94 |
- F |
-
-
- | 24 |
- GSM225685 |
- Temporal Cortex |
- Normal |
- C225685F87N |
- 87 |
- F |
-
-
- | 25 |
- GSM225686 |
- Temporal Cortex |
- Normal |
- C225686M74N |
- 74 |
- M |
-
-
- | 26 |
- GSM225687 |
- Temporal Cortex |
- Normal |
- C225687M85N |
- 85 |
- M |
-
-
- | 27 |
- GSM225688 |
- Temporal Cortex |
- Normal |
- C225688M75N |
- 75 |
- M |
-
-
- | 28 |
- GSM225689 |
- Temporal Cortex |
- Normal |
- C225689F86N |
- 86 |
- F |
-
-
- | 29 |
- GSM225690 |
- Temporal Cortex |
- Normal |
- C225690M75N |
- 75 |
- M |
-
-
- | 30 |
- GSM225691 |
- Temporal Cortex |
- Normal |
- C225691M81N |
- 81 |
- M |
-
-
- | 31 |
- GSM225692 |
- Temporal Cortex |
- Normal |
- C225692F72N |
- 72 |
- F |
-
-
- | 32 |
- GSM225693 |
- Temporal Cortex |
- Normal |
- C225693F81N |
- 81 |
- F |
-
-
- | 33 |
- GSM225695 |
- Temporal Cortex |
- Normal |
- C225695M81N |
- 81 |
- M |
-
-
- | 34 |
- GSM225696 |
- Temporal Cortex |
- Normal |
- C225696M81N |
- 81 |
- M |
-
-
- | 35 |
- GSM225697 |
- Temporal Cortex |
- Normal |
- C225697M91N |
- 91 |
- M |
-
-
- | 36 |
- GSM225698 |
- Temporal Cortex |
- Normal |
- C225698M84N |
- 84 |
- M |
-
-
- | 37 |
- GSM225699 |
- Temporal Cortex |
- Normal |
- C225699M96N |
- 96 |
- M |
-
-
- | 38 |
- GSM225700 |
- Temporal Cortex |
- Normal |
- C225700F97N |
- 97 |
- F |
-
-
- | 39 |
- GSM225701 |
- Temporal Cortex |
- Normal |
- C225701M90N |
- 90 |
- M |
-
-
- | 40 |
- GSM225702 |
- Temporal Cortex |
- Normal |
- C225702F67N |
- 67 |
- F |
-
-
- | 41 |
- GSM225703 |
- Temporal Cortex |
- Normal |
- C225703F83N |
- 83 |
- F |
-
-
- | 42 |
- GSM225704 |
- Temporal Cortex |
- Normal |
- C225704F82N |
- 82 |
- F |
-
-
- | 43 |
- GSM225705 |
- Temporal Cortex |
- Normal |
- C225705F66N |
- 66 |
- F |
-
-
- | 44 |
- GSM225706 |
- Temporal Cortex |
- Normal |
- C225706F72N |
- 72 |
- F |
-
-
- | 45 |
- GSM225707 |
- Temporal Cortex |
- Normal |
- C225707F65N |
- 65 |
- F |
-
-
- | 46 |
- GSM225708 |
- Temporal Cortex |
- Normal |
- C225708F75N |
- 75 |
- F |
-
-
- | 47 |
- GSM225709 |
- Temporal Cortex |
- Normal |
- C225709F74N |
- 74 |
- F |
-
-
- | 48 |
- GSM225711 |
- Temporal Cortex |
- Normal |
- C225711M68N |
- 68 |
- M |
-
-
- | 49 |
- GSM225713 |
- Temporal Cortex |
- Normal |
- C225713F80N |
- 80 |
- F |
-
-
- | 50 |
- GSM225714 |
- Temporal Cortex |
- Normal |
- C225714M80N |
- 80 |
- M |
-
-
- | 51 |
- GSM225715 |
- Temporal Cortex |
- Normal |
- C225715M66N |
- 66 |
- M |
-
-
- | 52 |
- GSM225717 |
- Temporal Cortex |
- Normal |
- C225717M88N |
- 88 |
- M |
-
-
- | 53 |
- GSM225718 |
- Temporal Cortex |
- Normal |
- C225718F91N |
- 91 |
- F |
-
-
- | 54 |
- GSM225719 |
- Temporal Cortex |
- Normal |
- C225719M73N |
- 73 |
- M |
-
-
- | 55 |
- GSM225720 |
- Temporal Cortex |
- Normal |
- C225720M76N |
- 76 |
- M |
-
-
- | 56 |
- GSM225721 |
- Temporal Cortex |
- Normal |
- C225721M75N |
- 75 |
- M |
-
-
- | 57 |
- GSM225722 |
- Temporal Cortex |
- Normal |
- C225722F86N |
- 86 |
- F |
-
-
- | 58 |
- GSM225723 |
- Temporal Cortex |
- Normal |
- C225723F72N |
- 72 |
- F |
-
-
- | 59 |
- GSM225724 |
- Temporal Cortex |
- Normal |
- C225724M97N |
- 97 |
- M |
-
-
- | 60 |
- GSM225725 |
- Temporal Cortex |
- Normal |
- C225725M86N |
- 86 |
- M |
-
-
- | 61 |
- GSM225726 |
- Temporal Cortex |
- Normal |
- C225726M82N |
- 82 |
- M |
-
-
- | 62 |
- GSM225727 |
- Temporal Cortex |
- Normal |
- C225727F95N |
- 95 |
- F |
-
-
- | 63 |
- GSM225728 |
- Temporal Cortex |
- Normal |
- C225728F76N |
- 76 |
- F |
-
-
- | 64 |
- GSM225729 |
- Temporal Cortex |
- Normal |
- C225729M76N |
- 76 |
- M |
-
-
- | 65 |
- GSM225730 |
- Temporal Cortex |
- Normal |
- C225730M69N |
- 69 |
- M |
-
-
- | 66 |
- GSM225731 |
- Temporal Cortex |
- Normal |
- C225731F80N |
- 80 |
- F |
-
-
- | 67 |
- GSM225732 |
- Temporal Cortex |
- Normal |
- C225732F99N |
- 99 |
- F |
-
-
- | 68 |
- GSM225733 |
- Temporal Cortex |
- Normal |
- C225733M68N |
- 68 |
- M |
-
-
- | 69 |
- GSM225734 |
- Temporal Cortex |
- Normal |
- C225734M70N |
- 70 |
- M |
-
-
- | 70 |
- GSM225735 |
- Temporal Cortex |
- Normal |
- C225735F87N |
- 87 |
- F |
-
-
- | 71 |
- GSM225736 |
- Temporal Cortex |
- Normal |
- C225736F99N |
- 99 |
- F |
-
-
- | 72 |
- GSM225737 |
- Temporal Cortex |
- Normal |
- C225737F88N |
- 88 |
- F |
-
-
- | 73 |
- GSM225739 |
- Temporal Cortex |
- Normal |
- C225739M65N |
- 65 |
- M |
-
-
- | 74 |
- GSM225741 |
- Temporal Cortex |
- Normal |
- C225741M82N |
- 82 |
- M |
-
-
- | 75 |
- GSM225742 |
- Temporal Cortex |
- Normal |
- C225742F78N |
- 78 |
- F |
-
-
- | 76 |
- GSM225743 |
- Temporal Cortex |
- Normal |
- C225743F85N |
- 85 |
- F |
-
-
- | 77 |
- GSM225744 |
- Temporal Cortex |
- Normal |
- C225744F100N |
- 100 |
- F |
-
-
- | 78 |
- GSM225745 |
- Temporal Cortex |
- Normal |
- C225745F87N |
- 87 |
- F |
-
-
- | 79 |
- GSM225746 |
- Temporal Cortex |
- Normal |
- C225746F85N |
- 85 |
- F |
-
-
- | 80 |
- GSM225747 |
- Temporal Cortex |
- Normal |
- C225747F97N |
- 97 |
- F |
-
-
- | 81 |
- GSM225748 |
- Temporal Cortex |
- Normal |
- C225748M65N |
- 65 |
- M |
-
-
- | 82 |
- GSM225749 |
- Temporal Cortex |
- Normal |
- C225749M65N |
- 65 |
- M |
-
-
- | 83 |
- GSM225751 |
- Temporal Cortex |
- Normal |
- C225751F87N |
- 87 |
- F |
-
-
- | 84 |
- GSM225752 |
- Temporal Cortex |
- Normal |
- C225752F85N |
- 85 |
- F |
-
-
- | 85 |
- GSM225753 |
- Temporal Cortex |
- Normal |
- C225753M68N |
- 68 |
- M |
-
-
- | 86 |
- GSM225754 |
- Temporal Cortex |
- Normal |
- C225754M71N |
- 71 |
- M |
-
-
- | 87 |
- GSM225755 |
- Temporal Cortex |
- Normal |
- C225755F83N |
- 83 |
- F |
-
-
- | 88 |
- GSM225756 |
- Temporal Cortex |
- Normal |
- C225756M76N |
- 76 |
- M |
-
-
- | 89 |
- GSM225757 |
- Temporal Cortex |
- Normal |
- C225757M67N |
- 67 |
- M |
-
-
- | 90 |
- GSM225758 |
- Temporal Cortex |
- Normal |
- C225758F100N |
- 100 |
- F |
-
-
- | 91 |
- GSM225759 |
- Temporal Cortex |
- Normal |
- C225759M79N |
- 79 |
- M |
-
-
- | 92 |
- GSM225760 |
- Temporal Cortex |
- Normal |
- C225760M74N |
- 74 |
- M |
-
-
- | 93 |
- GSM225761 |
- Temporal Cortex |
- Normal |
- C225761F88N |
- 88 |
- F |
-
-
- | 94 |
- GSM225762 |
- Temporal Cortex |
- Normal |
- C225762M70N |
- 70 |
- M |
-
-
- | 95 |
- GSM225763 |
- Temporal Cortex |
- Normal |
- C225763F97N |
- 97 |
- F |
-
-
- | 96 |
- GSM225764 |
- Temporal Cortex |
- Normal |
- C225764M69N |
- 69 |
- M |
-
-
- | 97 |
- GSM225915 |
- Temporal Cortex |
- Normal |
- C225915F99N |
- 99 |
- F |
-
-
- | 98 |
- GSM225916 |
- Temporal Cortex |
- Normal |
- C225916M81N |
- 81 |
- M |
-
-
- | 99 |
- GSM225917 |
- Temporal Cortex |
- Normal |
- C225917F85N |
- 85 |
- F |
-
-
- | 100 |
- GSM225918 |
- Temporal Cortex |
- Normal |
- C225918F82N |
- 82 |
- F |
-
-
- | 101 |
- GSM225919 |
- Temporal Cortex |
- Normal |
- C225919M70N |
- 70 |
- M |
-
-
- | 102 |
- GSM225920 |
- Temporal Cortex |
- Normal |
- C225920M73N |
- 73 |
- M |
-
-
- | 103 |
- GSM225921 |
- Temporal Cortex |
- Normal |
- C225921M83N |
- 83 |
- M |
-
-
- | 104 |
- GSM225922 |
- Temporal Cortex |
- Normal |
- C225922M74N |
- 74 |
- M |
-
-
- | 105 |
- GSM225923 |
- Temporal Cortex |
- Normal |
- C225923M77N |
- 77 |
- M |
-
-
- | 106 |
- GSM225924 |
- Temporal Cortex |
- Normal |
- C225924M81N |
- 81 |
- M |
-
-
- | 107 |
- GSM225925 |
- Temporal Cortex |
- Normal |
- C225925M65N |
- 65 |
- M |
-
-
- | 108 |
- GSM225926 |
- Temporal Cortex |
- Normal |
- C225926F73N |
- 73 |
- F |
-
-
- | 109 |
- GSM225927 |
- Temporal Cortex |
- Normal |
- C225927F85N |
- 85 |
- F |
-
-
- | 110 |
- GSM225928 |
- Temporal Cortex |
- Normal |
- C225928M69N |
- 69 |
- M |
-
-
- | 111 |
- GSM225929 |
- Temporal Cortex |
- Normal |
- C225929M72N |
- 72 |
- M |
-
-
- | 112 |
- GSM225930 |
- Temporal Cortex |
- Normal |
- C225930F76N |
- 76 |
- F |
-
-
- | 113 |
- GSM225931 |
- Temporal Cortex |
- Normal |
- C225931M73N |
- 73 |
- M |
-
-
- | 114 |
- GSM225932 |
- Temporal Cortex |
- Normal |
- C225932M66N |
- 66 |
- M |
-
-
- | 115 |
- GSM225933 |
- Temporal Cortex |
- Normal |
- C225933F85N |
- 85 |
- F |
-
-
- | 116 |
- GSM225934 |
- Temporal Cortex |
- Normal |
- C225934M87N |
- 87 |
- M |
-
-
- | 117 |
- GSM225935 |
- Temporal Cortex |
- Normal |
- C225935F86N |
- 86 |
- F |
-
-
- | 118 |
- GSM225936 |
- Temporal Cortex |
- Normal |
- C225936F73N |
- 73 |
- F |
-
-
- | 119 |
- GSM225937 |
- Temporal Cortex |
- Normal |
- C225937M86N |
- 86 |
- M |
-
-
- | 120 |
- GSM225938 |
- Temporal Cortex |
- Normal |
- C225938M72N |
- 72 |
- M |
-
-
- | 121 |
- GSM225939 |
- Temporal Cortex |
- Normal |
- C225939F69N |
- 69 |
- F |
-
-
- | 122 |
- GSM225940 |
- Temporal Cortex |
- Normal |
- C225940F88N |
- 88 |
- F |
-
-
- | 123 |
- GSM225941 |
- Temporal Cortex |
- Normal |
- C225941M77N |
- 77 |
- M |
-
-
- | 124 |
- GSM225942 |
- Temporal Cortex |
- Normal |
- C225942M96N |
- 96 |
- M |
-
-
- | 125 |
- GSM225943 |
- Temporal Cortex |
- Normal |
- C225943F78N |
- 78 |
- F |
-
-
- | 126 |
- GSM225944 |
- Temporal Cortex |
- Normal |
- C225944M77N |
- 77 |
- M |
-
-
- | 127 |
- GSM225945 |
- Temporal Cortex |
- Normal |
- C225945F99N |
- 99 |
- F |
-
-
- | 128 |
- GSM225946 |
- Temporal Cortex |
- Normal |
- C225946M78N |
- 78 |
- M |
-
-
- | 129 |
- GSM225947 |
- Temporal Cortex |
- Normal |
- C225947F76N |
- 76 |
- F |
-
-
- | 130 |
- GSM225948 |
- Temporal Cortex |
- Normal |
- C225948M78N |
- 78 |
- M |
-
-
- | 131 |
- GSM225949 |
- Temporal Cortex |
- Normal |
- C225949F97N |
- 97 |
- F |
-
-
- | 132 |
- GSM225950 |
- Temporal Cortex |
- Normal |
- C225950F86N |
- 86 |
- F |
-
-
- | 133 |
- GSM225951 |
- Temporal Cortex |
- Normal |
- C225951M77N |
- 77 |
- M |
-
-
- | 134 |
- GSM225952 |
- Temporal Cortex |
- Normal |
- C225952M87N |
- 87 |
- M |
-
-
- | 135 |
- GSM225953 |
- Temporal Cortex |
- Normal |
- C225953F72N |
- 72 |
- F |
-
-
- | 136 |
- GSM225954 |
- Temporal Cortex |
- Normal |
- C225954F91N |
- 91 |
- F |
-
-
- | 137 |
- GSM225955 |
- Temporal Cortex |
- Normal |
- C225955F85N |
- 85 |
- F |
-
-
- | 138 |
- GSM225956 |
- Temporal Cortex |
- Normal |
- C225956M88N |
- 88 |
- M |
-
-
- | 139 |
- GSM225957 |
- Temporal Cortex |
- Normal |
- C225957F86N |
- 86 |
- F |
-
-
- | 140 |
- GSM225958 |
- Temporal Cortex |
- Normal |
- C225958F93N |
- 93 |
- F |
-
-
- | 141 |
- GSM225959 |
- Temporal Cortex |
- Normal |
- C225959M82N |
- 82 |
- M |
-
-
- | 142 |
- GSM225961 |
- Temporal Cortex |
- Normal |
- C225961F72N |
- 72 |
- F |
-
-
- | 143 |
- GSM225962 |
- Temporal Cortex |
- Normal |
- C225962F85N |
- 85 |
- F |
-
-
- | 144 |
- GSM225963 |
- Temporal Cortex |
- Normal |
- C225963M70N |
- 70 |
- M |
-
-
- | 145 |
- GSM225964 |
- Temporal Cortex |
- Normal |
- C225964F67N |
- 67 |
- F |
-
-
- | 146 |
- GSM225965 |
- Temporal Cortex |
- Normal |
- C225965F74N |
- 74 |
- F |
-
-
- | 147 |
- GSM226034 |
- Temporal Cortex |
- Normal |
- C226034M69N |
- 69 |
- M |
-
-
- | 148 |
- GSM226035 |
- Temporal Cortex |
- Normal |
- C226035M85N |
- 85 |
- M |
-
-
- | 149 |
- GSM226037 |
- Temporal Cortex |
- Normal |
- C226037M89N |
- 89 |
- M |
-
-
- | 150 |
- GSM226038 |
- Temporal Cortex |
- Normal |
- C226038M86N |
- 86 |
- M |
-
-
- | 151 |
- GSM226039 |
- Temporal Cortex |
- Normal |
- C226039M90N |
- 90 |
- M |
-
-
- | 152 |
- GSM226040 |
- Temporal Cortex |
- Normal |
- C226040F94N |
- 94 |
- F |
-
-
- | 153 |
- GSM226041 |
- Temporal Cortex |
- Normal |
- C226041F91N |
- 91 |
- F |
-
-
- | 154 |
- GSM226042 |
- Temporal Cortex |
- Normal |
- C226042F91N |
- 91 |
- F |
-
-
- | 155 |
- GSM226044 |
- Temporal Cortex |
- Normal |
- C226044F95N |
- 95 |
- F |
-
-
- | 156 |
- GSM226045 |
- Temporal Cortex |
- Normal |
- C226045F95N |
- 95 |
- F |
-
-
- | 157 |
- GSM226046 |
- Temporal Cortex |
- Normal |
- C226046F91N |
- 91 |
- F |
-
-
- | 158 |
- GSM226047 |
- Temporal Cortex |
- Normal |
- C226047M80N |
- 80 |
- M |
-
-
- | 159 |
- GSM226048 |
- Temporal Cortex |
- Normal |
- C226048M83N |
- 83 |
- M |
-
-
- | 160 |
- GSM226049 |
- Temporal Cortex |
- Normal |
- C226049M67N |
- 67 |
- M |
-
-
- | 161 |
- GSM226050 |
- Temporal Cortex |
- Normal |
- C226050M76N |
- 76 |
- M |
-
-
- | 162 |
- GSM226051 |
- Temporal Cortex |
- Normal |
- C226051F86N |
- 86 |
- F |
-
-
- | 163 |
- GSM226052 |
- Temporal Cortex |
- Normal |
- C226052F86N |
- 86 |
- F |
-
-
- | 164 |
- GSM226053 |
- Temporal Cortex |
- Normal |
- C226053M83N |
- 83 |
- M |
-
-
- | 165 |
- GSM226055 |
- Temporal Cortex |
- Normal |
- C226055M84N |
- 84 |
- M |
-
-
- | 166 |
- GSM226056 |
- Temporal Cortex |
- Normal |
- C226056M80N |
- 80 |
- M |
-
-
- | 167 |
- GSM226082 |
- Temporal Cortex |
- Normal |
- C226082M72N |
- 72 |
- M |
-
-
- | 168 |
- GSM226145 |
- Temporal Cortex |
- Normal |
- C226145M67N |
- 67 |
- M |
-
-
- | 169 |
- GSM226146 |
- Temporal Cortex |
- Normal |
- C226146F96N |
- 96 |
- F |
-
-
- | 170 |
- GSM226147 |
- Temporal Cortex |
- Normal |
- C226147F75N |
- 75 |
- F |
-
-
- | 171 |
- GSM226148 |
- Temporal Cortex |
- Normal |
- C226148F89N |
- 89 |
- F |
-
-
- | 172 |
- GSM226149 |
- Temporal Cortex |
- Normal |
- C226149F86N |
- 86 |
- F |
-
-
- | 173 |
- GSM226150 |
- Temporal Cortex |
- Normal |
- C226150M67N |
- 67 |
- M |
-
-
- | 174 |
- GSM226151 |
- Temporal Cortex |
- Normal |
- C226151M77N |
- 77 |
- M |
-
-
- | 175 |
- GSM226154 |
- Temporal Cortex |
- Normal |
- C226154M65N |
- 65 |
- M |
-
-
- | 176 |
- GSM226155 |
- Temporal Cortex |
- Normal |
- C226155M69N |
- 69 |
- M |
-
-
- | 177 |
- GSM226156 |
- Temporal Cortex |
- Normal |
- C226156M84N |
- 84 |
- M |
-
-
- | 178 |
- GSM226157 |
- Temporal Cortex |
- Normal |
- C226157F85N |
- 85 |
- F |
-
-
- | 179 |
- GSM226158 |
- Temporal Cortex |
- Normal |
- C226158M94N |
- 94 |
- M |
-
-
- | 180 |
- GSM226159 |
- Temporal Cortex |
- Normal |
- C226159F89N |
- 89 |
- F |
-
-
- | 181 |
- GSM226160 |
- Temporal Cortex |
- Normal |
- C226160M87N |
- 87 |
- M |
-
-
- | 182 |
- GSM226162 |
- Temporal Cortex |
- Normal |
- C226162M90N |
- 90 |
- M |
-
-
- | 183 |
- GSM226163 |
- Temporal Cortex |
- Normal |
- C226163F88N |
- 88 |
- F |
-
-
- | 184 |
- GSM226164 |
- Temporal Cortex |
- Normal |
- C226164M94N |
- 94 |
- M |
-
-
- | 185 |
- GSM226165 |
- Temporal Cortex |
- Normal |
- C226165F86N |
- 86 |
- F |
-
-
- | 186 |
- GSM226167 |
- Temporal Cortex |
- Normal |
- C226167F93N |
- 93 |
- F |
-
-
- | 187 |
- GSM226168 |
- Temporal Cortex |
- Normal |
- C226168M91N |
- 91 |
- M |
-
-
- | 188 |
- GSM388217 |
- Cortical Tissue |
- Alzheimer's |
- C388217F97A |
- 97 |
- F |
-
-
- | 189 |
- GSM388218 |
- Cortical Tissue |
- Alzheimer's |
- C388218F101A |
- 101 |
- F |
-
-
- | 190 |
- GSM388219 |
- Cortical Tissue |
- Alzheimer's |
- C388219M84A |
- 84 |
- M |
-
-
- | 191 |
- GSM388220 |
- Cortical Tissue |
- Alzheimer's |
- C388220F95A |
- 95 |
- F |
-
-
- | 192 |
- GSM388221 |
- Cortical Tissue |
- Alzheimer's |
- C388221F97A |
- 97 |
- F |
-
-
- | 193 |
- GSM388222 |
- Cortical Tissue |
- Alzheimer's |
- C388222F102A |
- 102 |
- F |
-
-
- | 194 |
- GSM388223 |
- Cortical Tissue |
- Alzheimer's |
- C388223M87A |
- 87 |
- M |
-
-
- | 195 |
- GSM388224 |
- Cortical Tissue |
- Alzheimer's |
- C388224F77A |
- 77 |
- F |
-
-
- | 196 |
- GSM388225 |
- Cortical Tissue |
- Alzheimer's |
- C388225M87A |
- 87 |
- M |
-
-
- | 197 |
- GSM388226 |
- Cortical Tissue |
- Alzheimer's |
- C388226M84A |
- 84 |
- M |
-
-
- | 198 |
- GSM388228 |
- Cortical Tissue |
- Alzheimer's |
- C388228F92A |
- 92 |
- F |
-
-
- | 199 |
- GSM388229 |
- Cortical Tissue |
- Alzheimer's |
- C388229M93A |
- 93 |
- M |
-
-
- | 200 |
- GSM388230 |
- Cortical Tissue |
- Alzheimer's |
- C388230F93A |
- 93 |
- F |
-
-
- | 201 |
- GSM388231 |
- Cortical Tissue |
- Alzheimer's |
- C388231F87A |
- 87 |
- F |
-
-
- | 202 |
- GSM388232 |
- Cortical Tissue |
- Alzheimer's |
- C388232F90A |
- 90 |
- F |
-
-
- | 203 |
- GSM388233 |
- Cortical Tissue |
- Alzheimer's |
- C388233M75A |
- 75 |
- M |
-
-
- | 204 |
- GSM388234 |
- Cortical Tissue |
- Alzheimer's |
- C388234M92A |
- 92 |
- M |
-
-
- | 205 |
- GSM388235 |
- Cortical Tissue |
- Alzheimer's |
- C388235M83A |
- 83 |
- M |
-
-
- | 206 |
- GSM388236 |
- Cortical Tissue |
- Alzheimer's |
- C388236M88A |
- 88 |
- M |
-
-
- | 207 |
- GSM388237 |
- Cortical Tissue |
- Alzheimer's |
- C388237M89A |
- 89 |
- M |
-
-
- | 208 |
- GSM388238 |
- Cortical Tissue |
- Alzheimer's |
- C388238F74A |
- 74 |
- F |
-
-
- | 209 |
- GSM388239 |
- Cortical Tissue |
- Alzheimer's |
- C388239F79A |
- 79 |
- F |
-
-
- | 210 |
- GSM388240 |
- Cortical Tissue |
- Alzheimer's |
- C388240M80A |
- 80 |
- M |
-
-
- | 211 |
- GSM388241 |
- Cortical Tissue |
- Alzheimer's |
- C388241F97A |
- 97 |
- F |
-
-
- | 212 |
- GSM388242 |
- Cortical Tissue |
- Alzheimer's |
- C388242M87A |
- 87 |
- M |
-
-
- | 213 |
- GSM388243 |
- Cortical Tissue |
- Alzheimer's |
- C388243F89A |
- 89 |
- F |
-
-
- | 214 |
- GSM388244 |
- Cortical Tissue |
- Alzheimer's |
- C388244F90A |
- 90 |
- F |
-
-
- | 215 |
- GSM388245 |
- Cortical Tissue |
- Alzheimer's |
- C388245M90A |
- 90 |
- M |
-
-
- | 216 |
- GSM388246 |
- Cortical Tissue |
- Alzheimer's |
- C388246M78A |
- 78 |
- M |
-
-
- | 217 |
- GSM388247 |
- Cortical Tissue |
- Alzheimer's |
- C388247F80A |
- 80 |
- F |
-
-
- | 218 |
- GSM388248 |
- Cortical Tissue |
- Alzheimer's |
- C388248F79A |
- 79 |
- F |
-
-
- | 219 |
- GSM388249 |
- Cortical Tissue |
- Alzheimer's |
- C388249F87A |
- 87 |
- F |
-
-
- | 220 |
- GSM388250 |
- Cortical Tissue |
- Alzheimer's |
- C388250F88A |
- 88 |
- F |
-
-
- | 221 |
- GSM388251 |
- Cortical Tissue |
- Alzheimer's |
- C388251M86A |
- 86 |
- M |
-
-
- | 222 |
- GSM388252 |
- Cortical Tissue |
- Alzheimer's |
- C388252F74A |
- 74 |
- F |
-
-
- | 223 |
- GSM388253 |
- Cortical Tissue |
- Alzheimer's |
- C388253F72A |
- 72 |
- F |
-
-
- | 224 |
- GSM388254 |
- Cortical Tissue |
- Alzheimer's |
- C388254M81A |
- 81 |
- M |
-
-
- | 225 |
- GSM388255 |
- Cortical Tissue |
- Alzheimer's |
- C388255F68A |
- 68 |
- F |
-
-
- | 226 |
- GSM388256 |
- Cortical Tissue |
- Alzheimer's |
- C388256F81A |
- 81 |
- F |
-
-
- | 227 |
- GSM388257 |
- Cortical Tissue |
- Alzheimer's |
- C388257F82A |
- 82 |
- F |
-
-
- | 228 |
- GSM388258 |
- Cortical Tissue |
- Alzheimer's |
- C388258M78A |
- 78 |
- M |
-
-
- | 229 |
- GSM388259 |
- Cortical Tissue |
- Alzheimer's |
- C388259M74A |
- 74 |
- M |
-
-
- | 230 |
- GSM388260 |
- Cortical Tissue |
- Alzheimer's |
- C388260M88A |
- 88 |
- M |
-
-
- | 231 |
- GSM388261 |
- Cortical Tissue |
- Alzheimer's |
- C388261F78A |
- 78 |
- F |
-
-
- | 232 |
- GSM388262 |
- Cortical Tissue |
- Alzheimer's |
- C388262M83A |
- 83 |
- M |
-
-
- | 233 |
- GSM388263 |
- Cortical Tissue |
- Alzheimer's |
- C388263M83A |
- 83 |
- M |
-
-
- | 234 |
- GSM388264 |
- Cortical Tissue |
- Alzheimer's |
- C388264M80A |
- 80 |
- M |
-
-
- | 235 |
- GSM388265 |
- Cortical Tissue |
- Alzheimer's |
- C388265M84A |
- 84 |
- M |
-
-
- | 236 |
- GSM388266 |
- Cortical Tissue |
- Alzheimer's |
- C388266F79A |
- 79 |
- F |
-
-
- | 237 |
- GSM388267 |
- Cortical Tissue |
- Alzheimer's |
- C388267F86A |
- 86 |
- F |
-
-
- | 238 |
- GSM388268 |
- Cortical Tissue |
- Alzheimer's |
- C388268M92A |
- 92 |
- M |
-
-
- | 239 |
- GSM388269 |
- Cortical Tissue |
- Alzheimer's |
- C388269F81A |
- 81 |
- F |
-
-
- | 240 |
- GSM388270 |
- Cortical Tissue |
- Alzheimer's |
- C388270F79A |
- 79 |
- F |
-
-
- | 241 |
- GSM388271 |
- Cortical Tissue |
- Alzheimer's |
- C388271M74A |
- 74 |
- M |
-
-
- | 242 |
- GSM388272 |
- Cortical Tissue |
- Alzheimer's |
- C388272F73A |
- 73 |
- F |
-
-
- | 243 |
- GSM388273 |
- Cortical Tissue |
- Alzheimer's |
- C388273M87A |
- 87 |
- M |
-
-
- | 244 |
- GSM388274 |
- Cortical Tissue |
- Alzheimer's |
- C388274F86A |
- 86 |
- F |
-
-
- | 245 |
- GSM388275 |
- Cortical Tissue |
- Alzheimer's |
- C388275F86A |
- 86 |
- F |
-
-
- | 246 |
- GSM388276 |
- Cortical Tissue |
- Alzheimer's |
- C388276F87A |
- 87 |
- F |
-
-
- | 247 |
- GSM388277 |
- Cortical Tissue |
- Alzheimer's |
- C388277F92A |
- 92 |
- F |
-
-
- | 248 |
- GSM388278 |
- Cortical Tissue |
- Alzheimer's |
- C388278F78A |
- 78 |
- F |
-
-
- | 249 |
- GSM388279 |
- Cortical Tissue |
- Alzheimer's |
- C388279F94A |
- 94 |
- F |
-
-
- | 250 |
- GSM388281 |
- Cortical Tissue |
- Alzheimer's |
- C388281F94A |
- 94 |
- F |
-
-
- | 251 |
- GSM388282 |
- Cortical Tissue |
- Alzheimer's |
- C388282M76A |
- 76 |
- M |
-
-
- | 252 |
- GSM388284 |
- Cortical Tissue |
- Alzheimer's |
- C388284M91A |
- 91 |
- M |
-
-
- | 253 |
- GSM388285 |
- Cortical Tissue |
- Alzheimer's |
- C388285M86A |
- 86 |
- M |
-
-
- | 254 |
- GSM388286 |
- Cortical Tissue |
- Alzheimer's |
- C388286M77A |
- 77 |
- M |
-
-
- | 255 |
- GSM388287 |
- Cortical Tissue |
- Alzheimer's |
- C388287M82A |
- 82 |
- M |
-
-
- | 256 |
- GSM388288 |
- Cortical Tissue |
- Alzheimer's |
- C388288M78A |
- 78 |
- M |
-
-
- | 257 |
- GSM388289 |
- Cortical Tissue |
- Alzheimer's |
- C388289M79A |
- 79 |
- M |
-
-
- | 258 |
- GSM388290 |
- Cortical Tissue |
- Alzheimer's |
- C388290F84A |
- 84 |
- F |
-
-
- | 259 |
- GSM388291 |
- Cortical Tissue |
- Alzheimer's |
- C388291F87A |
- 87 |
- F |
-
-
- | 260 |
- GSM388292 |
- Cortical Tissue |
- Alzheimer's |
- C388292F86A |
- 86 |
- F |
-
-
- | 261 |
- GSM388294 |
- Cortical Tissue |
- Alzheimer's |
- C388294M83A |
- 83 |
- M |
-
-
- | 262 |
- GSM388295 |
- Cortical Tissue |
- Alzheimer's |
- C388295M83A |
- 83 |
- M |
-
-
- | 263 |
- GSM388296 |
- Cortical Tissue |
- Alzheimer's |
- C388296M81A |
- 81 |
- M |
-
-
- | 264 |
- GSM388297 |
- Cortical Tissue |
- Alzheimer's |
- C388297F93A |
- 93 |
- F |
-
-
- | 265 |
- GSM388298 |
- Cortical Tissue |
- Alzheimer's |
- C388298M71A |
- 71 |
- M |
-
-
- | 266 |
- GSM388299 |
- Cortical Tissue |
- Alzheimer's |
- C388299M78A |
- 78 |
- M |
-
-
- | 267 |
- GSM388300 |
- Cortical Tissue |
- Alzheimer's |
- C388300F75A |
- 75 |
- F |
-
-
- | 268 |
- GSM388301 |
- Cortical Tissue |
- Alzheimer's |
- C388301F84A |
- 84 |
- F |
-
-
- | 269 |
- GSM388302 |
- Cortical Tissue |
- Alzheimer's |
- C388302M73A |
- 73 |
- M |
-
-
- | 270 |
- GSM388303 |
- Cortical Tissue |
- Alzheimer's |
- C388303F89A |
- 89 |
- F |
-
-
- | 271 |
- GSM388304 |
- Cortical Tissue |
- Alzheimer's |
- C388304FNAA |
- NA |
- F |
-
-
- | 272 |
- GSM388305 |
- Cortical Tissue |
- Alzheimer's |
- C388305M69A |
- 69 |
- M |
-
-
- | 273 |
- GSM388306 |
- Cortical Tissue |
- Alzheimer's |
- C388306M83A |
- 83 |
- M |
-
-
- | 274 |
- GSM388307 |
- Cortical Tissue |
- Alzheimer's |
- C388307M71A |
- 71 |
- M |
-
-
- | 275 |
- GSM388308 |
- Cortical Tissue |
- Alzheimer's |
- C388308F86A |
- 86 |
- F |
-
-
- | 276 |
- GSM388309 |
- Cortical Tissue |
- Alzheimer's |
- C388309M82A |
- 82 |
- M |
-
-
- | 277 |
- GSM388310 |
- Cortical Tissue |
- Alzheimer's |
- C388310FNAA |
- NA |
- F |
-
-
- | 278 |
- GSM388311 |
- Cortical Tissue |
- Alzheimer's |
- C388311M88A |
- 88 |
- M |
-
-
- | 279 |
- GSM388312 |
- Cortical Tissue |
- Alzheimer's |
- C388312M77A |
- 77 |
- M |
-
-
- | 280 |
- GSM388313 |
- Cortical Tissue |
- Alzheimer's |
- C388313M85A |
- 85 |
- M |
-
-
- | 281 |
- GSM388314 |
- Cortical Tissue |
- Alzheimer's |
- C388314F81A |
- 81 |
- F |
-
-
- | 282 |
- GSM388315 |
- Cortical Tissue |
- Alzheimer's |
- C388315F86A |
- 86 |
- F |
-
-
- | 283 |
- GSM388316 |
- Cortical Tissue |
- Alzheimer's |
- C388316M89A |
- 89 |
- M |
-
-
- | 284 |
- GSM388317 |
- Cortical Tissue |
- Alzheimer's |
- C388317F73A |
- 73 |
- F |
-
-
- | 285 |
- GSM388318 |
- Cortical Tissue |
- Alzheimer's |
- C388318F96A |
- 96 |
- F |
-
-
- | 286 |
- GSM388319 |
- Cortical Tissue |
- Alzheimer's |
- C388319M73A |
- 73 |
- M |
-
-
- | 287 |
- GSM388320 |
- Cortical Tissue |
- Alzheimer's |
- C388320M81A |
- 81 |
- M |
-
-
- | 288 |
- GSM388321 |
- Cortical Tissue |
- Alzheimer's |
- C388321F84A |
- 84 |
- F |
-
-
- | 289 |
- GSM388322 |
- Cortical Tissue |
- Alzheimer's |
- C388322F93A |
- 93 |
- F |
-
-
- | 290 |
- GSM388323 |
- Cortical Tissue |
- Alzheimer's |
- C388323F82A |
- 82 |
- F |
-
-
- | 291 |
- GSM388324 |
- Cortical Tissue |
- Alzheimer's |
- C388324M76A |
- 76 |
- M |
-
-
- | 292 |
- GSM388325 |
- Cortical Tissue |
- Alzheimer's |
- C388325M77A |
- 77 |
- M |
-
-
- | 293 |
- GSM388326 |
- Cortical Tissue |
- Alzheimer's |
- C388326F86A |
- 86 |
- F |
-
-
- | 294 |
- GSM388327 |
- Cortical Tissue |
- Alzheimer's |
- C388327F85A |
- 85 |
- F |
-
-
- | 295 |
- GSM388328 |
- Cortical Tissue |
- Alzheimer's |
- C388328M83A |
- 83 |
- M |
-
-
- | 296 |
- GSM388329 |
- Cortical Tissue |
- Alzheimer's |
- C388329M76A |
- 76 |
- M |
-
-
- | 297 |
- GSM388330 |
- Cortical Tissue |
- Alzheimer's |
- C388330M81A |
- 81 |
- M |
-
-
- | 298 |
- GSM388331 |
- Cortical Tissue |
- Alzheimer's |
- C388331M79A |
- 79 |
- M |
-
-
- | 299 |
- GSM388332 |
- Cortical Tissue |
- Alzheimer's |
- C388332M81A |
- 81 |
- M |
-
-
- | 300 |
- GSM388333 |
- Cortical Tissue |
- Alzheimer's |
- C388333F78A |
- 78 |
- F |
-
-
- | 301 |
- GSM388334 |
- Cortical Tissue |
- Alzheimer's |
- C388334M80A |
- 80 |
- M |
-
-
- | 302 |
- GSM388335 |
- Cortical Tissue |
- Alzheimer's |
- C388335M84A |
- 84 |
- M |
-
-
- | 303 |
- GSM388336 |
- Cortical Tissue |
- Alzheimer's |
- C388336F85A |
- 85 |
- F |
-
-
- | 304 |
- GSM388337 |
- Cortical Tissue |
- Alzheimer's |
- C388337M75A |
- 75 |
- M |
-
-
- | 305 |
- GSM388338 |
- Cortical Tissue |
- Alzheimer's |
- C388338F80A |
- 80 |
- F |
-
-
- | 306 |
- GSM388339 |
- Cortical Tissue |
- Alzheimer's |
- C388339F97A |
- 97 |
- F |
-
-
- | 307 |
- GSM388340 |
- Cortical Tissue |
- Alzheimer's |
- C388340F82A |
- 82 |
- F |
-
-
- | 308 |
- GSM388341 |
- Cortical Tissue |
- Alzheimer's |
- C388341M82A |
- 82 |
- M |
-
-
- | 309 |
- GSM388342 |
- Cortical Tissue |
- Alzheimer's |
- C388342M77A |
- 77 |
- M |
-
-
- | 310 |
- GSM388343 |
- Cortical Tissue |
- Alzheimer's |
- C388343M81A |
- 81 |
- M |
-
-
- | 311 |
- GSM388345 |
- Cortical Tissue |
- Alzheimer's |
- C388345F96A |
- 96 |
- F |
-
-
- | 312 |
- GSM388346 |
- Cortical Tissue |
- Alzheimer's |
- C388346F90A |
- 90 |
- F |
-
-
- | 313 |
- GSM388347 |
- Cortical Tissue |
- Alzheimer's |
- C388347M86A |
- 86 |
- M |
-
-
- | 314 |
- GSM388348 |
- Cortical Tissue |
- Alzheimer's |
- C388348M88A |
- 88 |
- M |
-
-
- | 315 |
- GSM388349 |
- Cortical Tissue |
- Alzheimer's |
- C388349F90A |
- 90 |
- F |
-
-
- | 316 |
- GSM388350 |
- Cortical Tissue |
- Alzheimer's |
- C388350F90A |
- 90 |
- F |
-
-
- | 317 |
- GSM388351 |
- Cortical Tissue |
- Alzheimer's |
- C388351F84A |
- 84 |
- F |
-
-
- | 318 |
- GSM388352 |
- Cortical Tissue |
- Alzheimer's |
- C388352M84A |
- 84 |
- M |
-
-
- | 319 |
- GSM388353 |
- Cortical Tissue |
- Alzheimer's |
- C388353F91A |
- 91 |
- F |
-
-
- | 320 |
- GSM388354 |
- Cortical Tissue |
- Alzheimer's |
- C388354F81A |
- 81 |
- F |
-
-
- | 321 |
- GSM388355 |
- Cortical Tissue |
- Alzheimer's |
- C388355F84A |
- 84 |
- F |
-
-
- | 322 |
- GSM388356 |
- Cortical Tissue |
- Alzheimer's |
- C388356M80A |
- 80 |
- M |
-
-
- | 323 |
- GSM388357 |
- Cortical Tissue |
- Alzheimer's |
- C388357M81A |
- 81 |
- M |
-
-
- | 324 |
- GSM388358 |
- Cortical Tissue |
- Alzheimer's |
- C388358F87A |
- 87 |
- F |
-
-
- | 325 |
- GSM388359 |
- Cortical Tissue |
- Alzheimer's |
- C388359M85A |
- 85 |
- M |
-
-
- | 326 |
- GSM388360 |
- Cortical Tissue |
- Alzheimer's |
- C388360F90A |
- 90 |
- F |
-
-
- | 327 |
- GSM388361 |
- Cortical Tissue |
- Alzheimer's |
- C388361M79A |
- 79 |
- M |
-
-
- | 328 |
- GSM388362 |
- Cortical Tissue |
- Alzheimer's |
- C388362F87A |
- 87 |
- F |
-
-
- | 329 |
- GSM388363 |
- Cortical Tissue |
- Alzheimer's |
- C388363M75A |
- 75 |
- M |
-
-
- | 330 |
- GSM388364 |
- Cortical Tissue |
- Alzheimer's |
- C388364F92A |
- 92 |
- F |
-
-
- | 331 |
- GSM388365 |
- Cortical Tissue |
- Alzheimer's |
- C388365F84A |
- 84 |
- F |
-
-
- | 332 |
- GSM388366 |
- Cortical Tissue |
- Alzheimer's |
- C388366M75A |
- 75 |
- M |
-
-
- | 333 |
- GSM388367 |
- Cortical Tissue |
- Alzheimer's |
- C388367F76A |
- 76 |
- F |
-
-
- | 334 |
- GSM388368 |
- Cortical Tissue |
- Alzheimer's |
- C388368F86A |
- 86 |
- F |
-
-
- | 335 |
- GSM388369 |
- Cortical Tissue |
- Alzheimer's |
- C388369M82A |
- 82 |
- M |
-
-
- | 336 |
- GSM388370 |
- Cortical Tissue |
- Alzheimer's |
- C388370M76A |
- 76 |
- M |
-
-
- | 337 |
- GSM388371 |
- Cortical Tissue |
- Alzheimer's |
- C388371F81A |
- 81 |
- F |
-
-
- | 338 |
- GSM388372 |
- Cortical Tissue |
- Alzheimer's |
- C388372F80A |
- 80 |
- F |
-
-
- | 339 |
- GSM388373 |
- Cortical Tissue |
- Alzheimer's |
- C388373M83A |
- 83 |
- M |
-
-
- | 340 |
- GSM388374 |
- Cortical Tissue |
- Alzheimer's |
- C388374F83A |
- 83 |
- F |
-
-
- | 341 |
- GSM388375 |
- Cortical Tissue |
- Alzheimer's |
- C388375F84A |
- 84 |
- F |
-
-
- | 342 |
- GSM388376 |
- Cortical Tissue |
- Alzheimer's |
- C388376M93A |
- 93 |
- M |
-
-
- | 343 |
- GSM388377 |
- Cortical Tissue |
- Alzheimer's |
- C388377F92A |
- 92 |
- F |
-
-
- | 344 |
- GSM388378 |
- Cortical Tissue |
- Alzheimer's |
- C388378M78A |
- 78 |
- M |
-
-
- | 345 |
- GSM388379 |
- Cortical Tissue |
- Alzheimer's |
- C388379M90A |
- 90 |
- M |
-
-
- | 346 |
- GSM388380 |
- Cortical Tissue |
- Alzheimer's |
- C388380M83A |
- 83 |
- M |
-
-
- | 347 |
- GSM388381 |
- Cortical Tissue |
- Alzheimer's |
- C388381M79A |
- 79 |
- M |
-
-
- | 348 |
- GSM388382 |
- Cortical Tissue |
- Alzheimer's |
- C388382M84A |
- 84 |
- M |
-
-
- | 349 |
- GSM388383 |
- Cortical Tissue |
- Alzheimer's |
- C388383F90A |
- 90 |
- F |
-
-
- | 350 |
- GSM388384 |
- Cortical Tissue |
- Alzheimer's |
- C388384F88A |
- 88 |
- F |
-
-
- | 351 |
- GSM388385 |
- Cortical Tissue |
- Alzheimer's |
- C388385M77A |
- 77 |
- M |
-
-
- | 352 |
- GSM388386 |
- Cortical Tissue |
- Alzheimer's |
- C388386F80A |
- 80 |
- F |
-
-
- | 353 |
- GSM388387 |
- Cortical Tissue |
- Alzheimer's |
- C388387M87A |
- 87 |
- M |
-
-
- | 354 |
- GSM388388 |
- Cortical Tissue |
- Alzheimer's |
- C388388M86A |
- 86 |
- M |
-
-
- | 355 |
- GSM388389 |
- Cortical Tissue |
- Alzheimer's |
- C388389M74A |
- 74 |
- M |
-
-
- | 356 |
- GSM388390 |
- Cortical Tissue |
- Alzheimer's |
- C388390F86A |
- 86 |
- F |
-
-
- | 357 |
- GSM388391 |
- Cortical Tissue |
- Alzheimer's |
- C388391F81A |
- 81 |
- F |
-
-
- | 358 |
- GSM388392 |
- Cortical Tissue |
- Alzheimer's |
- C388392F73A |
- 73 |
- F |
-
-
- | 359 |
- GSM388393 |
- Cortical Tissue |
- Alzheimer's |
- C388393M83A |
- 83 |
- M |
-
-
- | 360 |
- GSM388394 |
- Cortical Tissue |
- Alzheimer's |
- C388394M86A |
- 86 |
- M |
-
-
- | 361 |
- GSM388395 |
- Cortical Tissue |
- Alzheimer's |
- C388395F86A |
- 86 |
- F |
-
-
- | 362 |
- GSM388396 |
- Cortical Tissue |
- Alzheimer's |
- C388396M78A |
- 78 |
- M |
-
-
- | 363 |
- GSM388397 |
- Cortical Tissue |
- Alzheimer's |
- C388397M83A |
- 83 |
- M |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GSE15222_F_RI_0409/experiment-design.rtf b/general/datasets/GSE15222_F_RI_0409/experiment-design.rtf
deleted file mode 100644
index 07d1b52..0000000
--- a/general/datasets/GSE15222_F_RI_0409/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Expression profiling by array
-
-We recently surveyed the relationship between the human brain transcriptome and genome in a series of neuropathologically normal postmortem samples. We now have analyzed additional samples with a confirmed pathologic diagnosis of late onset Alzheimer's disease (LOAD, final n=187 controls, 176 cases). Nine percent of the cortical transcripts we analyzed had expression profiles correlated with their genotypes in the combined cohort and approximately 5% of transcripts had SNP-transcript relationships that could distinguish LOAD samples. Two of these transcripts have been previously implicated in LOAD candidate gene SNP-expression screens. This study shows how the relationship between common inherited genetic variants and brain transcript expression can be used in the study of human brain disorders. We suggest that studying the transcriptome as a quantitative endo-phenotype has greater power to find risk SNPs influencing expression than the use of discrete diagnostic categories such as presence or absence of disease. see DOI:10.1016/j.ajhg.2009.03.011 for further details and complete author list.
-
-Expression quantitative trait loci study using human brain from 363 cortical samples. Affymetrix 500K chip for genotyping, Illumina Sentrix Human-ref 8 bead array chip for expression. Genotyping data will be available at dbGAP.
diff --git a/general/datasets/GSE15222_F_RI_0409/notes.rtf b/general/datasets/GSE15222_F_RI_0409/notes.rtf
deleted file mode 100644
index e7bd85c..0000000
--- a/general/datasets/GSE15222_F_RI_0409/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Access to the original data from Dr. Myers' laboratory
-or GEO GSE15222
-PMI = Post Mortem Interval
-Cannot find this record in the GEO website: WGACON-120
-
-This data is based on May 2004 (NCBI35/hg17).
diff --git a/general/datasets/GSE15222_F_RI_0409/platform.rtf b/general/datasets/GSE15222_F_RI_0409/platform.rtf
deleted file mode 100644
index 5bcda8b..0000000
--- a/general/datasets/GSE15222_F_RI_0409/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Illumina Human 50 mer probes. Total of 24357 probes according to Myers et al. A total of 24354 probes included in this GeneNetwork file.
-
-From the Methods section of the paper:
-
-Genotyping and Expression Proï¬ling DNA was hybridized to the Affymetrix GeneChip Human Mapping 500K Array Set (502,627 SNPs) as previously described.11,12 Genotypes were extracted with the use of both SNiPer-HD13 and BRLMM (Affymetrix, Santa Clara, CA) algorithms. Genotypes that exhibited less than 98% concordance between calls were excluded. SNPs with call rates less than 90% were excluded from the analysis. HardyWeinberg equilibrium (HWE) was assessed with exact tests and the PLINK analysis toolset.14 SNPs with HWE exact-test p values less than 0.05, as well as SNPs with minor-allele frequencies less than 1%, were excluded. Allele calls had a mean of 97% and a range of 90%–99%. cRNA was hybridized to Illumina Human Refseq-8 Expression BeadChip (24,357 transcripts) via standard protocols. Expression proï¬les were extracted and rank invariant normalized15–17 with the use of the BeadStudio software available from Illumina, with the Illumina custom error model used. Rankinvariant-normalized expression data were log10 transformed, and missing data were encoded as missing, rather than as a zero level of expression.
diff --git a/general/datasets/GSE15222_F_RI_0409/summary.rtf b/general/datasets/GSE15222_F_RI_0409/summary.rtf
deleted file mode 100644
index e99fa9e..0000000
--- a/general/datasets/GSE15222_F_RI_0409/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Myers and colleagues generated massive neocortical transcriptome data sets for a set of unrelated elderly neurologically and neuropathologically normal humans and from confirmed late onset Alzheimer's disease patients (LOAD, n = 187 normal and 176 LOAD cases, see DOI:10.1016/j.ajhg.2009.03.011 for detail). They used an Illumina Sentrix Bead array (HumanRef-8) that measures expression of approximately 19,730 curated RefSeq sequences (Human Build 34).
-
-Case identifiers: All case identifiers (IDs) in GeneNetwork begin with a capital C followed by a six digit GEO identifier, followed by the sex and age in years. Non-Alzheimer cases are labeled with the suffix letter N: C225652M85N. Alzheimer cases are labeled with the suffix letter A: C388217F97A.
-
-Data were initially downloaded from the NCBI GEO archive under the experiment ID GSE15222. All data were generated using the Illumina HumanRef-8 expression BeadChip (GPL2700) v2 Rev0. This data set in GeneNetwork includes data for 24,354 probes. We have realigned the 50-mer sequences by BLAT to the latest version of the human genome (Feb 2009, hg19) and reannotated the array (August 2009). The annotation in GN will differ from that provided in GEO for this platform. We were unable to obtain 50-mer sequences for several thousand probes (e.g., HTT), and these probes have therefore not been realigned to the human genome.
-
-The GEO data set was processed by Myers and colleagues using Illumina's Rank Invariant transform. We performed a series of QC and renormalization steps to the data to allow more facile comparison to other data sets in GeneNetwork. In brief, data is log2 transformed. We recentered each array to a mean expression of 8 units and a standard deviation of 2 units (2z + 8 transform). The values are therefore modified z scores and each unit represents roughly a two-fold difference in expression. Average expression across all 363 cases range from a low of 6 units (e.g., SYT15) to a high of 19 units for ARSK. APOE has an average expression of 15 units and APP has an average expression of 11.5 units.. The distribution is far from normal with a great excess of measurements of genes with low to moderate expression clustered between 6.5 and 8.5 units.
-
-A small number of arrays (n = 6, GSM226040, GSM226041, GSM226042, GSM226044, GSM226045, GSM226046) had a different distribution from the great majority of other arrays. This was probably due to a batch processing effect. Members of this minority group belonged to both normal and LOAD cases. This putative batch effect has been eliminated in the GeneNetwork rendition of the Myers data. To eliminate the putative batch effect, we simply computed a mean offset for each probe in the "minority set" relative to the remaining "majority set" and added or subtracted this offset to force the mean of each probe in the minority set to conform to mean of the same probe in the majority set.
diff --git a/general/datasets/GSE16780AB_UCLA_ML0911/summary.rtf b/general/datasets/GSE16780AB_UCLA_ML0911/summary.rtf
deleted file mode 100644
index 6ecd595..0000000
--- a/general/datasets/GSE16780AB_UCLA_ML0911/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 150, Name: GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11)
\ No newline at end of file
diff --git a/general/datasets/GSE16780BXH_UCLA_ML0911/summary.rtf b/general/datasets/GSE16780BXH_UCLA_ML0911/summary.rtf
deleted file mode 100644
index 9abf757..0000000
--- a/general/datasets/GSE16780BXH_UCLA_ML0911/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 151, Name: GSE16780 UCLA Mouse BXH Liver Affy HT M430A (Sep11)
\ No newline at end of file
diff --git a/general/datasets/GSE16780MDP_UCLA_ML0911/summary.rtf b/general/datasets/GSE16780MDP_UCLA_ML0911/summary.rtf
deleted file mode 100644
index 24e1d40..0000000
--- a/general/datasets/GSE16780MDP_UCLA_ML0911/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-The following is an excerpt from The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits
-
-
-
-The Hybrid Mouse Diversity Panel (HMDP) is a collection of approximately 100 well-characterized inbred strains of mice that can be used to analyze the genetic and environmental factors underlying complex traits. While not nearly as powerful for mapping genetic loci contributing to the traits as human genome-wide association studies, it has some important advantages. First, environmental factors can be controlled. Second, relevant tissues are accessible for global molecular phenotyping. Finally, because inbred strains are renewable, results from separate studies can be integrated. Thus far, the HMDP has been studied for traits relevant to obesity, diabetes, atherosclerosis, osteoporosis, heart failure, immune regulation, fatty liver disease, and host-gut microbiota interactions. High-throughput technologies have been used to examine the genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes of the mice under various environmental conditions. All of the published data are available and can be readily used to formulate hypotheses about genes, pathways and interactions.
-
-The HMDP was developed as a systems genetics resource similar to recombinant inbred (RI) strain sets (2, 3) or chromosome substitution strains (4), but with the added advantage of high-resolution association mapping (1). It consists of a set of 30 classic inbred strains chosen for diversity plus 70 or more RI strains derived primarily from strains C57BL/6J and DBA/2J (the BxD RI set) and A/J and C57BL/6J (the AxB and BxA RI sets). The classic strains provide mapping resolution, while the RI strains provide power. All of the chosen strains are commercially available from the Jackson Laboratory (https://www.jax.org) and all have been either sequenced (www.sanger.ac.uk/science/data/mouse-genomes-project) or densely genotyped (5).
diff --git a/general/datasets/GSE16780_UCLA_ML0911/acknowledgment.rtf b/general/datasets/GSE16780_UCLA_ML0911/acknowledgment.rtf
deleted file mode 100644
index 83eca40..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Bennett BJ, Ghazalpour A
diff --git a/general/datasets/GSE16780_UCLA_ML0911/cases.rtf b/general/datasets/GSE16780_UCLA_ML0911/cases.rtf
deleted file mode 100644
index 6eefb7b..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-For complete information please refer to Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, Siemers N, Neubauer M, Neuhaus I, Yordanova R, Guan B, Truong A, Yang WP, He A, Kayne P, Gargalovic P, Kirchgessner T, Pan C, Castellani LW, Kostem E, Furlotte N, Drake TA, Eskin E, Lusis AJ (2010) A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Research 20:281-90 PMID: 20054062
diff --git a/general/datasets/GSE16780_UCLA_ML0911/experiment-design.rtf b/general/datasets/GSE16780_UCLA_ML0911/experiment-design.rtf
deleted file mode 100644
index 40c5b94..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Expression profiling by array.
-
-Expression Profiles from 99 strains of inbred and recombinant inbred mice. Most assayed in triplicate. Two of 288 chips were excluded from the final analysis due to low QC scores.
diff --git a/general/datasets/GSE16780_UCLA_ML0911/notes.rtf b/general/datasets/GSE16780_UCLA_ML0911/notes.rtf
deleted file mode 100644
index 51b03e3..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Raw data provided as supplementary file at GEO Series GSE16780
diff --git a/general/datasets/GSE16780_UCLA_ML0911/platform.rtf b/general/datasets/GSE16780_UCLA_ML0911/platform.rtf
deleted file mode 100644
index 17c2cc4..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Platform GPL8759 [HT_MG-430A] Affymetrix HT Mouse Genome 430A Array
-
-The probe sets were selected from sequences derived from GenBank®, dbEST and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute Center for Genome Research (MSCG, April 2002).
-
-Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the array. Eleven pairs of oligonucleotide probes, including a perfect match and mismatch probe, are used to measure the level of transcription of each sequence represented on the GeneChip® HT Mouse Genome 430 Array Plate Set.
diff --git a/general/datasets/GSE16780_UCLA_ML0911/processing.rtf b/general/datasets/GSE16780_UCLA_ML0911/processing.rtf
deleted file mode 100644
index 7617e4f..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-For complete information please refer to A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 2010 Feb;20(2):281-90. PMID: 20054062
diff --git a/general/datasets/GSE16780_UCLA_ML0911/summary.rtf b/general/datasets/GSE16780_UCLA_ML0911/summary.rtf
deleted file mode 100644
index 2d0ff54..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Novel, systems-based approach to mouse genetics.
diff --git a/general/datasets/GSE16780_UCLA_ML0911/tissue.rtf b/general/datasets/GSE16780_UCLA_ML0911/tissue.rtf
deleted file mode 100644
index 4628b5b..0000000
--- a/general/datasets/GSE16780_UCLA_ML0911/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Hybrid Mouse diversity Panel Liver Expression Profile
diff --git a/general/datasets/GSE5281_F_RMA0709/acknowledgment.rtf b/general/datasets/GSE5281_F_RMA0709/acknowledgment.rtf
deleted file mode 100644
index 8ce4f5c..0000000
--- a/general/datasets/GSE5281_F_RMA0709/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Please cite: Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, Grover A, Niedzielko TL, Schneider LE, Mastroeni D, Caselli R, Kukull W, Morris JC, Hulette CM, Schmechel D, Rogers J, Stephan DA (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc Natl Acad Sci USA 105:4441-4446.
diff --git a/general/datasets/GSE5281_F_RMA0709/experiment-design.rtf b/general/datasets/GSE5281_F_RMA0709/experiment-design.rtf
deleted file mode 100644
index bc54b5c..0000000
--- a/general/datasets/GSE5281_F_RMA0709/experiment-design.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Human brain expression data in patients with Alzheimer's disease and age-matched elderly control subjects. This cortical expression data set is taken from GEO GSE5281 (Liang et al. 2006, Liang et al. 2008). Samples were laser-captured from cortical regions of 16 normal elderly humans (10 males and 4 females) and from 33 AD cases (15 males and 18 females). Mean age of cases and controls was 80 years. All samples were run on the Affymetrix U133 Plus 2.0 array. We renormalized the RMA data to an average expression of 8 units on a log2 scale. Two versions of the data have been entered in GeneNetwork: one consisting of 157 of 161 arrays (full set minus 4 arrays we consider of poor quality); the second consisting of what we regard as the best 102 arrays (those with mean correlations of better than 0.88 with all other arrays). Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex area 17 layer III. GeneNetwork does not yet allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example, expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-NOTE: We detected a minimum of 7.6% case assignment error rate (12 of 158 arrays) in this data set. Twelve cases are assigned to the wrong sex (see XIST probe set 224588_at, the figure below, and table 1). This raises the possibility that some cases are also misassigned by cortical brain region and disease status.
-
-
-
-
-
-Legend: Expression of the sex-specific gene XIST reveals about 10 sex assignment errors in this data set.
-
-Samples were laser-captured from cortical layer 3 (except the hippocampus) and run on the Affymetrix U133 Plus 2.0 array. We renormalized the data to an average expression of 8 units on a log2 scale. Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex layer III. A total of 16 normal subjects were used (10 M and 4 female). The AD samples. GeneNetwork does not allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-Information about the genes that are preferentially expressed during the course of Alzheimer's disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
diff --git a/general/datasets/GSE5281_F_RMA0709/platform.rtf b/general/datasets/GSE5281_F_RMA0709/platform.rtf
deleted file mode 100644
index 6c2af02..0000000
--- a/general/datasets/GSE5281_F_RMA0709/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
-
-In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).
diff --git a/general/datasets/GSE5281_F_RMA0709/summary.rtf b/general/datasets/GSE5281_F_RMA0709/summary.rtf
deleted file mode 100644
index 5db3978..0000000
--- a/general/datasets/GSE5281_F_RMA0709/summary.rtf
+++ /dev/null
@@ -1,1484 +0,0 @@
-(Taken verbatim from the GEO record)
-
-Information about the genes that are preferentially expressed during the course of Alzheimer’s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
-
-Aim 1. Collect brain samples from three Alzheimer’s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels.
-
-Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology.
-
-We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis.
-
-
-
-Bad arrays excluded: Four samples, highlighted in the table below, are bad arrays. For quality control, they should be excluded.
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM119615 |
- Entorhinal Cortex |
- Normal |
- E119615M63N |
- 63 |
- M |
-
-
- | 2 |
- GSM119616 |
- Entorhinal Cortex |
- Normal |
- E119616M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM119617 |
- Entorhinal Cortex |
- Normal |
- E119617M80N |
- 80 |
- M |
-
-
- | 4 |
- GSM119618 |
- Entorhinal Cortex |
- Normal |
- E119618M->F80N |
- 80 |
- M |
-
-
- | 5 |
- GSM119619 |
- Entorhinal Cortex |
- Normal |
- E119619F->M102N |
- 102 |
- F |
-
-
- | 6 |
- GSM119620 |
- Entorhinal Cortex |
- Normal |
- E119620M79N |
- 79 |
- M |
-
-
- | 7 |
- GSM119621 |
- Entorhinal Cortex |
- Normal |
- E119621M76N |
- 76 |
- M |
-
-
- | 8 |
- GSM119622 |
- Entorhinal Cortex |
- Normal |
- E119622M83N |
- 83 |
- M |
-
-
- | 9 |
- GSM119623 |
- Entorhinal Cortex |
- Normal |
- E119623M79N |
- 79 |
- M |
-
-
- | 10 |
- GSM119624 |
- Entorhinal Cortex |
- Normal |
- E119624F88N |
- 88 |
- F |
-
-
- | 11 |
- GSM119625 |
- Entorhinal Cortex |
- Normal |
- E119625F82N |
- 82 |
- F |
-
-
- | 12 |
- GSM119626 |
- Entorhinal Cortex |
- Normal |
- E119626M69N |
- 69 |
- M |
-
-
- | 13 |
- GSM119627 |
- Entorhinal Cortex |
- Normal |
- E119627M78N |
- 78 |
- M |
-
-
- | 14 |
- GSM238763 |
- Entorhinal Cortex |
- Alzheimer's |
- E238763F82A |
- 82 |
- F |
-
-
- | 15 |
- GSM238790 |
- Entorhinal Cortex |
- Alzheimer's |
- E238790F86A |
- 86 |
- F |
-
-
- | 16 |
- GSM238791 |
- Entorhinal Cortex |
- Alzheimer's |
- E238791F93A |
- 93 |
- F |
-
-
- | 17 |
- GSM238792 |
- Entorhinal Cortex |
- Alzheimer's |
- E238792M84A |
- 84 |
- M |
-
-
- | 18 |
- GSM238793 |
- Entorhinal Cortex |
- Alzheimer's |
- E238793F79A |
- 79 |
- F |
-
-
- | 19 |
- GSM238794 |
- Entorhinal Cortex |
- Alzheimer's |
- E238794F78A |
- 78 |
- F |
-
-
- | 20 |
- GSM238795 |
- Entorhinal Cortex |
- Alzheimer's |
- E238795F91A |
- 91 |
- F |
-
-
- | 21 |
- GSM238796 |
- Entorhinal Cortex |
- Alzheimer's |
- E238796M86A |
- 86 |
- M |
-
-
- | 22 |
- GSM238797 |
- Entorhinal Cortex |
- Alzheimer's |
- E238797NA0A |
- N/A |
- N/A |
-
-
- | 23 |
- GSM238798 |
- Entorhinal Cortex |
- Alzheimer's |
- E238798M80A |
- 80 |
- M |
-
-
- | 24 |
- GSM119628 |
- Hippocampus |
- Normal |
- H119628M85N |
- 85 |
- M |
-
-
- | 25 |
- GSM119629 |
- Hippocampus |
- Normal |
- H119629M80N |
- 80 |
- M |
-
-
- | 26 |
- GSM119630 |
- Hippocampus |
- Normal |
- H119630M80N |
- 80 |
- M |
-
-
- | 27 |
- GSM119631 |
- Hippocampus |
- Normal |
- H119631F102N |
- 102 |
- F |
-
-
- | 28 |
- GSM119632 |
- Hippocampus |
- Normal |
- H119632M63N |
- 63 |
- M |
-
-
- | 29 |
- GSM119633 |
- Hippocampus |
- Normal |
- H119633M79N |
- 79 |
- M |
-
-
- | 30 |
- GSM119634 |
- Hippocampus |
- Normal |
- H119634M76N |
- 76 |
- M |
-
-
- | 31 |
- GSM119635 |
- Hippocampus |
- Normal |
- H119635M83N |
- 83 |
- M |
-
-
- | 32 |
- GSM119636 |
- Hippocampus |
- Normal |
- H119636M79N |
- 79 |
- M |
-
-
- | 33 |
- GSM119637 |
- Hippocampus |
- Normal |
- H119637F88N |
- 88 |
- F |
-
-
- | 34 |
- GSM119638 |
- Hippocampus |
- Normal |
- H119638F73N |
- 73 |
- F |
-
-
- | 35 |
- GSM119639 |
- Hippocampus |
- Normal |
- H119639M69N |
- 69 |
- M |
-
-
- | 36 |
- GSM119640 |
- Hippocampus |
- Normal |
- H119640M78N |
- 78 |
- M |
-
-
- | 37 |
- GSM238799 |
- Hippocampus |
- Alzheimer's |
- H238799F73A |
- 73 |
- F |
-
-
- | 38 |
- GSM238800 |
- Hippocampus |
- Alzheimer's |
- H238800M81A |
- 81 |
- M |
-
-
- | 39 |
- GSM238801 |
- Hippocampus |
- Alzheimer's |
- H238801M78A |
- 78 |
- M |
-
-
- | 40 |
- GSM238802 |
- Hippocampus |
- Alzheimer's |
- H238802M75A |
- 75 |
- M |
-
-
- | 41 |
- GSM238803 |
- Hippocampus |
- Alzheimer's |
- H238803F70A |
- 70 |
- F |
-
-
- | 42 |
- GSM238804 |
- Hippocampus |
- Alzheimer's |
- H238804F85A |
- 85 |
- F |
-
-
- | 43 |
- GSM238805 |
- Hippocampus |
- Alzheimer's |
- H238805F77A |
- 77 |
- F |
-
-
- | 44 |
- GSM238806 |
- Hippocampus |
- Alzheimer's |
- H238806M79A |
- 79 |
- M |
-
-
- | 45 |
- GSM238807 |
- Hippocampus |
- Alzheimer's |
- H238807M88A |
- 88 |
- M |
-
-
- | 46 |
- GSM238808 |
- Hippocampus |
- Alzheimer's |
- H238808M72A |
- 72 |
- M |
-
-
- | 47 |
- GSM119641 |
- Medial Temporal Gyrus |
- Normal |
- MT119641M85N |
- 85 |
- M |
-
-
- | 48 |
- GSM119642 |
- Medial Temporal Gyrus |
- Normal |
- MT119642M80N |
- 80 |
- M |
-
-
- | 49 |
- GSM119643 |
- Medial Temporal Gyrus |
- Normal |
- MT119643F102N |
- 102 |
- F |
-
-
- | 50 |
- GSM119644 |
- Medial Temporal Gyrus |
- Normal |
- MT119644M63N |
- 63 |
- M |
-
-
- | 51 |
- GSM119645 |
- Medial Temporal Gyrus |
- Normal |
- MT119645M79N |
- 79 |
- M |
-
-
- | 52 |
- GSM119646 |
- Medial Temporal Gyrus |
- Normal |
- MT119646M83N |
- 83 |
- M |
-
-
- | 53 |
- GSM119647 |
- Medial Temporal Gyrus |
- Normal |
- MT119647M79N |
- 79 |
- M |
-
-
- | 54 |
- GSM119648 |
- Medial Temporal Gyrus |
- Normal |
- MT119648F88N |
- 88 |
- F |
-
-
- | 55 |
- GSM119649 |
- Medial Temporal Gyrus |
- Normal |
- MT119649F82N |
- 82 |
- F |
-
-
- | 56 |
- GSM119650 |
- Medial Temporal Gyrus |
- Normal |
- MT119650F73N |
- 73 |
- F |
-
-
- | 57 |
- GSM119651 |
- Medial Temporal Gyrus |
- Normal |
- MT119651M69N |
- 69 |
- M |
-
-
- | 58 |
- GSM119652 |
- Medial Temporal Gyrus |
- Normal |
- MT119652M->F78N |
- 78 |
- M |
-
-
- | 59 |
- GSM238809 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238809M81A |
- 81 |
- M |
-
-
- | 60 |
- GSM238810 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238810M72A |
- 72 |
- M |
-
-
- | 61 |
- GSM238811 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238811M75A |
- 75 |
- M |
-
-
- | 62 |
- GSM238812 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238812M78A |
- 78 |
- M |
-
-
- | 63 |
- GSM238813 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238813M75A |
- 75 |
- M |
-
-
- | 64 |
- GSM238815 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238815F95A |
- 95 |
- F |
-
-
- | 65 |
- GSM238816 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238816F81A |
- 81 |
- F |
-
-
- | 66 |
- GSM238817 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238817F85A |
- 85 |
- F |
-
-
- | 67 |
- GSM238818 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238818M79A |
- 79 |
- M |
-
-
- | 68 |
- GSM238819 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238819F82A |
- 82 |
- F |
-
-
- | 69 |
- GSM238820 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238820M88A |
- 88 |
- M |
-
-
- | 70 |
- GSM238821 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238821M72A |
- 72 |
- M |
-
-
- | 71 |
- GSM238822 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238822F73A |
- 73 |
- F |
-
-
- | 72 |
- GSM238823 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238823M87A |
- 87 |
- M |
-
-
- | 73 |
- GSM238824 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238824M68A |
- 68 |
- M |
-
-
- | 74 |
- GSM238825 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238825F80A |
- 80 |
- F |
-
-
- | 75 |
- GSM119653 |
- Posterior Cingulate |
- Normal |
- PC119653M85N |
- 85 |
- M |
-
-
- | 76 |
- GSM119654 |
- Posterior Cingulate |
- Normal |
- PC119654M80N |
- 80 |
- M |
-
-
- | 77 |
- GSM119655 |
- Posterior Cingulate |
- Normal |
- PC119655F102N |
- 102 |
- F |
-
-
- | 78 |
- GSM119656 |
- Posterior Cingulate |
- Normal |
- PC119656M63N |
- 63 |
- M |
-
-
- | 79 |
- GSM119657 |
- Posterior Cingulate |
- Normal |
- PC119657M79N |
- 79 |
- M |
-
-
- | 80 |
- GSM119658 |
- Posterior Cingulate |
- Normal |
- PC119658M->F76N |
- 76 |
- M |
-
-
- | 81 |
- GSM119659 |
- Posterior Cingulate |
- Normal |
- PC119659M83N |
- 83 |
- M |
-
-
- | 82 |
- GSM119660 |
- Posterior Cingulate |
- Normal |
- PC119660M79N |
- 79 |
- M |
-
-
- | 83 |
- GSM119661 |
- Posterior Cingulate |
- Normal |
- PC119661F88N |
- 88 |
- F |
-
-
- | 84 |
- GSM119662 |
- Posterior Cingulate |
- Normal |
- PC119662F82N |
- 82 |
- F |
-
-
- | 85 |
- GSM119663 |
- Posterior Cingulate |
- Normal |
- PC119663F73N |
- 73 |
- F |
-
-
- | 86 |
- GSM119664 |
- Posterior Cingulate |
- Normal |
- PC119664M69N |
- 69 |
- M |
-
-
- | 87 |
- GSM119665 |
- Posterior Cingulate |
- Normal |
- PC119665M78N |
- 78 |
- M |
-
-
- | 88 |
- GSM238826 |
- Posterior Cingulate |
- Alzheimer's |
- PC238826F73A |
- 73 |
- F |
-
-
- | 89 |
- GSM238827 |
- Posterior Cingulate |
- Alzheimer's |
- PC238827M81A |
- 81 |
- M |
-
-
- | 90 |
- GSM238834 |
- Posterior Cingulate |
- Alzheimer's |
- PC238834M78A |
- 78 |
- M |
-
-
- | 91 |
- GSM238835 |
- Posterior Cingulate |
- Alzheimer's |
- PC238835M75A |
- 75 |
- M |
-
-
- | 92 |
- GSM238837 |
- Posterior Cingulate |
- Alzheimer's |
- PC238837M68A |
- 68 |
- M |
-
-
- | 93 |
- GSM238838 |
- Posterior Cingulate |
- Alzheimer's |
- PC238838F70A |
- 70 |
- F |
-
-
- | 94 |
- GSM238839 |
- Posterior Cingulate |
- Alzheimer's |
- PC238839F85A |
- 85 |
- F |
-
-
- | 95 |
- GSM238840 |
- Posterior Cingulate |
- Alzheimer's |
- PC238840M79A |
- 79 |
- M |
-
-
- | 96 |
- GSM238841 |
- Posterior Cingulate |
- Alzheimer's |
- PC238841M88A |
- 88 |
- M |
-
-
- | 97 |
- GSM119666 |
- Superior Frontal Gyrus |
- Normal |
- SF119666M79N |
- 79 |
- M |
-
-
- | 98 |
- GSM119667 |
- Superior Frontal Gyrus |
- Normal |
- SF119667F->M88N |
- 88 |
- F |
-
-
- | 99 |
- GSM119668 |
- Superior Frontal Gyrus |
- Normal |
- SF119668F->M82N |
- 82 |
- F |
-
-
- | 100 |
- GSM119669 |
- Superior Frontal Gyrus |
- Normal |
- SF119669F->M73N |
- 73 |
- F |
-
-
- | 101 |
- GSM119670 |
- Superior Frontal Gyrus |
- Normal |
- SF119670F->M102N |
- 102 |
- F |
-
-
- | 102 |
- GSM119671 |
- Superior Frontal Gyrus |
- Normal |
- SF119671M63N |
- 63 |
- M |
-
-
- | 103 |
- GSM119672 |
- Superior Frontal Gyrus |
- Normal |
- SF119672M->F79N |
- 79 |
- M |
-
-
- | 104 |
- GSM119673 |
- Superior Frontal Gyrus |
- Normal |
- SF119673M->F76N |
- 76 |
- M |
-
-
- | 105 |
- GSM119674 |
- Superior Frontal Gyrus |
- Normal |
- SF119674M->F83N |
- 83 |
- M |
-
-
- | 106 |
- GSM119675 |
- Superior Frontal Gyrus |
- Normal |
- SF119675M69N |
- 69 |
- M |
-
-
- | 107 |
- GSM119676 |
- Superior Frontal Gyrus |
- Normal |
- SF119676M78N |
- 78 |
- M |
-
-
- | 108 |
- GSM238842 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238842F73A |
- 73 |
- F |
-
-
- | 109 |
- GSM238843 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238843M81A |
- 81 |
- M |
-
-
- | 110 |
- GSM238844 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238844M72A |
- 72 |
- M |
-
-
- | 111 |
- GSM238845 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238845M75A |
- 75 |
- M |
-
-
- | 112 |
- GSM238846 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238846M78A |
- 78 |
- M |
-
-
- | 113 |
- GSM238847 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238847M75A |
- 75 |
- M |
-
-
- | 114 |
- GSM238848 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238848M87A |
- 87 |
- M |
-
-
- | 115 |
- GSM238851 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238851F95A |
- 95 |
- F |
-
-
- | 116 |
- GSM238854 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238854M68A |
- 68 |
- M |
-
-
- | 117 |
- GSM238855 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238855F95A |
- 95 |
- F |
-
-
- | 118 |
- GSM238856 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238856F70A |
- 70 |
- F |
-
-
- | 119 |
- GSM238857 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238857F85A |
- 85 |
- F |
-
-
- | 120 |
- GSM238858 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238858F83A |
- 83 |
- F |
-
-
- | 121 |
- GSM238860 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238860F77A |
- 77 |
- F |
-
-
- | 122 |
- GSM238861 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238861F83A |
- 83 |
- F |
-
-
- | 123 |
- GSM238862 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238862M68A |
- 68 |
- M |
-
-
- | 124 |
- GSM238863 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238863M79A |
- 79 |
- M |
-
-
- | 125 |
- GSM238864 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238864F82A |
- 82 |
- F |
-
-
- | 126 |
- GSM238865 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238865M88A |
- 88 |
- M |
-
-
- | 127 |
- GSM238867 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238867F80A |
- 80 |
- F |
-
-
- | 128 |
- GSM238868 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238868M74A |
- 74 |
- M |
-
-
- | 129 |
- GSM238870 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238870M72A |
- 72 |
- M |
-
-
- | 130 |
- GSM238871 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238871M80A |
- 80 |
- M |
-
-
- | 131 |
- GSM119677 |
- Primary Visual Cortex |
- Normal |
- V119677M85N |
- 85 |
- M |
-
-
- | 132 |
- GSM119678 |
- Primary Visual Cortex |
- Normal |
- V119678M80N |
- 80 |
- M |
-
-
- | 133 |
- GSM119679 |
- Primary Visual Cortex |
- Normal |
- V119679M63N |
- 63 |
- M |
-
-
- | 134 |
- GSM119680 |
- Primary Visual Cortex |
- Normal |
- V119680M79N |
- 79 |
- M |
-
-
- | 135 |
- GSM119681 |
- Primary Visual Cortex |
- Normal |
- V119681M76N |
- 76 |
- M |
-
-
- | 136 |
- GSM119682 |
- Primary Visual Cortex |
- Normal |
- V119682M83N |
- 83 |
- M |
-
-
- | 137 |
- GSM119683 |
- Primary Visual Cortex |
- Normal |
- V119683M79N |
- 79 |
- M |
-
-
- | 138 |
- GSM119684 |
- Primary Visual Cortex |
- Normal |
- V119684F88N |
- 88 |
- F |
-
-
- | 139 |
- GSM119685 |
- Primary Visual Cortex |
- Normal |
- V119685F82N |
- 82 |
- F |
-
-
- | 140 |
- GSM119686 |
- Primary Visual Cortex |
- Normal |
- V119686F73N |
- 73 |
- F |
-
-
- | 141 |
- GSM119687 |
- Primary Visual Cortex |
- Normal |
- V119687M69N |
- 69 |
- M |
-
-
- | 142 |
- GSM119688 |
- Primary Visual Cortex |
- Normal |
- V119688M78N |
- 78 |
- M |
-
-
- | 143 |
- GSM238872 |
- Primary Visual Cortex |
- Alzheimer's |
- V238872F73A |
- 73 |
- F |
-
-
- | 144 |
- GSM238873 |
- Primary Visual Cortex |
- Alzheimer's |
- V238873M81A |
- 81 |
- M |
-
-
- | 145 |
- GSM238874 |
- Primary Visual Cortex |
- Alzheimer's |
- V238874M75A |
- 75 |
- M |
-
-
- | 146 |
- GSM238875 |
- Primary Visual Cortex |
- Alzheimer's |
- V238875M78A |
- 78 |
- M |
-
-
- | 147 |
- GSM238877 |
- Primary Visual Cortex |
- Alzheimer's |
- V238877M75A |
- 75 |
- M |
-
-
- | 148 |
- GSM238941 |
- Primary Visual Cortex |
- Alzheimer's |
- V238941M87A |
- 87 |
- M |
-
-
- | 149 |
- GSM238942 |
- Primary Visual Cortex |
- Alzheimer's |
- V238942F95A |
- 95 |
- F |
-
-
- | 150 |
- GSM238943 |
- Primary Visual Cortex |
- Alzheimer's |
- V238943M68A |
- 68 |
- M |
-
-
- | 151 |
- GSM238944 |
- Primary Visual Cortex |
- Alzheimer's |
- V238944F70A |
- 70 |
- F |
-
-
- | 152 |
- GSM238945 |
- Primary Visual Cortex |
- Alzheimer's |
- V238945F81A |
- 81 |
- F |
-
-
- | 153 |
- GSM238946 |
- Primary Visual Cortex |
- Alzheimer's |
- V238946F85A |
- 85 |
- F |
-
-
- | 154 |
- GSM238947 |
- Primary Visual Cortex |
- Alzheimer's |
- V238947M68A |
- 68 |
- M |
-
-
- | 155 |
- GSM238948 |
- Primary Visual Cortex |
- Alzheimer's |
- V238948M79A |
- 79 |
- M |
-
-
- | 156 |
- GSM238949 |
- Primary Visual Cortex |
- Alzheimer's |
- V238949F82A |
- 82 |
- F |
-
-
- | 157 |
- GSM238951 |
- Primary Visual Cortex |
- Alzheimer's |
- V238951M88A |
- 88 |
- M |
-
-
- | 158 |
- GSM238952 |
- Primary Visual Cortex |
- Alzheimer's |
- V238952M74A |
- 74 |
- M |
-
-
- | 159 |
- GSM238953 |
- Primary Visual Cortex |
- Alzheimer's |
- V238953M72A |
- 72 |
- M |
-
-
- | 160 |
- GSM238955 |
- Primary Visual Cortex |
- Alzheimer's |
- V238955M->F68A |
- 68 |
- M |
-
-
- | 161 |
- GSM238963 |
- Primary Visual Cortex |
- Alzheimer's |
- V238963F80A |
- 80 |
- F |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GSE5281_F_RMA_Alzh_0709/acknowledgment.rtf b/general/datasets/GSE5281_F_RMA_Alzh_0709/acknowledgment.rtf
deleted file mode 100644
index 8ce4f5c..0000000
--- a/general/datasets/GSE5281_F_RMA_Alzh_0709/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Please cite: Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, Grover A, Niedzielko TL, Schneider LE, Mastroeni D, Caselli R, Kukull W, Morris JC, Hulette CM, Schmechel D, Rogers J, Stephan DA (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc Natl Acad Sci USA 105:4441-4446.
diff --git a/general/datasets/GSE5281_F_RMA_Alzh_0709/experiment-design.rtf b/general/datasets/GSE5281_F_RMA_Alzh_0709/experiment-design.rtf
deleted file mode 100644
index bc54b5c..0000000
--- a/general/datasets/GSE5281_F_RMA_Alzh_0709/experiment-design.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Human brain expression data in patients with Alzheimer's disease and age-matched elderly control subjects. This cortical expression data set is taken from GEO GSE5281 (Liang et al. 2006, Liang et al. 2008). Samples were laser-captured from cortical regions of 16 normal elderly humans (10 males and 4 females) and from 33 AD cases (15 males and 18 females). Mean age of cases and controls was 80 years. All samples were run on the Affymetrix U133 Plus 2.0 array. We renormalized the RMA data to an average expression of 8 units on a log2 scale. Two versions of the data have been entered in GeneNetwork: one consisting of 157 of 161 arrays (full set minus 4 arrays we consider of poor quality); the second consisting of what we regard as the best 102 arrays (those with mean correlations of better than 0.88 with all other arrays). Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex area 17 layer III. GeneNetwork does not yet allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example, expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-NOTE: We detected a minimum of 7.6% case assignment error rate (12 of 158 arrays) in this data set. Twelve cases are assigned to the wrong sex (see XIST probe set 224588_at, the figure below, and table 1). This raises the possibility that some cases are also misassigned by cortical brain region and disease status.
-
-
-
-
-
-Legend: Expression of the sex-specific gene XIST reveals about 10 sex assignment errors in this data set.
-
-Samples were laser-captured from cortical layer 3 (except the hippocampus) and run on the Affymetrix U133 Plus 2.0 array. We renormalized the data to an average expression of 8 units on a log2 scale. Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex layer III. A total of 16 normal subjects were used (10 M and 4 female). The AD samples. GeneNetwork does not allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-Information about the genes that are preferentially expressed during the course of Alzheimer's disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
diff --git a/general/datasets/GSE5281_F_RMA_Alzh_0709/platform.rtf b/general/datasets/GSE5281_F_RMA_Alzh_0709/platform.rtf
deleted file mode 100644
index 6c2af02..0000000
--- a/general/datasets/GSE5281_F_RMA_Alzh_0709/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
-
-In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).
diff --git a/general/datasets/GSE5281_F_RMA_Alzh_0709/summary.rtf b/general/datasets/GSE5281_F_RMA_Alzh_0709/summary.rtf
deleted file mode 100644
index 5db3978..0000000
--- a/general/datasets/GSE5281_F_RMA_Alzh_0709/summary.rtf
+++ /dev/null
@@ -1,1484 +0,0 @@
-(Taken verbatim from the GEO record)
-
-Information about the genes that are preferentially expressed during the course of Alzheimer’s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
-
-Aim 1. Collect brain samples from three Alzheimer’s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels.
-
-Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology.
-
-We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis.
-
-
-
-Bad arrays excluded: Four samples, highlighted in the table below, are bad arrays. For quality control, they should be excluded.
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM119615 |
- Entorhinal Cortex |
- Normal |
- E119615M63N |
- 63 |
- M |
-
-
- | 2 |
- GSM119616 |
- Entorhinal Cortex |
- Normal |
- E119616M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM119617 |
- Entorhinal Cortex |
- Normal |
- E119617M80N |
- 80 |
- M |
-
-
- | 4 |
- GSM119618 |
- Entorhinal Cortex |
- Normal |
- E119618M->F80N |
- 80 |
- M |
-
-
- | 5 |
- GSM119619 |
- Entorhinal Cortex |
- Normal |
- E119619F->M102N |
- 102 |
- F |
-
-
- | 6 |
- GSM119620 |
- Entorhinal Cortex |
- Normal |
- E119620M79N |
- 79 |
- M |
-
-
- | 7 |
- GSM119621 |
- Entorhinal Cortex |
- Normal |
- E119621M76N |
- 76 |
- M |
-
-
- | 8 |
- GSM119622 |
- Entorhinal Cortex |
- Normal |
- E119622M83N |
- 83 |
- M |
-
-
- | 9 |
- GSM119623 |
- Entorhinal Cortex |
- Normal |
- E119623M79N |
- 79 |
- M |
-
-
- | 10 |
- GSM119624 |
- Entorhinal Cortex |
- Normal |
- E119624F88N |
- 88 |
- F |
-
-
- | 11 |
- GSM119625 |
- Entorhinal Cortex |
- Normal |
- E119625F82N |
- 82 |
- F |
-
-
- | 12 |
- GSM119626 |
- Entorhinal Cortex |
- Normal |
- E119626M69N |
- 69 |
- M |
-
-
- | 13 |
- GSM119627 |
- Entorhinal Cortex |
- Normal |
- E119627M78N |
- 78 |
- M |
-
-
- | 14 |
- GSM238763 |
- Entorhinal Cortex |
- Alzheimer's |
- E238763F82A |
- 82 |
- F |
-
-
- | 15 |
- GSM238790 |
- Entorhinal Cortex |
- Alzheimer's |
- E238790F86A |
- 86 |
- F |
-
-
- | 16 |
- GSM238791 |
- Entorhinal Cortex |
- Alzheimer's |
- E238791F93A |
- 93 |
- F |
-
-
- | 17 |
- GSM238792 |
- Entorhinal Cortex |
- Alzheimer's |
- E238792M84A |
- 84 |
- M |
-
-
- | 18 |
- GSM238793 |
- Entorhinal Cortex |
- Alzheimer's |
- E238793F79A |
- 79 |
- F |
-
-
- | 19 |
- GSM238794 |
- Entorhinal Cortex |
- Alzheimer's |
- E238794F78A |
- 78 |
- F |
-
-
- | 20 |
- GSM238795 |
- Entorhinal Cortex |
- Alzheimer's |
- E238795F91A |
- 91 |
- F |
-
-
- | 21 |
- GSM238796 |
- Entorhinal Cortex |
- Alzheimer's |
- E238796M86A |
- 86 |
- M |
-
-
- | 22 |
- GSM238797 |
- Entorhinal Cortex |
- Alzheimer's |
- E238797NA0A |
- N/A |
- N/A |
-
-
- | 23 |
- GSM238798 |
- Entorhinal Cortex |
- Alzheimer's |
- E238798M80A |
- 80 |
- M |
-
-
- | 24 |
- GSM119628 |
- Hippocampus |
- Normal |
- H119628M85N |
- 85 |
- M |
-
-
- | 25 |
- GSM119629 |
- Hippocampus |
- Normal |
- H119629M80N |
- 80 |
- M |
-
-
- | 26 |
- GSM119630 |
- Hippocampus |
- Normal |
- H119630M80N |
- 80 |
- M |
-
-
- | 27 |
- GSM119631 |
- Hippocampus |
- Normal |
- H119631F102N |
- 102 |
- F |
-
-
- | 28 |
- GSM119632 |
- Hippocampus |
- Normal |
- H119632M63N |
- 63 |
- M |
-
-
- | 29 |
- GSM119633 |
- Hippocampus |
- Normal |
- H119633M79N |
- 79 |
- M |
-
-
- | 30 |
- GSM119634 |
- Hippocampus |
- Normal |
- H119634M76N |
- 76 |
- M |
-
-
- | 31 |
- GSM119635 |
- Hippocampus |
- Normal |
- H119635M83N |
- 83 |
- M |
-
-
- | 32 |
- GSM119636 |
- Hippocampus |
- Normal |
- H119636M79N |
- 79 |
- M |
-
-
- | 33 |
- GSM119637 |
- Hippocampus |
- Normal |
- H119637F88N |
- 88 |
- F |
-
-
- | 34 |
- GSM119638 |
- Hippocampus |
- Normal |
- H119638F73N |
- 73 |
- F |
-
-
- | 35 |
- GSM119639 |
- Hippocampus |
- Normal |
- H119639M69N |
- 69 |
- M |
-
-
- | 36 |
- GSM119640 |
- Hippocampus |
- Normal |
- H119640M78N |
- 78 |
- M |
-
-
- | 37 |
- GSM238799 |
- Hippocampus |
- Alzheimer's |
- H238799F73A |
- 73 |
- F |
-
-
- | 38 |
- GSM238800 |
- Hippocampus |
- Alzheimer's |
- H238800M81A |
- 81 |
- M |
-
-
- | 39 |
- GSM238801 |
- Hippocampus |
- Alzheimer's |
- H238801M78A |
- 78 |
- M |
-
-
- | 40 |
- GSM238802 |
- Hippocampus |
- Alzheimer's |
- H238802M75A |
- 75 |
- M |
-
-
- | 41 |
- GSM238803 |
- Hippocampus |
- Alzheimer's |
- H238803F70A |
- 70 |
- F |
-
-
- | 42 |
- GSM238804 |
- Hippocampus |
- Alzheimer's |
- H238804F85A |
- 85 |
- F |
-
-
- | 43 |
- GSM238805 |
- Hippocampus |
- Alzheimer's |
- H238805F77A |
- 77 |
- F |
-
-
- | 44 |
- GSM238806 |
- Hippocampus |
- Alzheimer's |
- H238806M79A |
- 79 |
- M |
-
-
- | 45 |
- GSM238807 |
- Hippocampus |
- Alzheimer's |
- H238807M88A |
- 88 |
- M |
-
-
- | 46 |
- GSM238808 |
- Hippocampus |
- Alzheimer's |
- H238808M72A |
- 72 |
- M |
-
-
- | 47 |
- GSM119641 |
- Medial Temporal Gyrus |
- Normal |
- MT119641M85N |
- 85 |
- M |
-
-
- | 48 |
- GSM119642 |
- Medial Temporal Gyrus |
- Normal |
- MT119642M80N |
- 80 |
- M |
-
-
- | 49 |
- GSM119643 |
- Medial Temporal Gyrus |
- Normal |
- MT119643F102N |
- 102 |
- F |
-
-
- | 50 |
- GSM119644 |
- Medial Temporal Gyrus |
- Normal |
- MT119644M63N |
- 63 |
- M |
-
-
- | 51 |
- GSM119645 |
- Medial Temporal Gyrus |
- Normal |
- MT119645M79N |
- 79 |
- M |
-
-
- | 52 |
- GSM119646 |
- Medial Temporal Gyrus |
- Normal |
- MT119646M83N |
- 83 |
- M |
-
-
- | 53 |
- GSM119647 |
- Medial Temporal Gyrus |
- Normal |
- MT119647M79N |
- 79 |
- M |
-
-
- | 54 |
- GSM119648 |
- Medial Temporal Gyrus |
- Normal |
- MT119648F88N |
- 88 |
- F |
-
-
- | 55 |
- GSM119649 |
- Medial Temporal Gyrus |
- Normal |
- MT119649F82N |
- 82 |
- F |
-
-
- | 56 |
- GSM119650 |
- Medial Temporal Gyrus |
- Normal |
- MT119650F73N |
- 73 |
- F |
-
-
- | 57 |
- GSM119651 |
- Medial Temporal Gyrus |
- Normal |
- MT119651M69N |
- 69 |
- M |
-
-
- | 58 |
- GSM119652 |
- Medial Temporal Gyrus |
- Normal |
- MT119652M->F78N |
- 78 |
- M |
-
-
- | 59 |
- GSM238809 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238809M81A |
- 81 |
- M |
-
-
- | 60 |
- GSM238810 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238810M72A |
- 72 |
- M |
-
-
- | 61 |
- GSM238811 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238811M75A |
- 75 |
- M |
-
-
- | 62 |
- GSM238812 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238812M78A |
- 78 |
- M |
-
-
- | 63 |
- GSM238813 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238813M75A |
- 75 |
- M |
-
-
- | 64 |
- GSM238815 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238815F95A |
- 95 |
- F |
-
-
- | 65 |
- GSM238816 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238816F81A |
- 81 |
- F |
-
-
- | 66 |
- GSM238817 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238817F85A |
- 85 |
- F |
-
-
- | 67 |
- GSM238818 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238818M79A |
- 79 |
- M |
-
-
- | 68 |
- GSM238819 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238819F82A |
- 82 |
- F |
-
-
- | 69 |
- GSM238820 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238820M88A |
- 88 |
- M |
-
-
- | 70 |
- GSM238821 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238821M72A |
- 72 |
- M |
-
-
- | 71 |
- GSM238822 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238822F73A |
- 73 |
- F |
-
-
- | 72 |
- GSM238823 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238823M87A |
- 87 |
- M |
-
-
- | 73 |
- GSM238824 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238824M68A |
- 68 |
- M |
-
-
- | 74 |
- GSM238825 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238825F80A |
- 80 |
- F |
-
-
- | 75 |
- GSM119653 |
- Posterior Cingulate |
- Normal |
- PC119653M85N |
- 85 |
- M |
-
-
- | 76 |
- GSM119654 |
- Posterior Cingulate |
- Normal |
- PC119654M80N |
- 80 |
- M |
-
-
- | 77 |
- GSM119655 |
- Posterior Cingulate |
- Normal |
- PC119655F102N |
- 102 |
- F |
-
-
- | 78 |
- GSM119656 |
- Posterior Cingulate |
- Normal |
- PC119656M63N |
- 63 |
- M |
-
-
- | 79 |
- GSM119657 |
- Posterior Cingulate |
- Normal |
- PC119657M79N |
- 79 |
- M |
-
-
- | 80 |
- GSM119658 |
- Posterior Cingulate |
- Normal |
- PC119658M->F76N |
- 76 |
- M |
-
-
- | 81 |
- GSM119659 |
- Posterior Cingulate |
- Normal |
- PC119659M83N |
- 83 |
- M |
-
-
- | 82 |
- GSM119660 |
- Posterior Cingulate |
- Normal |
- PC119660M79N |
- 79 |
- M |
-
-
- | 83 |
- GSM119661 |
- Posterior Cingulate |
- Normal |
- PC119661F88N |
- 88 |
- F |
-
-
- | 84 |
- GSM119662 |
- Posterior Cingulate |
- Normal |
- PC119662F82N |
- 82 |
- F |
-
-
- | 85 |
- GSM119663 |
- Posterior Cingulate |
- Normal |
- PC119663F73N |
- 73 |
- F |
-
-
- | 86 |
- GSM119664 |
- Posterior Cingulate |
- Normal |
- PC119664M69N |
- 69 |
- M |
-
-
- | 87 |
- GSM119665 |
- Posterior Cingulate |
- Normal |
- PC119665M78N |
- 78 |
- M |
-
-
- | 88 |
- GSM238826 |
- Posterior Cingulate |
- Alzheimer's |
- PC238826F73A |
- 73 |
- F |
-
-
- | 89 |
- GSM238827 |
- Posterior Cingulate |
- Alzheimer's |
- PC238827M81A |
- 81 |
- M |
-
-
- | 90 |
- GSM238834 |
- Posterior Cingulate |
- Alzheimer's |
- PC238834M78A |
- 78 |
- M |
-
-
- | 91 |
- GSM238835 |
- Posterior Cingulate |
- Alzheimer's |
- PC238835M75A |
- 75 |
- M |
-
-
- | 92 |
- GSM238837 |
- Posterior Cingulate |
- Alzheimer's |
- PC238837M68A |
- 68 |
- M |
-
-
- | 93 |
- GSM238838 |
- Posterior Cingulate |
- Alzheimer's |
- PC238838F70A |
- 70 |
- F |
-
-
- | 94 |
- GSM238839 |
- Posterior Cingulate |
- Alzheimer's |
- PC238839F85A |
- 85 |
- F |
-
-
- | 95 |
- GSM238840 |
- Posterior Cingulate |
- Alzheimer's |
- PC238840M79A |
- 79 |
- M |
-
-
- | 96 |
- GSM238841 |
- Posterior Cingulate |
- Alzheimer's |
- PC238841M88A |
- 88 |
- M |
-
-
- | 97 |
- GSM119666 |
- Superior Frontal Gyrus |
- Normal |
- SF119666M79N |
- 79 |
- M |
-
-
- | 98 |
- GSM119667 |
- Superior Frontal Gyrus |
- Normal |
- SF119667F->M88N |
- 88 |
- F |
-
-
- | 99 |
- GSM119668 |
- Superior Frontal Gyrus |
- Normal |
- SF119668F->M82N |
- 82 |
- F |
-
-
- | 100 |
- GSM119669 |
- Superior Frontal Gyrus |
- Normal |
- SF119669F->M73N |
- 73 |
- F |
-
-
- | 101 |
- GSM119670 |
- Superior Frontal Gyrus |
- Normal |
- SF119670F->M102N |
- 102 |
- F |
-
-
- | 102 |
- GSM119671 |
- Superior Frontal Gyrus |
- Normal |
- SF119671M63N |
- 63 |
- M |
-
-
- | 103 |
- GSM119672 |
- Superior Frontal Gyrus |
- Normal |
- SF119672M->F79N |
- 79 |
- M |
-
-
- | 104 |
- GSM119673 |
- Superior Frontal Gyrus |
- Normal |
- SF119673M->F76N |
- 76 |
- M |
-
-
- | 105 |
- GSM119674 |
- Superior Frontal Gyrus |
- Normal |
- SF119674M->F83N |
- 83 |
- M |
-
-
- | 106 |
- GSM119675 |
- Superior Frontal Gyrus |
- Normal |
- SF119675M69N |
- 69 |
- M |
-
-
- | 107 |
- GSM119676 |
- Superior Frontal Gyrus |
- Normal |
- SF119676M78N |
- 78 |
- M |
-
-
- | 108 |
- GSM238842 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238842F73A |
- 73 |
- F |
-
-
- | 109 |
- GSM238843 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238843M81A |
- 81 |
- M |
-
-
- | 110 |
- GSM238844 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238844M72A |
- 72 |
- M |
-
-
- | 111 |
- GSM238845 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238845M75A |
- 75 |
- M |
-
-
- | 112 |
- GSM238846 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238846M78A |
- 78 |
- M |
-
-
- | 113 |
- GSM238847 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238847M75A |
- 75 |
- M |
-
-
- | 114 |
- GSM238848 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238848M87A |
- 87 |
- M |
-
-
- | 115 |
- GSM238851 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238851F95A |
- 95 |
- F |
-
-
- | 116 |
- GSM238854 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238854M68A |
- 68 |
- M |
-
-
- | 117 |
- GSM238855 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238855F95A |
- 95 |
- F |
-
-
- | 118 |
- GSM238856 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238856F70A |
- 70 |
- F |
-
-
- | 119 |
- GSM238857 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238857F85A |
- 85 |
- F |
-
-
- | 120 |
- GSM238858 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238858F83A |
- 83 |
- F |
-
-
- | 121 |
- GSM238860 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238860F77A |
- 77 |
- F |
-
-
- | 122 |
- GSM238861 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238861F83A |
- 83 |
- F |
-
-
- | 123 |
- GSM238862 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238862M68A |
- 68 |
- M |
-
-
- | 124 |
- GSM238863 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238863M79A |
- 79 |
- M |
-
-
- | 125 |
- GSM238864 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238864F82A |
- 82 |
- F |
-
-
- | 126 |
- GSM238865 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238865M88A |
- 88 |
- M |
-
-
- | 127 |
- GSM238867 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238867F80A |
- 80 |
- F |
-
-
- | 128 |
- GSM238868 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238868M74A |
- 74 |
- M |
-
-
- | 129 |
- GSM238870 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238870M72A |
- 72 |
- M |
-
-
- | 130 |
- GSM238871 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238871M80A |
- 80 |
- M |
-
-
- | 131 |
- GSM119677 |
- Primary Visual Cortex |
- Normal |
- V119677M85N |
- 85 |
- M |
-
-
- | 132 |
- GSM119678 |
- Primary Visual Cortex |
- Normal |
- V119678M80N |
- 80 |
- M |
-
-
- | 133 |
- GSM119679 |
- Primary Visual Cortex |
- Normal |
- V119679M63N |
- 63 |
- M |
-
-
- | 134 |
- GSM119680 |
- Primary Visual Cortex |
- Normal |
- V119680M79N |
- 79 |
- M |
-
-
- | 135 |
- GSM119681 |
- Primary Visual Cortex |
- Normal |
- V119681M76N |
- 76 |
- M |
-
-
- | 136 |
- GSM119682 |
- Primary Visual Cortex |
- Normal |
- V119682M83N |
- 83 |
- M |
-
-
- | 137 |
- GSM119683 |
- Primary Visual Cortex |
- Normal |
- V119683M79N |
- 79 |
- M |
-
-
- | 138 |
- GSM119684 |
- Primary Visual Cortex |
- Normal |
- V119684F88N |
- 88 |
- F |
-
-
- | 139 |
- GSM119685 |
- Primary Visual Cortex |
- Normal |
- V119685F82N |
- 82 |
- F |
-
-
- | 140 |
- GSM119686 |
- Primary Visual Cortex |
- Normal |
- V119686F73N |
- 73 |
- F |
-
-
- | 141 |
- GSM119687 |
- Primary Visual Cortex |
- Normal |
- V119687M69N |
- 69 |
- M |
-
-
- | 142 |
- GSM119688 |
- Primary Visual Cortex |
- Normal |
- V119688M78N |
- 78 |
- M |
-
-
- | 143 |
- GSM238872 |
- Primary Visual Cortex |
- Alzheimer's |
- V238872F73A |
- 73 |
- F |
-
-
- | 144 |
- GSM238873 |
- Primary Visual Cortex |
- Alzheimer's |
- V238873M81A |
- 81 |
- M |
-
-
- | 145 |
- GSM238874 |
- Primary Visual Cortex |
- Alzheimer's |
- V238874M75A |
- 75 |
- M |
-
-
- | 146 |
- GSM238875 |
- Primary Visual Cortex |
- Alzheimer's |
- V238875M78A |
- 78 |
- M |
-
-
- | 147 |
- GSM238877 |
- Primary Visual Cortex |
- Alzheimer's |
- V238877M75A |
- 75 |
- M |
-
-
- | 148 |
- GSM238941 |
- Primary Visual Cortex |
- Alzheimer's |
- V238941M87A |
- 87 |
- M |
-
-
- | 149 |
- GSM238942 |
- Primary Visual Cortex |
- Alzheimer's |
- V238942F95A |
- 95 |
- F |
-
-
- | 150 |
- GSM238943 |
- Primary Visual Cortex |
- Alzheimer's |
- V238943M68A |
- 68 |
- M |
-
-
- | 151 |
- GSM238944 |
- Primary Visual Cortex |
- Alzheimer's |
- V238944F70A |
- 70 |
- F |
-
-
- | 152 |
- GSM238945 |
- Primary Visual Cortex |
- Alzheimer's |
- V238945F81A |
- 81 |
- F |
-
-
- | 153 |
- GSM238946 |
- Primary Visual Cortex |
- Alzheimer's |
- V238946F85A |
- 85 |
- F |
-
-
- | 154 |
- GSM238947 |
- Primary Visual Cortex |
- Alzheimer's |
- V238947M68A |
- 68 |
- M |
-
-
- | 155 |
- GSM238948 |
- Primary Visual Cortex |
- Alzheimer's |
- V238948M79A |
- 79 |
- M |
-
-
- | 156 |
- GSM238949 |
- Primary Visual Cortex |
- Alzheimer's |
- V238949F82A |
- 82 |
- F |
-
-
- | 157 |
- GSM238951 |
- Primary Visual Cortex |
- Alzheimer's |
- V238951M88A |
- 88 |
- M |
-
-
- | 158 |
- GSM238952 |
- Primary Visual Cortex |
- Alzheimer's |
- V238952M74A |
- 74 |
- M |
-
-
- | 159 |
- GSM238953 |
- Primary Visual Cortex |
- Alzheimer's |
- V238953M72A |
- 72 |
- M |
-
-
- | 160 |
- GSM238955 |
- Primary Visual Cortex |
- Alzheimer's |
- V238955M->F68A |
- 68 |
- M |
-
-
- | 161 |
- GSM238963 |
- Primary Visual Cortex |
- Alzheimer's |
- V238963F80A |
- 80 |
- F |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GSE5281_F_RMA_N_0709/acknowledgment.rtf b/general/datasets/GSE5281_F_RMA_N_0709/acknowledgment.rtf
deleted file mode 100644
index 8ce4f5c..0000000
--- a/general/datasets/GSE5281_F_RMA_N_0709/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Please cite: Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, Grover A, Niedzielko TL, Schneider LE, Mastroeni D, Caselli R, Kukull W, Morris JC, Hulette CM, Schmechel D, Rogers J, Stephan DA (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc Natl Acad Sci USA 105:4441-4446.
diff --git a/general/datasets/GSE5281_F_RMA_N_0709/experiment-design.rtf b/general/datasets/GSE5281_F_RMA_N_0709/experiment-design.rtf
deleted file mode 100644
index bc54b5c..0000000
--- a/general/datasets/GSE5281_F_RMA_N_0709/experiment-design.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Human brain expression data in patients with Alzheimer's disease and age-matched elderly control subjects. This cortical expression data set is taken from GEO GSE5281 (Liang et al. 2006, Liang et al. 2008). Samples were laser-captured from cortical regions of 16 normal elderly humans (10 males and 4 females) and from 33 AD cases (15 males and 18 females). Mean age of cases and controls was 80 years. All samples were run on the Affymetrix U133 Plus 2.0 array. We renormalized the RMA data to an average expression of 8 units on a log2 scale. Two versions of the data have been entered in GeneNetwork: one consisting of 157 of 161 arrays (full set minus 4 arrays we consider of poor quality); the second consisting of what we regard as the best 102 arrays (those with mean correlations of better than 0.88 with all other arrays). Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex area 17 layer III. GeneNetwork does not yet allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example, expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-NOTE: We detected a minimum of 7.6% case assignment error rate (12 of 158 arrays) in this data set. Twelve cases are assigned to the wrong sex (see XIST probe set 224588_at, the figure below, and table 1). This raises the possibility that some cases are also misassigned by cortical brain region and disease status.
-
-
-
-
-
-Legend: Expression of the sex-specific gene XIST reveals about 10 sex assignment errors in this data set.
-
-Samples were laser-captured from cortical layer 3 (except the hippocampus) and run on the Affymetrix U133 Plus 2.0 array. We renormalized the data to an average expression of 8 units on a log2 scale. Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex layer III. A total of 16 normal subjects were used (10 M and 4 female). The AD samples. GeneNetwork does not allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-Information about the genes that are preferentially expressed during the course of Alzheimer's disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
diff --git a/general/datasets/GSE5281_F_RMA_N_0709/platform.rtf b/general/datasets/GSE5281_F_RMA_N_0709/platform.rtf
deleted file mode 100644
index 6c2af02..0000000
--- a/general/datasets/GSE5281_F_RMA_N_0709/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
-
-In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).
diff --git a/general/datasets/GSE5281_F_RMA_N_0709/summary.rtf b/general/datasets/GSE5281_F_RMA_N_0709/summary.rtf
deleted file mode 100644
index 5db3978..0000000
--- a/general/datasets/GSE5281_F_RMA_N_0709/summary.rtf
+++ /dev/null
@@ -1,1484 +0,0 @@
-(Taken verbatim from the GEO record)
-
-Information about the genes that are preferentially expressed during the course of Alzheimer’s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
-
-Aim 1. Collect brain samples from three Alzheimer’s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels.
-
-Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology.
-
-We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis.
-
-
-
-Bad arrays excluded: Four samples, highlighted in the table below, are bad arrays. For quality control, they should be excluded.
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM119615 |
- Entorhinal Cortex |
- Normal |
- E119615M63N |
- 63 |
- M |
-
-
- | 2 |
- GSM119616 |
- Entorhinal Cortex |
- Normal |
- E119616M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM119617 |
- Entorhinal Cortex |
- Normal |
- E119617M80N |
- 80 |
- M |
-
-
- | 4 |
- GSM119618 |
- Entorhinal Cortex |
- Normal |
- E119618M->F80N |
- 80 |
- M |
-
-
- | 5 |
- GSM119619 |
- Entorhinal Cortex |
- Normal |
- E119619F->M102N |
- 102 |
- F |
-
-
- | 6 |
- GSM119620 |
- Entorhinal Cortex |
- Normal |
- E119620M79N |
- 79 |
- M |
-
-
- | 7 |
- GSM119621 |
- Entorhinal Cortex |
- Normal |
- E119621M76N |
- 76 |
- M |
-
-
- | 8 |
- GSM119622 |
- Entorhinal Cortex |
- Normal |
- E119622M83N |
- 83 |
- M |
-
-
- | 9 |
- GSM119623 |
- Entorhinal Cortex |
- Normal |
- E119623M79N |
- 79 |
- M |
-
-
- | 10 |
- GSM119624 |
- Entorhinal Cortex |
- Normal |
- E119624F88N |
- 88 |
- F |
-
-
- | 11 |
- GSM119625 |
- Entorhinal Cortex |
- Normal |
- E119625F82N |
- 82 |
- F |
-
-
- | 12 |
- GSM119626 |
- Entorhinal Cortex |
- Normal |
- E119626M69N |
- 69 |
- M |
-
-
- | 13 |
- GSM119627 |
- Entorhinal Cortex |
- Normal |
- E119627M78N |
- 78 |
- M |
-
-
- | 14 |
- GSM238763 |
- Entorhinal Cortex |
- Alzheimer's |
- E238763F82A |
- 82 |
- F |
-
-
- | 15 |
- GSM238790 |
- Entorhinal Cortex |
- Alzheimer's |
- E238790F86A |
- 86 |
- F |
-
-
- | 16 |
- GSM238791 |
- Entorhinal Cortex |
- Alzheimer's |
- E238791F93A |
- 93 |
- F |
-
-
- | 17 |
- GSM238792 |
- Entorhinal Cortex |
- Alzheimer's |
- E238792M84A |
- 84 |
- M |
-
-
- | 18 |
- GSM238793 |
- Entorhinal Cortex |
- Alzheimer's |
- E238793F79A |
- 79 |
- F |
-
-
- | 19 |
- GSM238794 |
- Entorhinal Cortex |
- Alzheimer's |
- E238794F78A |
- 78 |
- F |
-
-
- | 20 |
- GSM238795 |
- Entorhinal Cortex |
- Alzheimer's |
- E238795F91A |
- 91 |
- F |
-
-
- | 21 |
- GSM238796 |
- Entorhinal Cortex |
- Alzheimer's |
- E238796M86A |
- 86 |
- M |
-
-
- | 22 |
- GSM238797 |
- Entorhinal Cortex |
- Alzheimer's |
- E238797NA0A |
- N/A |
- N/A |
-
-
- | 23 |
- GSM238798 |
- Entorhinal Cortex |
- Alzheimer's |
- E238798M80A |
- 80 |
- M |
-
-
- | 24 |
- GSM119628 |
- Hippocampus |
- Normal |
- H119628M85N |
- 85 |
- M |
-
-
- | 25 |
- GSM119629 |
- Hippocampus |
- Normal |
- H119629M80N |
- 80 |
- M |
-
-
- | 26 |
- GSM119630 |
- Hippocampus |
- Normal |
- H119630M80N |
- 80 |
- M |
-
-
- | 27 |
- GSM119631 |
- Hippocampus |
- Normal |
- H119631F102N |
- 102 |
- F |
-
-
- | 28 |
- GSM119632 |
- Hippocampus |
- Normal |
- H119632M63N |
- 63 |
- M |
-
-
- | 29 |
- GSM119633 |
- Hippocampus |
- Normal |
- H119633M79N |
- 79 |
- M |
-
-
- | 30 |
- GSM119634 |
- Hippocampus |
- Normal |
- H119634M76N |
- 76 |
- M |
-
-
- | 31 |
- GSM119635 |
- Hippocampus |
- Normal |
- H119635M83N |
- 83 |
- M |
-
-
- | 32 |
- GSM119636 |
- Hippocampus |
- Normal |
- H119636M79N |
- 79 |
- M |
-
-
- | 33 |
- GSM119637 |
- Hippocampus |
- Normal |
- H119637F88N |
- 88 |
- F |
-
-
- | 34 |
- GSM119638 |
- Hippocampus |
- Normal |
- H119638F73N |
- 73 |
- F |
-
-
- | 35 |
- GSM119639 |
- Hippocampus |
- Normal |
- H119639M69N |
- 69 |
- M |
-
-
- | 36 |
- GSM119640 |
- Hippocampus |
- Normal |
- H119640M78N |
- 78 |
- M |
-
-
- | 37 |
- GSM238799 |
- Hippocampus |
- Alzheimer's |
- H238799F73A |
- 73 |
- F |
-
-
- | 38 |
- GSM238800 |
- Hippocampus |
- Alzheimer's |
- H238800M81A |
- 81 |
- M |
-
-
- | 39 |
- GSM238801 |
- Hippocampus |
- Alzheimer's |
- H238801M78A |
- 78 |
- M |
-
-
- | 40 |
- GSM238802 |
- Hippocampus |
- Alzheimer's |
- H238802M75A |
- 75 |
- M |
-
-
- | 41 |
- GSM238803 |
- Hippocampus |
- Alzheimer's |
- H238803F70A |
- 70 |
- F |
-
-
- | 42 |
- GSM238804 |
- Hippocampus |
- Alzheimer's |
- H238804F85A |
- 85 |
- F |
-
-
- | 43 |
- GSM238805 |
- Hippocampus |
- Alzheimer's |
- H238805F77A |
- 77 |
- F |
-
-
- | 44 |
- GSM238806 |
- Hippocampus |
- Alzheimer's |
- H238806M79A |
- 79 |
- M |
-
-
- | 45 |
- GSM238807 |
- Hippocampus |
- Alzheimer's |
- H238807M88A |
- 88 |
- M |
-
-
- | 46 |
- GSM238808 |
- Hippocampus |
- Alzheimer's |
- H238808M72A |
- 72 |
- M |
-
-
- | 47 |
- GSM119641 |
- Medial Temporal Gyrus |
- Normal |
- MT119641M85N |
- 85 |
- M |
-
-
- | 48 |
- GSM119642 |
- Medial Temporal Gyrus |
- Normal |
- MT119642M80N |
- 80 |
- M |
-
-
- | 49 |
- GSM119643 |
- Medial Temporal Gyrus |
- Normal |
- MT119643F102N |
- 102 |
- F |
-
-
- | 50 |
- GSM119644 |
- Medial Temporal Gyrus |
- Normal |
- MT119644M63N |
- 63 |
- M |
-
-
- | 51 |
- GSM119645 |
- Medial Temporal Gyrus |
- Normal |
- MT119645M79N |
- 79 |
- M |
-
-
- | 52 |
- GSM119646 |
- Medial Temporal Gyrus |
- Normal |
- MT119646M83N |
- 83 |
- M |
-
-
- | 53 |
- GSM119647 |
- Medial Temporal Gyrus |
- Normal |
- MT119647M79N |
- 79 |
- M |
-
-
- | 54 |
- GSM119648 |
- Medial Temporal Gyrus |
- Normal |
- MT119648F88N |
- 88 |
- F |
-
-
- | 55 |
- GSM119649 |
- Medial Temporal Gyrus |
- Normal |
- MT119649F82N |
- 82 |
- F |
-
-
- | 56 |
- GSM119650 |
- Medial Temporal Gyrus |
- Normal |
- MT119650F73N |
- 73 |
- F |
-
-
- | 57 |
- GSM119651 |
- Medial Temporal Gyrus |
- Normal |
- MT119651M69N |
- 69 |
- M |
-
-
- | 58 |
- GSM119652 |
- Medial Temporal Gyrus |
- Normal |
- MT119652M->F78N |
- 78 |
- M |
-
-
- | 59 |
- GSM238809 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238809M81A |
- 81 |
- M |
-
-
- | 60 |
- GSM238810 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238810M72A |
- 72 |
- M |
-
-
- | 61 |
- GSM238811 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238811M75A |
- 75 |
- M |
-
-
- | 62 |
- GSM238812 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238812M78A |
- 78 |
- M |
-
-
- | 63 |
- GSM238813 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238813M75A |
- 75 |
- M |
-
-
- | 64 |
- GSM238815 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238815F95A |
- 95 |
- F |
-
-
- | 65 |
- GSM238816 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238816F81A |
- 81 |
- F |
-
-
- | 66 |
- GSM238817 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238817F85A |
- 85 |
- F |
-
-
- | 67 |
- GSM238818 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238818M79A |
- 79 |
- M |
-
-
- | 68 |
- GSM238819 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238819F82A |
- 82 |
- F |
-
-
- | 69 |
- GSM238820 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238820M88A |
- 88 |
- M |
-
-
- | 70 |
- GSM238821 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238821M72A |
- 72 |
- M |
-
-
- | 71 |
- GSM238822 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238822F73A |
- 73 |
- F |
-
-
- | 72 |
- GSM238823 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238823M87A |
- 87 |
- M |
-
-
- | 73 |
- GSM238824 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238824M68A |
- 68 |
- M |
-
-
- | 74 |
- GSM238825 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238825F80A |
- 80 |
- F |
-
-
- | 75 |
- GSM119653 |
- Posterior Cingulate |
- Normal |
- PC119653M85N |
- 85 |
- M |
-
-
- | 76 |
- GSM119654 |
- Posterior Cingulate |
- Normal |
- PC119654M80N |
- 80 |
- M |
-
-
- | 77 |
- GSM119655 |
- Posterior Cingulate |
- Normal |
- PC119655F102N |
- 102 |
- F |
-
-
- | 78 |
- GSM119656 |
- Posterior Cingulate |
- Normal |
- PC119656M63N |
- 63 |
- M |
-
-
- | 79 |
- GSM119657 |
- Posterior Cingulate |
- Normal |
- PC119657M79N |
- 79 |
- M |
-
-
- | 80 |
- GSM119658 |
- Posterior Cingulate |
- Normal |
- PC119658M->F76N |
- 76 |
- M |
-
-
- | 81 |
- GSM119659 |
- Posterior Cingulate |
- Normal |
- PC119659M83N |
- 83 |
- M |
-
-
- | 82 |
- GSM119660 |
- Posterior Cingulate |
- Normal |
- PC119660M79N |
- 79 |
- M |
-
-
- | 83 |
- GSM119661 |
- Posterior Cingulate |
- Normal |
- PC119661F88N |
- 88 |
- F |
-
-
- | 84 |
- GSM119662 |
- Posterior Cingulate |
- Normal |
- PC119662F82N |
- 82 |
- F |
-
-
- | 85 |
- GSM119663 |
- Posterior Cingulate |
- Normal |
- PC119663F73N |
- 73 |
- F |
-
-
- | 86 |
- GSM119664 |
- Posterior Cingulate |
- Normal |
- PC119664M69N |
- 69 |
- M |
-
-
- | 87 |
- GSM119665 |
- Posterior Cingulate |
- Normal |
- PC119665M78N |
- 78 |
- M |
-
-
- | 88 |
- GSM238826 |
- Posterior Cingulate |
- Alzheimer's |
- PC238826F73A |
- 73 |
- F |
-
-
- | 89 |
- GSM238827 |
- Posterior Cingulate |
- Alzheimer's |
- PC238827M81A |
- 81 |
- M |
-
-
- | 90 |
- GSM238834 |
- Posterior Cingulate |
- Alzheimer's |
- PC238834M78A |
- 78 |
- M |
-
-
- | 91 |
- GSM238835 |
- Posterior Cingulate |
- Alzheimer's |
- PC238835M75A |
- 75 |
- M |
-
-
- | 92 |
- GSM238837 |
- Posterior Cingulate |
- Alzheimer's |
- PC238837M68A |
- 68 |
- M |
-
-
- | 93 |
- GSM238838 |
- Posterior Cingulate |
- Alzheimer's |
- PC238838F70A |
- 70 |
- F |
-
-
- | 94 |
- GSM238839 |
- Posterior Cingulate |
- Alzheimer's |
- PC238839F85A |
- 85 |
- F |
-
-
- | 95 |
- GSM238840 |
- Posterior Cingulate |
- Alzheimer's |
- PC238840M79A |
- 79 |
- M |
-
-
- | 96 |
- GSM238841 |
- Posterior Cingulate |
- Alzheimer's |
- PC238841M88A |
- 88 |
- M |
-
-
- | 97 |
- GSM119666 |
- Superior Frontal Gyrus |
- Normal |
- SF119666M79N |
- 79 |
- M |
-
-
- | 98 |
- GSM119667 |
- Superior Frontal Gyrus |
- Normal |
- SF119667F->M88N |
- 88 |
- F |
-
-
- | 99 |
- GSM119668 |
- Superior Frontal Gyrus |
- Normal |
- SF119668F->M82N |
- 82 |
- F |
-
-
- | 100 |
- GSM119669 |
- Superior Frontal Gyrus |
- Normal |
- SF119669F->M73N |
- 73 |
- F |
-
-
- | 101 |
- GSM119670 |
- Superior Frontal Gyrus |
- Normal |
- SF119670F->M102N |
- 102 |
- F |
-
-
- | 102 |
- GSM119671 |
- Superior Frontal Gyrus |
- Normal |
- SF119671M63N |
- 63 |
- M |
-
-
- | 103 |
- GSM119672 |
- Superior Frontal Gyrus |
- Normal |
- SF119672M->F79N |
- 79 |
- M |
-
-
- | 104 |
- GSM119673 |
- Superior Frontal Gyrus |
- Normal |
- SF119673M->F76N |
- 76 |
- M |
-
-
- | 105 |
- GSM119674 |
- Superior Frontal Gyrus |
- Normal |
- SF119674M->F83N |
- 83 |
- M |
-
-
- | 106 |
- GSM119675 |
- Superior Frontal Gyrus |
- Normal |
- SF119675M69N |
- 69 |
- M |
-
-
- | 107 |
- GSM119676 |
- Superior Frontal Gyrus |
- Normal |
- SF119676M78N |
- 78 |
- M |
-
-
- | 108 |
- GSM238842 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238842F73A |
- 73 |
- F |
-
-
- | 109 |
- GSM238843 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238843M81A |
- 81 |
- M |
-
-
- | 110 |
- GSM238844 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238844M72A |
- 72 |
- M |
-
-
- | 111 |
- GSM238845 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238845M75A |
- 75 |
- M |
-
-
- | 112 |
- GSM238846 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238846M78A |
- 78 |
- M |
-
-
- | 113 |
- GSM238847 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238847M75A |
- 75 |
- M |
-
-
- | 114 |
- GSM238848 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238848M87A |
- 87 |
- M |
-
-
- | 115 |
- GSM238851 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238851F95A |
- 95 |
- F |
-
-
- | 116 |
- GSM238854 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238854M68A |
- 68 |
- M |
-
-
- | 117 |
- GSM238855 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238855F95A |
- 95 |
- F |
-
-
- | 118 |
- GSM238856 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238856F70A |
- 70 |
- F |
-
-
- | 119 |
- GSM238857 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238857F85A |
- 85 |
- F |
-
-
- | 120 |
- GSM238858 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238858F83A |
- 83 |
- F |
-
-
- | 121 |
- GSM238860 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238860F77A |
- 77 |
- F |
-
-
- | 122 |
- GSM238861 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238861F83A |
- 83 |
- F |
-
-
- | 123 |
- GSM238862 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238862M68A |
- 68 |
- M |
-
-
- | 124 |
- GSM238863 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238863M79A |
- 79 |
- M |
-
-
- | 125 |
- GSM238864 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238864F82A |
- 82 |
- F |
-
-
- | 126 |
- GSM238865 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238865M88A |
- 88 |
- M |
-
-
- | 127 |
- GSM238867 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238867F80A |
- 80 |
- F |
-
-
- | 128 |
- GSM238868 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238868M74A |
- 74 |
- M |
-
-
- | 129 |
- GSM238870 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238870M72A |
- 72 |
- M |
-
-
- | 130 |
- GSM238871 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238871M80A |
- 80 |
- M |
-
-
- | 131 |
- GSM119677 |
- Primary Visual Cortex |
- Normal |
- V119677M85N |
- 85 |
- M |
-
-
- | 132 |
- GSM119678 |
- Primary Visual Cortex |
- Normal |
- V119678M80N |
- 80 |
- M |
-
-
- | 133 |
- GSM119679 |
- Primary Visual Cortex |
- Normal |
- V119679M63N |
- 63 |
- M |
-
-
- | 134 |
- GSM119680 |
- Primary Visual Cortex |
- Normal |
- V119680M79N |
- 79 |
- M |
-
-
- | 135 |
- GSM119681 |
- Primary Visual Cortex |
- Normal |
- V119681M76N |
- 76 |
- M |
-
-
- | 136 |
- GSM119682 |
- Primary Visual Cortex |
- Normal |
- V119682M83N |
- 83 |
- M |
-
-
- | 137 |
- GSM119683 |
- Primary Visual Cortex |
- Normal |
- V119683M79N |
- 79 |
- M |
-
-
- | 138 |
- GSM119684 |
- Primary Visual Cortex |
- Normal |
- V119684F88N |
- 88 |
- F |
-
-
- | 139 |
- GSM119685 |
- Primary Visual Cortex |
- Normal |
- V119685F82N |
- 82 |
- F |
-
-
- | 140 |
- GSM119686 |
- Primary Visual Cortex |
- Normal |
- V119686F73N |
- 73 |
- F |
-
-
- | 141 |
- GSM119687 |
- Primary Visual Cortex |
- Normal |
- V119687M69N |
- 69 |
- M |
-
-
- | 142 |
- GSM119688 |
- Primary Visual Cortex |
- Normal |
- V119688M78N |
- 78 |
- M |
-
-
- | 143 |
- GSM238872 |
- Primary Visual Cortex |
- Alzheimer's |
- V238872F73A |
- 73 |
- F |
-
-
- | 144 |
- GSM238873 |
- Primary Visual Cortex |
- Alzheimer's |
- V238873M81A |
- 81 |
- M |
-
-
- | 145 |
- GSM238874 |
- Primary Visual Cortex |
- Alzheimer's |
- V238874M75A |
- 75 |
- M |
-
-
- | 146 |
- GSM238875 |
- Primary Visual Cortex |
- Alzheimer's |
- V238875M78A |
- 78 |
- M |
-
-
- | 147 |
- GSM238877 |
- Primary Visual Cortex |
- Alzheimer's |
- V238877M75A |
- 75 |
- M |
-
-
- | 148 |
- GSM238941 |
- Primary Visual Cortex |
- Alzheimer's |
- V238941M87A |
- 87 |
- M |
-
-
- | 149 |
- GSM238942 |
- Primary Visual Cortex |
- Alzheimer's |
- V238942F95A |
- 95 |
- F |
-
-
- | 150 |
- GSM238943 |
- Primary Visual Cortex |
- Alzheimer's |
- V238943M68A |
- 68 |
- M |
-
-
- | 151 |
- GSM238944 |
- Primary Visual Cortex |
- Alzheimer's |
- V238944F70A |
- 70 |
- F |
-
-
- | 152 |
- GSM238945 |
- Primary Visual Cortex |
- Alzheimer's |
- V238945F81A |
- 81 |
- F |
-
-
- | 153 |
- GSM238946 |
- Primary Visual Cortex |
- Alzheimer's |
- V238946F85A |
- 85 |
- F |
-
-
- | 154 |
- GSM238947 |
- Primary Visual Cortex |
- Alzheimer's |
- V238947M68A |
- 68 |
- M |
-
-
- | 155 |
- GSM238948 |
- Primary Visual Cortex |
- Alzheimer's |
- V238948M79A |
- 79 |
- M |
-
-
- | 156 |
- GSM238949 |
- Primary Visual Cortex |
- Alzheimer's |
- V238949F82A |
- 82 |
- F |
-
-
- | 157 |
- GSM238951 |
- Primary Visual Cortex |
- Alzheimer's |
- V238951M88A |
- 88 |
- M |
-
-
- | 158 |
- GSM238952 |
- Primary Visual Cortex |
- Alzheimer's |
- V238952M74A |
- 74 |
- M |
-
-
- | 159 |
- GSM238953 |
- Primary Visual Cortex |
- Alzheimer's |
- V238953M72A |
- 72 |
- M |
-
-
- | 160 |
- GSM238955 |
- Primary Visual Cortex |
- Alzheimer's |
- V238955M->F68A |
- 68 |
- M |
-
-
- | 161 |
- GSM238963 |
- Primary Visual Cortex |
- Alzheimer's |
- V238963F80A |
- 80 |
- F |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GSE5281_RMA0709/acknowledgment.rtf b/general/datasets/GSE5281_RMA0709/acknowledgment.rtf
deleted file mode 100644
index 8ce4f5c..0000000
--- a/general/datasets/GSE5281_RMA0709/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Please cite: Liang WS, Reiman EM, Valla J, Dunckley T, Beach TG, Grover A, Niedzielko TL, Schneider LE, Mastroeni D, Caselli R, Kukull W, Morris JC, Hulette CM, Schmechel D, Rogers J, Stephan DA (2008) Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc Natl Acad Sci USA 105:4441-4446.
diff --git a/general/datasets/GSE5281_RMA0709/experiment-design.rtf b/general/datasets/GSE5281_RMA0709/experiment-design.rtf
deleted file mode 100644
index bc54b5c..0000000
--- a/general/datasets/GSE5281_RMA0709/experiment-design.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Human brain expression data in patients with Alzheimer's disease and age-matched elderly control subjects. This cortical expression data set is taken from GEO GSE5281 (Liang et al. 2006, Liang et al. 2008). Samples were laser-captured from cortical regions of 16 normal elderly humans (10 males and 4 females) and from 33 AD cases (15 males and 18 females). Mean age of cases and controls was 80 years. All samples were run on the Affymetrix U133 Plus 2.0 array. We renormalized the RMA data to an average expression of 8 units on a log2 scale. Two versions of the data have been entered in GeneNetwork: one consisting of 157 of 161 arrays (full set minus 4 arrays we consider of poor quality); the second consisting of what we regard as the best 102 arrays (those with mean correlations of better than 0.88 with all other arrays). Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex area 17 layer III. GeneNetwork does not yet allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example, expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-NOTE: We detected a minimum of 7.6% case assignment error rate (12 of 158 arrays) in this data set. Twelve cases are assigned to the wrong sex (see XIST probe set 224588_at, the figure below, and table 1). This raises the possibility that some cases are also misassigned by cortical brain region and disease status.
-
-
-
-
-
-Legend: Expression of the sex-specific gene XIST reveals about 10 sex assignment errors in this data set.
-
-Samples were laser-captured from cortical layer 3 (except the hippocampus) and run on the Affymetrix U133 Plus 2.0 array. We renormalized the data to an average expression of 8 units on a log2 scale. Case IDs have the following code structure: Brain Region, GEO ID, Sex, Age, Disease Status. E119615M63N is a sample of the entorhinal cortex of case GSM119615, a male 63 year old normal case. The tissue codes are E = enorhinal cortex layer II, H = hippocampus CA1 pyramidal layer, MT = medial temporal cortex layer III, PC = porterior cingulate cortex layer III, SP = supeior frontal cortex layer III, V = primary visual cortex layer III. A total of 16 normal subjects were used (10 M and 4 female). The AD samples. GeneNetwork does not allow sophisticated display of the data, but you can perform correlation analyses of any of the 56,000 probe sets. For example expression of the APP transcript is higher in the AD cases and correlates well with many other AD related genes.
-
-Information about the genes that are preferentially expressed during the course of Alzheimer's disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
diff --git a/general/datasets/GSE5281_RMA0709/platform.rtf b/general/datasets/GSE5281_RMA0709/platform.rtf
deleted file mode 100644
index 6c2af02..0000000
--- a/general/datasets/GSE5281_RMA0709/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
-
-In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).
diff --git a/general/datasets/GSE5281_RMA0709/summary.rtf b/general/datasets/GSE5281_RMA0709/summary.rtf
deleted file mode 100644
index 5db3978..0000000
--- a/general/datasets/GSE5281_RMA0709/summary.rtf
+++ /dev/null
@@ -1,1484 +0,0 @@
-(Taken verbatim from the GEO record)
-
-Information about the genes that are preferentially expressed during the course of Alzheimer’s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.
-
-Aim 1. Collect brain samples from three Alzheimer’s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels.
-
-Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology.
-
-We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis.
-
-
-
-Bad arrays excluded: Four samples, highlighted in the table below, are bad arrays. For quality control, they should be excluded.
-
-
-
-
-
-
-
-
- | Index |
- GEO Series |
- Organ Region |
- Tissue |
- Case ID |
- Age |
- Sex |
-
-
- | 1 |
- GSM119615 |
- Entorhinal Cortex |
- Normal |
- E119615M63N |
- 63 |
- M |
-
-
- | 2 |
- GSM119616 |
- Entorhinal Cortex |
- Normal |
- E119616M85N |
- 85 |
- M |
-
-
- | 3 |
- GSM119617 |
- Entorhinal Cortex |
- Normal |
- E119617M80N |
- 80 |
- M |
-
-
- | 4 |
- GSM119618 |
- Entorhinal Cortex |
- Normal |
- E119618M->F80N |
- 80 |
- M |
-
-
- | 5 |
- GSM119619 |
- Entorhinal Cortex |
- Normal |
- E119619F->M102N |
- 102 |
- F |
-
-
- | 6 |
- GSM119620 |
- Entorhinal Cortex |
- Normal |
- E119620M79N |
- 79 |
- M |
-
-
- | 7 |
- GSM119621 |
- Entorhinal Cortex |
- Normal |
- E119621M76N |
- 76 |
- M |
-
-
- | 8 |
- GSM119622 |
- Entorhinal Cortex |
- Normal |
- E119622M83N |
- 83 |
- M |
-
-
- | 9 |
- GSM119623 |
- Entorhinal Cortex |
- Normal |
- E119623M79N |
- 79 |
- M |
-
-
- | 10 |
- GSM119624 |
- Entorhinal Cortex |
- Normal |
- E119624F88N |
- 88 |
- F |
-
-
- | 11 |
- GSM119625 |
- Entorhinal Cortex |
- Normal |
- E119625F82N |
- 82 |
- F |
-
-
- | 12 |
- GSM119626 |
- Entorhinal Cortex |
- Normal |
- E119626M69N |
- 69 |
- M |
-
-
- | 13 |
- GSM119627 |
- Entorhinal Cortex |
- Normal |
- E119627M78N |
- 78 |
- M |
-
-
- | 14 |
- GSM238763 |
- Entorhinal Cortex |
- Alzheimer's |
- E238763F82A |
- 82 |
- F |
-
-
- | 15 |
- GSM238790 |
- Entorhinal Cortex |
- Alzheimer's |
- E238790F86A |
- 86 |
- F |
-
-
- | 16 |
- GSM238791 |
- Entorhinal Cortex |
- Alzheimer's |
- E238791F93A |
- 93 |
- F |
-
-
- | 17 |
- GSM238792 |
- Entorhinal Cortex |
- Alzheimer's |
- E238792M84A |
- 84 |
- M |
-
-
- | 18 |
- GSM238793 |
- Entorhinal Cortex |
- Alzheimer's |
- E238793F79A |
- 79 |
- F |
-
-
- | 19 |
- GSM238794 |
- Entorhinal Cortex |
- Alzheimer's |
- E238794F78A |
- 78 |
- F |
-
-
- | 20 |
- GSM238795 |
- Entorhinal Cortex |
- Alzheimer's |
- E238795F91A |
- 91 |
- F |
-
-
- | 21 |
- GSM238796 |
- Entorhinal Cortex |
- Alzheimer's |
- E238796M86A |
- 86 |
- M |
-
-
- | 22 |
- GSM238797 |
- Entorhinal Cortex |
- Alzheimer's |
- E238797NA0A |
- N/A |
- N/A |
-
-
- | 23 |
- GSM238798 |
- Entorhinal Cortex |
- Alzheimer's |
- E238798M80A |
- 80 |
- M |
-
-
- | 24 |
- GSM119628 |
- Hippocampus |
- Normal |
- H119628M85N |
- 85 |
- M |
-
-
- | 25 |
- GSM119629 |
- Hippocampus |
- Normal |
- H119629M80N |
- 80 |
- M |
-
-
- | 26 |
- GSM119630 |
- Hippocampus |
- Normal |
- H119630M80N |
- 80 |
- M |
-
-
- | 27 |
- GSM119631 |
- Hippocampus |
- Normal |
- H119631F102N |
- 102 |
- F |
-
-
- | 28 |
- GSM119632 |
- Hippocampus |
- Normal |
- H119632M63N |
- 63 |
- M |
-
-
- | 29 |
- GSM119633 |
- Hippocampus |
- Normal |
- H119633M79N |
- 79 |
- M |
-
-
- | 30 |
- GSM119634 |
- Hippocampus |
- Normal |
- H119634M76N |
- 76 |
- M |
-
-
- | 31 |
- GSM119635 |
- Hippocampus |
- Normal |
- H119635M83N |
- 83 |
- M |
-
-
- | 32 |
- GSM119636 |
- Hippocampus |
- Normal |
- H119636M79N |
- 79 |
- M |
-
-
- | 33 |
- GSM119637 |
- Hippocampus |
- Normal |
- H119637F88N |
- 88 |
- F |
-
-
- | 34 |
- GSM119638 |
- Hippocampus |
- Normal |
- H119638F73N |
- 73 |
- F |
-
-
- | 35 |
- GSM119639 |
- Hippocampus |
- Normal |
- H119639M69N |
- 69 |
- M |
-
-
- | 36 |
- GSM119640 |
- Hippocampus |
- Normal |
- H119640M78N |
- 78 |
- M |
-
-
- | 37 |
- GSM238799 |
- Hippocampus |
- Alzheimer's |
- H238799F73A |
- 73 |
- F |
-
-
- | 38 |
- GSM238800 |
- Hippocampus |
- Alzheimer's |
- H238800M81A |
- 81 |
- M |
-
-
- | 39 |
- GSM238801 |
- Hippocampus |
- Alzheimer's |
- H238801M78A |
- 78 |
- M |
-
-
- | 40 |
- GSM238802 |
- Hippocampus |
- Alzheimer's |
- H238802M75A |
- 75 |
- M |
-
-
- | 41 |
- GSM238803 |
- Hippocampus |
- Alzheimer's |
- H238803F70A |
- 70 |
- F |
-
-
- | 42 |
- GSM238804 |
- Hippocampus |
- Alzheimer's |
- H238804F85A |
- 85 |
- F |
-
-
- | 43 |
- GSM238805 |
- Hippocampus |
- Alzheimer's |
- H238805F77A |
- 77 |
- F |
-
-
- | 44 |
- GSM238806 |
- Hippocampus |
- Alzheimer's |
- H238806M79A |
- 79 |
- M |
-
-
- | 45 |
- GSM238807 |
- Hippocampus |
- Alzheimer's |
- H238807M88A |
- 88 |
- M |
-
-
- | 46 |
- GSM238808 |
- Hippocampus |
- Alzheimer's |
- H238808M72A |
- 72 |
- M |
-
-
- | 47 |
- GSM119641 |
- Medial Temporal Gyrus |
- Normal |
- MT119641M85N |
- 85 |
- M |
-
-
- | 48 |
- GSM119642 |
- Medial Temporal Gyrus |
- Normal |
- MT119642M80N |
- 80 |
- M |
-
-
- | 49 |
- GSM119643 |
- Medial Temporal Gyrus |
- Normal |
- MT119643F102N |
- 102 |
- F |
-
-
- | 50 |
- GSM119644 |
- Medial Temporal Gyrus |
- Normal |
- MT119644M63N |
- 63 |
- M |
-
-
- | 51 |
- GSM119645 |
- Medial Temporal Gyrus |
- Normal |
- MT119645M79N |
- 79 |
- M |
-
-
- | 52 |
- GSM119646 |
- Medial Temporal Gyrus |
- Normal |
- MT119646M83N |
- 83 |
- M |
-
-
- | 53 |
- GSM119647 |
- Medial Temporal Gyrus |
- Normal |
- MT119647M79N |
- 79 |
- M |
-
-
- | 54 |
- GSM119648 |
- Medial Temporal Gyrus |
- Normal |
- MT119648F88N |
- 88 |
- F |
-
-
- | 55 |
- GSM119649 |
- Medial Temporal Gyrus |
- Normal |
- MT119649F82N |
- 82 |
- F |
-
-
- | 56 |
- GSM119650 |
- Medial Temporal Gyrus |
- Normal |
- MT119650F73N |
- 73 |
- F |
-
-
- | 57 |
- GSM119651 |
- Medial Temporal Gyrus |
- Normal |
- MT119651M69N |
- 69 |
- M |
-
-
- | 58 |
- GSM119652 |
- Medial Temporal Gyrus |
- Normal |
- MT119652M->F78N |
- 78 |
- M |
-
-
- | 59 |
- GSM238809 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238809M81A |
- 81 |
- M |
-
-
- | 60 |
- GSM238810 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238810M72A |
- 72 |
- M |
-
-
- | 61 |
- GSM238811 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238811M75A |
- 75 |
- M |
-
-
- | 62 |
- GSM238812 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238812M78A |
- 78 |
- M |
-
-
- | 63 |
- GSM238813 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238813M75A |
- 75 |
- M |
-
-
- | 64 |
- GSM238815 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238815F95A |
- 95 |
- F |
-
-
- | 65 |
- GSM238816 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238816F81A |
- 81 |
- F |
-
-
- | 66 |
- GSM238817 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238817F85A |
- 85 |
- F |
-
-
- | 67 |
- GSM238818 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238818M79A |
- 79 |
- M |
-
-
- | 68 |
- GSM238819 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238819F82A |
- 82 |
- F |
-
-
- | 69 |
- GSM238820 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238820M88A |
- 88 |
- M |
-
-
- | 70 |
- GSM238821 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238821M72A |
- 72 |
- M |
-
-
- | 71 |
- GSM238822 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238822F73A |
- 73 |
- F |
-
-
- | 72 |
- GSM238823 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238823M87A |
- 87 |
- M |
-
-
- | 73 |
- GSM238824 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238824M68A |
- 68 |
- M |
-
-
- | 74 |
- GSM238825 |
- Medial Temporal Gyrus |
- Alzheimer's |
- MT238825F80A |
- 80 |
- F |
-
-
- | 75 |
- GSM119653 |
- Posterior Cingulate |
- Normal |
- PC119653M85N |
- 85 |
- M |
-
-
- | 76 |
- GSM119654 |
- Posterior Cingulate |
- Normal |
- PC119654M80N |
- 80 |
- M |
-
-
- | 77 |
- GSM119655 |
- Posterior Cingulate |
- Normal |
- PC119655F102N |
- 102 |
- F |
-
-
- | 78 |
- GSM119656 |
- Posterior Cingulate |
- Normal |
- PC119656M63N |
- 63 |
- M |
-
-
- | 79 |
- GSM119657 |
- Posterior Cingulate |
- Normal |
- PC119657M79N |
- 79 |
- M |
-
-
- | 80 |
- GSM119658 |
- Posterior Cingulate |
- Normal |
- PC119658M->F76N |
- 76 |
- M |
-
-
- | 81 |
- GSM119659 |
- Posterior Cingulate |
- Normal |
- PC119659M83N |
- 83 |
- M |
-
-
- | 82 |
- GSM119660 |
- Posterior Cingulate |
- Normal |
- PC119660M79N |
- 79 |
- M |
-
-
- | 83 |
- GSM119661 |
- Posterior Cingulate |
- Normal |
- PC119661F88N |
- 88 |
- F |
-
-
- | 84 |
- GSM119662 |
- Posterior Cingulate |
- Normal |
- PC119662F82N |
- 82 |
- F |
-
-
- | 85 |
- GSM119663 |
- Posterior Cingulate |
- Normal |
- PC119663F73N |
- 73 |
- F |
-
-
- | 86 |
- GSM119664 |
- Posterior Cingulate |
- Normal |
- PC119664M69N |
- 69 |
- M |
-
-
- | 87 |
- GSM119665 |
- Posterior Cingulate |
- Normal |
- PC119665M78N |
- 78 |
- M |
-
-
- | 88 |
- GSM238826 |
- Posterior Cingulate |
- Alzheimer's |
- PC238826F73A |
- 73 |
- F |
-
-
- | 89 |
- GSM238827 |
- Posterior Cingulate |
- Alzheimer's |
- PC238827M81A |
- 81 |
- M |
-
-
- | 90 |
- GSM238834 |
- Posterior Cingulate |
- Alzheimer's |
- PC238834M78A |
- 78 |
- M |
-
-
- | 91 |
- GSM238835 |
- Posterior Cingulate |
- Alzheimer's |
- PC238835M75A |
- 75 |
- M |
-
-
- | 92 |
- GSM238837 |
- Posterior Cingulate |
- Alzheimer's |
- PC238837M68A |
- 68 |
- M |
-
-
- | 93 |
- GSM238838 |
- Posterior Cingulate |
- Alzheimer's |
- PC238838F70A |
- 70 |
- F |
-
-
- | 94 |
- GSM238839 |
- Posterior Cingulate |
- Alzheimer's |
- PC238839F85A |
- 85 |
- F |
-
-
- | 95 |
- GSM238840 |
- Posterior Cingulate |
- Alzheimer's |
- PC238840M79A |
- 79 |
- M |
-
-
- | 96 |
- GSM238841 |
- Posterior Cingulate |
- Alzheimer's |
- PC238841M88A |
- 88 |
- M |
-
-
- | 97 |
- GSM119666 |
- Superior Frontal Gyrus |
- Normal |
- SF119666M79N |
- 79 |
- M |
-
-
- | 98 |
- GSM119667 |
- Superior Frontal Gyrus |
- Normal |
- SF119667F->M88N |
- 88 |
- F |
-
-
- | 99 |
- GSM119668 |
- Superior Frontal Gyrus |
- Normal |
- SF119668F->M82N |
- 82 |
- F |
-
-
- | 100 |
- GSM119669 |
- Superior Frontal Gyrus |
- Normal |
- SF119669F->M73N |
- 73 |
- F |
-
-
- | 101 |
- GSM119670 |
- Superior Frontal Gyrus |
- Normal |
- SF119670F->M102N |
- 102 |
- F |
-
-
- | 102 |
- GSM119671 |
- Superior Frontal Gyrus |
- Normal |
- SF119671M63N |
- 63 |
- M |
-
-
- | 103 |
- GSM119672 |
- Superior Frontal Gyrus |
- Normal |
- SF119672M->F79N |
- 79 |
- M |
-
-
- | 104 |
- GSM119673 |
- Superior Frontal Gyrus |
- Normal |
- SF119673M->F76N |
- 76 |
- M |
-
-
- | 105 |
- GSM119674 |
- Superior Frontal Gyrus |
- Normal |
- SF119674M->F83N |
- 83 |
- M |
-
-
- | 106 |
- GSM119675 |
- Superior Frontal Gyrus |
- Normal |
- SF119675M69N |
- 69 |
- M |
-
-
- | 107 |
- GSM119676 |
- Superior Frontal Gyrus |
- Normal |
- SF119676M78N |
- 78 |
- M |
-
-
- | 108 |
- GSM238842 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238842F73A |
- 73 |
- F |
-
-
- | 109 |
- GSM238843 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238843M81A |
- 81 |
- M |
-
-
- | 110 |
- GSM238844 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238844M72A |
- 72 |
- M |
-
-
- | 111 |
- GSM238845 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238845M75A |
- 75 |
- M |
-
-
- | 112 |
- GSM238846 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238846M78A |
- 78 |
- M |
-
-
- | 113 |
- GSM238847 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238847M75A |
- 75 |
- M |
-
-
- | 114 |
- GSM238848 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238848M87A |
- 87 |
- M |
-
-
- | 115 |
- GSM238851 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238851F95A |
- 95 |
- F |
-
-
- | 116 |
- GSM238854 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238854M68A |
- 68 |
- M |
-
-
- | 117 |
- GSM238855 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238855F95A |
- 95 |
- F |
-
-
- | 118 |
- GSM238856 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238856F70A |
- 70 |
- F |
-
-
- | 119 |
- GSM238857 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238857F85A |
- 85 |
- F |
-
-
- | 120 |
- GSM238858 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238858F83A |
- 83 |
- F |
-
-
- | 121 |
- GSM238860 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238860F77A |
- 77 |
- F |
-
-
- | 122 |
- GSM238861 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238861F83A |
- 83 |
- F |
-
-
- | 123 |
- GSM238862 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238862M68A |
- 68 |
- M |
-
-
- | 124 |
- GSM238863 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238863M79A |
- 79 |
- M |
-
-
- | 125 |
- GSM238864 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238864F82A |
- 82 |
- F |
-
-
- | 126 |
- GSM238865 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238865M88A |
- 88 |
- M |
-
-
- | 127 |
- GSM238867 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238867F80A |
- 80 |
- F |
-
-
- | 128 |
- GSM238868 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238868M74A |
- 74 |
- M |
-
-
- | 129 |
- GSM238870 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238870M72A |
- 72 |
- M |
-
-
- | 130 |
- GSM238871 |
- Superior Frontal Gyrus |
- Alzheimer's |
- SF238871M80A |
- 80 |
- M |
-
-
- | 131 |
- GSM119677 |
- Primary Visual Cortex |
- Normal |
- V119677M85N |
- 85 |
- M |
-
-
- | 132 |
- GSM119678 |
- Primary Visual Cortex |
- Normal |
- V119678M80N |
- 80 |
- M |
-
-
- | 133 |
- GSM119679 |
- Primary Visual Cortex |
- Normal |
- V119679M63N |
- 63 |
- M |
-
-
- | 134 |
- GSM119680 |
- Primary Visual Cortex |
- Normal |
- V119680M79N |
- 79 |
- M |
-
-
- | 135 |
- GSM119681 |
- Primary Visual Cortex |
- Normal |
- V119681M76N |
- 76 |
- M |
-
-
- | 136 |
- GSM119682 |
- Primary Visual Cortex |
- Normal |
- V119682M83N |
- 83 |
- M |
-
-
- | 137 |
- GSM119683 |
- Primary Visual Cortex |
- Normal |
- V119683M79N |
- 79 |
- M |
-
-
- | 138 |
- GSM119684 |
- Primary Visual Cortex |
- Normal |
- V119684F88N |
- 88 |
- F |
-
-
- | 139 |
- GSM119685 |
- Primary Visual Cortex |
- Normal |
- V119685F82N |
- 82 |
- F |
-
-
- | 140 |
- GSM119686 |
- Primary Visual Cortex |
- Normal |
- V119686F73N |
- 73 |
- F |
-
-
- | 141 |
- GSM119687 |
- Primary Visual Cortex |
- Normal |
- V119687M69N |
- 69 |
- M |
-
-
- | 142 |
- GSM119688 |
- Primary Visual Cortex |
- Normal |
- V119688M78N |
- 78 |
- M |
-
-
- | 143 |
- GSM238872 |
- Primary Visual Cortex |
- Alzheimer's |
- V238872F73A |
- 73 |
- F |
-
-
- | 144 |
- GSM238873 |
- Primary Visual Cortex |
- Alzheimer's |
- V238873M81A |
- 81 |
- M |
-
-
- | 145 |
- GSM238874 |
- Primary Visual Cortex |
- Alzheimer's |
- V238874M75A |
- 75 |
- M |
-
-
- | 146 |
- GSM238875 |
- Primary Visual Cortex |
- Alzheimer's |
- V238875M78A |
- 78 |
- M |
-
-
- | 147 |
- GSM238877 |
- Primary Visual Cortex |
- Alzheimer's |
- V238877M75A |
- 75 |
- M |
-
-
- | 148 |
- GSM238941 |
- Primary Visual Cortex |
- Alzheimer's |
- V238941M87A |
- 87 |
- M |
-
-
- | 149 |
- GSM238942 |
- Primary Visual Cortex |
- Alzheimer's |
- V238942F95A |
- 95 |
- F |
-
-
- | 150 |
- GSM238943 |
- Primary Visual Cortex |
- Alzheimer's |
- V238943M68A |
- 68 |
- M |
-
-
- | 151 |
- GSM238944 |
- Primary Visual Cortex |
- Alzheimer's |
- V238944F70A |
- 70 |
- F |
-
-
- | 152 |
- GSM238945 |
- Primary Visual Cortex |
- Alzheimer's |
- V238945F81A |
- 81 |
- F |
-
-
- | 153 |
- GSM238946 |
- Primary Visual Cortex |
- Alzheimer's |
- V238946F85A |
- 85 |
- F |
-
-
- | 154 |
- GSM238947 |
- Primary Visual Cortex |
- Alzheimer's |
- V238947M68A |
- 68 |
- M |
-
-
- | 155 |
- GSM238948 |
- Primary Visual Cortex |
- Alzheimer's |
- V238948M79A |
- 79 |
- M |
-
-
- | 156 |
- GSM238949 |
- Primary Visual Cortex |
- Alzheimer's |
- V238949F82A |
- 82 |
- F |
-
-
- | 157 |
- GSM238951 |
- Primary Visual Cortex |
- Alzheimer's |
- V238951M88A |
- 88 |
- M |
-
-
- | 158 |
- GSM238952 |
- Primary Visual Cortex |
- Alzheimer's |
- V238952M74A |
- 74 |
- M |
-
-
- | 159 |
- GSM238953 |
- Primary Visual Cortex |
- Alzheimer's |
- V238953M72A |
- 72 |
- M |
-
-
- | 160 |
- GSM238955 |
- Primary Visual Cortex |
- Alzheimer's |
- V238955M->F68A |
- 68 |
- M |
-
-
- | 161 |
- GSM238963 |
- Primary Visual Cortex |
- Alzheimer's |
- V238963F80A |
- 80 |
- F |
-
-
-
- |
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverEt_M5F_0912/notes.rtf b/general/datasets/GenEx_BXD_liverEt_M5F_0912/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverEt_M5F_0912/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverEt_M5F_0912/summary.rtf b/general/datasets/GenEx_BXD_liverEt_M5F_0912/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverEt_M5F_0912/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverEt_M5M_0912/notes.rtf b/general/datasets/GenEx_BXD_liverEt_M5M_0912/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverEt_M5M_0912/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverEt_M5M_0912/summary.rtf b/general/datasets/GenEx_BXD_liverEt_M5M_0912/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverEt_M5M_0912/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverEt_M5_0912/notes.rtf b/general/datasets/GenEx_BXD_liverEt_M5_0912/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverEt_M5_0912/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverEt_M5_0912/summary.rtf b/general/datasets/GenEx_BXD_liverEt_M5_0912/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverEt_M5_0912/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverEt_RMA_0211/notes.rtf b/general/datasets/GenEx_BXD_liverEt_RMA_0211/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverEt_RMA_0211/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverEt_RMA_0211/summary.rtf b/general/datasets/GenEx_BXD_liverEt_RMA_0211/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverEt_RMA_0211/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverEt_RMA_F_0211/notes.rtf b/general/datasets/GenEx_BXD_liverEt_RMA_F_0211/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverEt_RMA_F_0211/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverEt_RMA_F_0211/summary.rtf b/general/datasets/GenEx_BXD_liverEt_RMA_F_0211/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverEt_RMA_F_0211/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverEt_RMA_M_0211/notes.rtf b/general/datasets/GenEx_BXD_liverEt_RMA_M_0211/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverEt_RMA_M_0211/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverEt_RMA_M_0211/summary.rtf b/general/datasets/GenEx_BXD_liverEt_RMA_M_0211/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverEt_RMA_M_0211/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverSal_RMA_0211/notes.rtf b/general/datasets/GenEx_BXD_liverSal_RMA_0211/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverSal_RMA_0211/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverSal_RMA_0211/summary.rtf b/general/datasets/GenEx_BXD_liverSal_RMA_0211/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverSal_RMA_0211/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverSal_RMA_F_0211/notes.rtf b/general/datasets/GenEx_BXD_liverSal_RMA_F_0211/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverSal_RMA_F_0211/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverSal_RMA_F_0211/summary.rtf b/general/datasets/GenEx_BXD_liverSal_RMA_F_0211/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverSal_RMA_F_0211/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/GenEx_BXD_liverSal_RMA_M_0211/notes.rtf b/general/datasets/GenEx_BXD_liverSal_RMA_M_0211/notes.rtf
deleted file mode 100644
index 3c8d261..0000000
--- a/general/datasets/GenEx_BXD_liverSal_RMA_M_0211/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-A total of 239 probe sets have LRS >46. Maximum LRS of 124.5. Perfect concordance between phenotype of probe set and genotype for St3gal4 on Chr 9 at 34.9 Mb.
-
-Xist expression is uniformly high in BXD55 and BXD70 using probe set 1427262_at, but this is probably due to ethanol effect. Note that Eif2s3y indicates all strains have balanced male and female data.
diff --git a/general/datasets/GenEx_BXD_liverSal_RMA_M_0211/summary.rtf b/general/datasets/GenEx_BXD_liverSal_RMA_M_0211/summary.rtf
deleted file mode 100644
index 60d23d4..0000000
--- a/general/datasets/GenEx_BXD_liverSal_RMA_M_0211/summary.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-These data generated by Dr. Robert Rooney, Kristin Hamre, Divyen Patel, and colleagues at Genome Explorations as part of an SBIR from NIAAA (2010-2011).
-
-Data entered by Arthur Centeno, Jan and Feb 2011.
-
-Data error checked by Robert W. Williams, Jan-May 2011.
-
-eQTLs with LOD > 10
-
-
-
-
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females: 303
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males: 279
- - UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes: 493
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females: 320
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males: 207
- - GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 513
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females: 189
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males: 97
- - GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes: 327
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Females: 274
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Males: 175
- - GenEx BXD Sal Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 444
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Females: 139
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Males: 73
- - GenEx BXD EtOH Liver Affy M430 2.0 (Jan11) RMA Both Sexes: 230
-
-
-
diff --git a/general/datasets/Gn10/experiment-type.rtf b/general/datasets/Gn10/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Gn10/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/HBTRC-MLC_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLC_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLC_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLC_0611/cases.rtf b/general/datasets/HBTRC-MLC_0611/cases.rtf
deleted file mode 100644
index e64114d..0000000
--- a/general/datasets/HBTRC-MLC_0611/cases.rtf
+++ /dev/null
@@ -1,4156 +0,0 @@
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLC_0611/experiment-design.rtf b/general/datasets/HBTRC-MLC_0611/experiment-design.rtf
deleted file mode 100644
index 3b0c224..0000000
--- a/general/datasets/HBTRC-MLC_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
diff --git a/general/datasets/HBTRC-MLC_0611/notes.rtf b/general/datasets/HBTRC-MLC_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLC_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLC_0611/summary.rtf b/general/datasets/HBTRC-MLC_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLC_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLC_AD_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLC_AD_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLC_AD_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLC_AD_0611/cases.rtf b/general/datasets/HBTRC-MLC_AD_0611/cases.rtf
deleted file mode 100644
index e64114d..0000000
--- a/general/datasets/HBTRC-MLC_AD_0611/cases.rtf
+++ /dev/null
@@ -1,4156 +0,0 @@
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLC_AD_0611/experiment-design.rtf b/general/datasets/HBTRC-MLC_AD_0611/experiment-design.rtf
deleted file mode 100644
index 3b0c224..0000000
--- a/general/datasets/HBTRC-MLC_AD_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
diff --git a/general/datasets/HBTRC-MLC_AD_0611/notes.rtf b/general/datasets/HBTRC-MLC_AD_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLC_AD_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLC_AD_0611/summary.rtf b/general/datasets/HBTRC-MLC_AD_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLC_AD_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLC_HD_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLC_HD_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLC_HD_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLC_HD_0611/cases.rtf b/general/datasets/HBTRC-MLC_HD_0611/cases.rtf
deleted file mode 100644
index e64114d..0000000
--- a/general/datasets/HBTRC-MLC_HD_0611/cases.rtf
+++ /dev/null
@@ -1,4156 +0,0 @@
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLC_HD_0611/experiment-design.rtf b/general/datasets/HBTRC-MLC_HD_0611/experiment-design.rtf
deleted file mode 100644
index 3b0c224..0000000
--- a/general/datasets/HBTRC-MLC_HD_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
diff --git a/general/datasets/HBTRC-MLC_HD_0611/notes.rtf b/general/datasets/HBTRC-MLC_HD_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLC_HD_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLC_HD_0611/summary.rtf b/general/datasets/HBTRC-MLC_HD_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLC_HD_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLC_N_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLC_N_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLC_N_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLC_N_0611/cases.rtf b/general/datasets/HBTRC-MLC_N_0611/cases.rtf
deleted file mode 100644
index e64114d..0000000
--- a/general/datasets/HBTRC-MLC_N_0611/cases.rtf
+++ /dev/null
@@ -1,4156 +0,0 @@
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLC_N_0611/experiment-design.rtf b/general/datasets/HBTRC-MLC_N_0611/experiment-design.rtf
deleted file mode 100644
index 3b0c224..0000000
--- a/general/datasets/HBTRC-MLC_N_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
diff --git a/general/datasets/HBTRC-MLC_N_0611/notes.rtf b/general/datasets/HBTRC-MLC_N_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLC_N_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLC_N_0611/summary.rtf b/general/datasets/HBTRC-MLC_N_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLC_N_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLPFC_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLPFC_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLPFC_0611/cases.rtf b/general/datasets/HBTRC-MLPFC_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLPFC_0611/experiment-design.rtf b/general/datasets/HBTRC-MLPFC_0611/experiment-design.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_0611/notes.rtf b/general/datasets/HBTRC-MLPFC_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLPFC_0611/platform.rtf b/general/datasets/HBTRC-MLPFC_0611/platform.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_0611/processing.rtf b/general/datasets/HBTRC-MLPFC_0611/processing.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_0611/summary.rtf b/general/datasets/HBTRC-MLPFC_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLPFC_0611/tissue.rtf b/general/datasets/HBTRC-MLPFC_0611/tissue.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_0611/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/cases.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/experiment-design.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/experiment-design.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/notes.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/platform.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/platform.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/processing.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/processing.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/summary.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLPFC_AD_0611/tissue.rtf b/general/datasets/HBTRC-MLPFC_AD_0611/tissue.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_AD_0611/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/cases.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/experiment-design.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/experiment-design.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/notes.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/platform.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/platform.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/processing.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/processing.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/summary.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLPFC_HD_0611/tissue.rtf b/general/datasets/HBTRC-MLPFC_HD_0611/tissue.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_HD_0611/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLPFC_N_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/cases.rtf b/general/datasets/HBTRC-MLPFC_N_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/experiment-design.rtf b/general/datasets/HBTRC-MLPFC_N_0611/experiment-design.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/notes.rtf b/general/datasets/HBTRC-MLPFC_N_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/platform.rtf b/general/datasets/HBTRC-MLPFC_N_0611/platform.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/processing.rtf b/general/datasets/HBTRC-MLPFC_N_0611/processing.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/summary.rtf b/general/datasets/HBTRC-MLPFC_N_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLPFC_N_0611/tissue.rtf b/general/datasets/HBTRC-MLPFC_N_0611/tissue.rtf
deleted file mode 100644
index 4ee3070..0000000
--- a/general/datasets/HBTRC-MLPFC_N_0611/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-See PMID: 25080494
diff --git a/general/datasets/HBTRC-MLVC_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLVC_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLVC_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLVC_0611/cases.rtf b/general/datasets/HBTRC-MLVC_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLVC_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLVC_0611/notes.rtf b/general/datasets/HBTRC-MLVC_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLVC_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLVC_0611/summary.rtf b/general/datasets/HBTRC-MLVC_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLVC_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLVC_AD_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLVC_AD_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLVC_AD_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLVC_AD_0611/cases.rtf b/general/datasets/HBTRC-MLVC_AD_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLVC_AD_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLVC_AD_0611/notes.rtf b/general/datasets/HBTRC-MLVC_AD_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLVC_AD_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLVC_AD_0611/summary.rtf b/general/datasets/HBTRC-MLVC_AD_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLVC_AD_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLVC_HD_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLVC_HD_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLVC_HD_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLVC_HD_0611/cases.rtf b/general/datasets/HBTRC-MLVC_HD_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLVC_HD_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLVC_HD_0611/notes.rtf b/general/datasets/HBTRC-MLVC_HD_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLVC_HD_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLVC_HD_0611/summary.rtf b/general/datasets/HBTRC-MLVC_HD_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLVC_HD_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HBTRC-MLVC_N_0611/acknowledgment.rtf b/general/datasets/HBTRC-MLVC_N_0611/acknowledgment.rtf
deleted file mode 100644
index 208cb6e..0000000
--- a/general/datasets/HBTRC-MLVC_N_0611/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The Harvard Brain dataset was contributed by Merck Pharmaceutical through the Sage Bionetworks Repository. The tissues were provided by Harvard Brain Tissue Resource Center which is supported in part by PHS grant R24 MH068855 (http://www.brainbank.mclean.org/).
diff --git a/general/datasets/HBTRC-MLVC_N_0611/cases.rtf b/general/datasets/HBTRC-MLVC_N_0611/cases.rtf
deleted file mode 100644
index 86ed08e..0000000
--- a/general/datasets/HBTRC-MLVC_N_0611/cases.rtf
+++ /dev/null
@@ -1,4166 +0,0 @@
-This data packet contains genotypes, clinical traits, as well as expression traits measured in three regions of the brain: visual cortex, cerebellum, prefrontal cortex. Samples were collected from 803 participants including 388 diagnosed with Alzheimer's disease and 220 diagnosed with Huntington's disease. Genotypes were run using two platforms (Illumina and Perlagen). Expression traits were profiled using a custom Agilent platform. Western-IRB has confirmed that this dataset residing in Sage Bionetworks Repository is 'exempt' under federal regulation 45 CFR 46.101(b)4 and does not involve human subject research as defined by OHRP guidelines.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- | Series |
- Cerebellum in GN |
- Condition |
- Gender |
- BioSample Name |
-
-
- | 1 |
- HB_029_N |
- N |
- NA |
- 3405_VC_N_0859 |
-
-
- | 2 |
- HB_058_N |
- N |
- NA |
- 4021_VC_N_0854 |
-
-
- | 3 |
- HB_064_N |
- N |
- NA |
- 4338_VC_N_0861 |
-
-
- | 4 |
- HB_086_N |
- N |
- NA |
- 4729_PF_N_0756 |
-
-
- | 5 |
- HB_091_N |
- N |
- NA |
- 4741_VC_N_0864 |
-
-
- | 6 |
- HB_092_N |
- N |
- NA |
- 4744_VC_N_0865 |
-
-
- | 7 |
- HB_102_N |
- N |
- NA |
- 4810_VC_N_0869 |
-
-
- | 8 |
- HB_119_N |
- N |
- NA |
- 4872_VC_N_0878 |
-
-
- | 9 |
- HB_147_N |
- N |
- NA |
- 5021_VC_N_0852 |
-
-
- | 10 |
- HB_161_N |
- N |
- NA |
- 5077_VC_N_0851 |
-
-
- | 11 |
- HB_162_N |
- N |
- NA |
- 5081_VC_N_1021 |
-
-
- | 12 |
- HB_166_N |
- N |
- NA |
- 5095_VC_N_1024 |
-
-
- | 13 |
- HB_183_N |
- N |
- NA |
- 5162_VC_N_0850 |
-
-
- | 14 |
- HB_206_N |
- N |
- NA |
- 5245_VC_N_0849 |
-
-
- | 15 |
- HB_215_N |
- N |
- NA |
- 5270_VC_N_0848 |
-
-
- | 16 |
- HB_218_N |
- N |
- NA |
- 5276_CR_N_0912 |
-
-
- | 17 |
- HB_223_N |
- N |
- NA |
- 5287_VC_N_0916 |
-
-
- | 18 |
- HB_226_N |
- N |
- NA |
- 5294_VC_N_0919 |
-
-
- | 19 |
- HB_241_N |
- N |
- NA |
- 5326_CR_N_0652 |
-
-
- | 20 |
- HB_243_N |
- N |
- NA |
- 5333_VC_N_1262 |
-
-
- | 21 |
- HB_247_N |
- N |
- NA |
- 5341_VC_N_0923 |
-
-
- | 22 |
- HB_257_N |
- N |
- NA |
- 5368_PF_N_1032 |
-
-
- | 23 |
- HB_264_N |
- N |
- NA |
- 5384_VC_N_0924 |
-
-
- | 24 |
- HB_295_N |
- N |
- NA |
- 5452_VC_N_1268 |
-
-
- | 25 |
- HB_300_N |
- N |
- NA |
- 5463_VC_N_0845 |
-
-
- | 26 |
- HB_311_N |
- N |
- NA |
- 5489_CR_N_0942 |
-
-
- | 27 |
- HB_324_N |
- N |
- NA |
- 5531_VC_N_0844 |
-
-
- | 28 |
- HB_332_N |
- N |
- NA |
- 5547_VC_N_0843 |
-
-
- | 29 |
- HB_340_N |
- N |
- NA |
- 5568_VC_N_0842 |
-
-
- | 30 |
- HB_360_N |
- N |
- NA |
- 5619_CR_N_0645 |
-
-
- | 31 |
- HB_365_N |
- N |
- NA |
- 5632_VC_N_0838 |
-
-
- | 32 |
- HB_367_N |
- N |
- NA |
- 5637_VC_N_0837 |
-
-
- | 33 |
- HB_382_N |
- N |
- NA |
- 5684_PF_N_1270 |
-
-
- | 34 |
- HB_396_N |
- N |
- NA |
- 5718_VC_N_0956 |
-
-
- | 35 |
- HB_398_N |
- N |
- NA |
- 5722_VC_N_1044 |
-
-
- | 36 |
- HB_400_N |
- N |
- NA |
- 5726_VC_N_0834_Bis |
-
-
- | 37 |
- HB_403_N |
- N |
- NA |
- 5734_VC_N_0833 |
-
-
- | 38 |
- HB_414_N |
- N |
- NA |
- 5772_VC_N_0832_Bis |
-
-
- | 39 |
- HB_416_N |
- N |
- NA |
- 5778_CR_N_0962 |
-
-
- | 40 |
- HB_418_N |
- N |
- NA |
- 5789_PF_N_1273 |
-
-
- | 41 |
- HB_421_N |
- N |
- NA |
- 5799_VC_N_1058 |
-
-
- | 42 |
- HB_423_N |
- N |
- NA |
- 5803_VC_N_0966 |
-
-
- | 43 |
- HB_426_N |
- N |
- NA |
- 5806_PF_N_1064 |
-
-
- | 44 |
- HB_427_N |
- N |
- NA |
- 5810_CR_N_0636 |
-
-
- | 45 |
- HB_431_N |
- N |
- NA |
- 5823_VC_N_0829 |
-
-
- | 46 |
- HB_432_N |
- N |
- NA |
- 5826_VC_N_0828 |
-
-
- | 47 |
- HB_433_N |
- N |
- NA |
- 5827_VC_N_0827 |
-
-
- | 48 |
- HB_436_N |
- N |
- NA |
- 5832_PF_N_1145 |
-
-
- | 49 |
- HB_443_N |
- N |
- NA |
- 5852_VC_N_0826 |
-
-
- | 50 |
- HB_446_N |
- N |
- NA |
- 5859_VC_N_0825 |
-
-
- | 51 |
- HB_449_N |
- N |
- NA |
- 5866_VC_N_0824 |
-
-
- | 52 |
- HB_450_N |
- N |
- NA |
- 5867_VC_N_1277 |
-
-
- | 53 |
- HB_453_N |
- N |
- NA |
- 5876_VC_N_0823 |
-
-
- | 54 |
- HB_462_N |
- N |
- NA |
- 5903_VC_N_0822 |
-
-
- | 55 |
- HB_464_N |
- N |
- NA |
- 5905_VC_N_0820 |
-
-
- | 56 |
- HB_468_N |
- N |
- NA |
- 5912_VC_N_1286 |
-
-
- | 57 |
- HB_472_N |
- N |
- NA |
- 5925_VC_N_1289 |
-
-
- | 58 |
- HB_475_N |
- N |
- NA |
- 5936_VC_N_0979 |
-
-
- | 59 |
- HB_476_N |
- N |
- NA |
- 5938_VC_N_0819 |
-
-
- | 60 |
- HB_480_N |
- N |
- NA |
- 5946_VC_N_0985 |
-
-
- | 61 |
- HB_485_N |
- N |
- NA |
- 5959_VC_N_0818 |
-
-
- | 62 |
- HB_486_N |
- N |
- NA |
- 5963_VC_N_0987 |
-
-
- | 63 |
- HB_495_N |
- N |
- NA |
- 5980_VC_N_0989 |
-
-
- | 64 |
- HB_497_N |
- N |
- NA |
- 5985_VC_N_0990 |
-
-
- | 65 |
- HB_500_N |
- N |
- NA |
- 5990_VC_N_0817 |
-
-
- | 66 |
- HB_501_N |
- N |
- NA |
- 5991_VC_N_0816 |
-
-
- | 67 |
- HB_504_N |
- N |
- NA |
- 5996_VC_N_0815 |
-
-
- | 68 |
- HB_505_N |
- N |
- NA |
- 5998_VC_N_0814 |
-
-
- | 69 |
- HB_507_N |
- N |
- NA |
- 6006_VC_N_0813 |
-
-
- | 70 |
- HB_508_N |
- N |
- NA |
- 6007_CR_N_0618 |
-
-
- | 71 |
- HB_509_N |
- N |
- NA |
- 6008_PF_N_1081 |
-
-
- | 72 |
- HB_512_N |
- N |
- NA |
- 6023_PF_N_1155 |
-
-
- | 73 |
- HB_516_N |
- N |
- NA |
- 6030_VC_N_0810 |
-
-
- | 74 |
- HB_519_N |
- N |
- NA |
- 6034_VC_N_0809 |
-
-
- | 75 |
- HB_532_N |
- N |
- NA |
- 6060_VC_N_1292 |
-
-
- | 76 |
- HB_541_N |
- N |
- NA |
- 6092_VC_N_1001 |
-
-
- | 77 |
- HB_542_N |
- N |
- NA |
- 6096_VC_N_0807 |
-
-
- | 78 |
- HB_544_N |
- N |
- NA |
- 6101_CR_N_1161 |
-
-
- | 79 |
- HB_547_N |
- N |
- NA |
- 6110_VC_N_1295 |
-
-
- | 80 |
- HB_551_N |
- N |
- NA |
- 6124_VC_N_0806 |
-
-
- | 81 |
- HB_557_N |
- N |
- NA |
- 6134_PF_N_1297 |
-
-
- | 82 |
- HB_560_N |
- N |
- NA |
- 6142_VC_N_0805 |
-
-
- | 83 |
- HB_569_N |
- N |
- NA |
- 6166_VC_N_0804 |
-
-
- | 84 |
- HB_570_N |
- N |
- NA |
- 6170_VC_N_0803 |
-
-
- | 85 |
- HB_572_N |
- N |
- NA |
- 6172_VC_N_1008 |
-
-
- | 86 |
- HB_577_N |
- N |
- NA |
- 6182_VC_N_1166 |
-
-
- | 87 |
- HB_579_N |
- N |
- NA |
- 6187_CR_N_0607 |
-
-
- | 88 |
- HB_581_N |
- N |
- NA |
- 6191_VC_N_1010 |
-
-
- | 89 |
- HB_584_N |
- N |
- NA |
- 6196_CR_N_0605 |
-
-
- | 90 |
- HB_586_N |
- N |
- NA |
- 6200_VC_N_0799 |
-
-
- | 91 |
- HB_587_N |
- N |
- NA |
- 6206_PF_N_1176 |
-
-
- | 92 |
- HB_589_N |
- N |
- NA |
- 6213_VC_N_0798 |
-
-
- | 93 |
- HB_601_N |
- N |
- NA |
- 6241_VC_N_0796 |
-
-
- | 94 |
- HB_604_N |
- N |
- NA |
- 6260_VC_N_0794 |
-
-
- | 95 |
- HB_609_N |
- N |
- NA |
- 6270_VC_N_0793 |
-
-
- | 96 |
- HB_618_N |
- N |
- NA |
- 6289_VC_N_0791 |
-
-
- | 97 |
- HB_622_N |
- N |
- NA |
- 6310_VC_N_0790 |
-
-
- | 98 |
- HB_625_N |
- N |
- NA |
- 6314_VC_N_0789 |
-
-
- | 99 |
- HB_637_N |
- N |
- NA |
- 6340_VC_N_0786 |
-
-
- | 100 |
- HB_638_N |
- N |
- NA |
- 6341_VC_N_0785 |
-
-
- | 101 |
- HB_640_N |
- N |
- NA |
- 6347_VC_N_0784 |
-
-
- | 102 |
- HB_641_N |
- N |
- NA |
- 6356_VC_N_0783 |
-
-
- | 103 |
- HB_643_N |
- N |
- NA |
- 6363_VC_N_0781 |
-
-
- | 104 |
- HB_644_N |
- N |
- NA |
- 6366_VC_N_0780 |
-
-
- | 105 |
- HB_645_N |
- N |
- NA |
- 6374_VC_N_0779 |
-
-
- | 106 |
- HB_650_N |
- N |
- NA |
- 6384_VC_N_0777 |
-
-
- | 107 |
- HB_651_N |
- N |
- NA |
- 6386_VC_N_0776 |
-
-
- | 108 |
- HB_653_N |
- N |
- NA |
- 6388_VC_N_0775 |
-
-
- | 109 |
- HB_659_N |
- N |
- NA |
- 6406_VC_N_1180 |
-
-
- | 110 |
- HB_662_N |
- N |
- NA |
- 6411_VC_N_0771 |
-
-
- | 111 |
- HB_663_N |
- N |
- NA |
- 6415_VC_N_0770 |
-
-
- | 112 |
- HB_670_N |
- N |
- NA |
- 6436_VC_N_0769 |
-
-
- | 113 |
- HB_687_N |
- N |
- NA |
- 6484_VC_N_0765 |
-
-
- | 114 |
- HB_689_N |
- N |
- NA |
- 6486_VC_N_0764 |
-
-
- | 115 |
- HB_694_N |
- N |
- NA |
- 6500_VC_N_0763 |
-
-
- | 116 |
- HB_697_N |
- N |
- NA |
- 6512_VC_N_0762 |
-
-
- | 117 |
- HB_700_N |
- N |
- NA |
- 6520_VC_N_0761 |
-
-
- | 118 |
- HB_711_N |
- N |
- NA |
- 6543_PF_N_1191 |
-
-
- | 119 |
- HB_714_N |
- N |
- NA |
- 6549_VC_N_1198 |
-
-
- | 120 |
- HB_717_N |
- N |
- NA |
- 6553_PF_N_2284 |
-
-
- | 121 |
- HB_721_N |
- N |
- NA |
- 6560_VC_N_2578 |
-
-
- | 122 |
- HB_726_N |
- N |
- NA |
- 6573_PF_N_2293 |
-
-
- | 123 |
- HB_730_N |
- N |
- NA |
- 6580_VC_N_2306 |
-
-
- | 124 |
- HB_735_N |
- N |
- NA |
- 6588_VC_N_1213 |
-
-
- | 125 |
- HB_737_N |
- N |
- NA |
- 6593_VC_N_1219 |
-
-
- | 126 |
- HB_738_N |
- N |
- NA |
- 6594_VC_N_1222 |
-
-
- | 127 |
- HB_759_N |
- N |
- NA |
- 6645_VC_N_1231 |
-
-
- | 128 |
- HB_764_N |
- N |
- NA |
- 6655_VC_N_1240 |
-
-
- | 129 |
- HB_765_N |
- N |
- NA |
- 6656_VC_N_1243 |
-
-
- | 130 |
- HB_767_N |
- N |
- NA |
- 6661_PF_N_2341 |
-
-
- | 131 |
- HB_770_N |
- N |
- NA |
- 6669_VC_N_1246 |
-
-
- | 132 |
- HB_772_N |
- N |
- NA |
- 6676_PF_N_1248 |
-
-
- | 133 |
- HB_001_HD |
- HD |
- F |
- 2028_CR_H_2282 |
-
-
- | 134 |
- HB_003_HD |
- HD |
- F |
- 2685_PF_H_2212 |
-
-
- | 135 |
- HB_004_HD |
- HD |
- M |
- 2706_CR_H_2432 |
-
-
- | 136 |
- HB_006_HD |
- HD |
- M |
- 2737_VC_H_2194 |
-
-
- | 137 |
- HB_007_HD |
- HD |
- NA |
- 2769_VC_H_2193 |
-
-
- | 138 |
- HB_008_HD |
- HD |
- F |
- 2790_CR_H_1890 |
-
-
- | 139 |
- HB_009_HD |
- HD |
- NA |
- 2879_VC_H_2192 |
-
-
- | 140 |
- HB_010_HD |
- HD |
- M |
- 2960_VC_H_2002 |
-
-
- | 141 |
- HB_011_HD |
- HD |
- F |
- 3053_VC_H_2001 |
-
-
- | 142 |
- HB_012_HD |
- HD |
- F |
- 3128_VC_H_1999 |
-
-
- | 143 |
- HB_014_HD |
- HD |
- F |
- 3149_PF_H_2110 |
-
-
- | 144 |
- HB_015_HD |
- HD |
- F |
- 3150_VC_H_1996 |
-
-
- | 145 |
- HB_016_HD |
- HD |
- F |
- 3177_VC_H_2191 |
-
-
- | 146 |
- HB_017_HD |
- HD |
- NA |
- 3195_VC_H_2190 |
-
-
- | 147 |
- HB_018_HD |
- HD |
- M |
- 3200_VC_H_2189 |
-
-
- | 148 |
- HB_019_HD |
- HD |
- M |
- 3209_VC_H_2188 |
-
-
- | 149 |
- HB_020_HD |
- HD |
- M |
- 3224_VC_H_1994 |
-
-
- | 150 |
- HB_022_HD |
- HD |
- F |
- 3242_PF_H_2105 |
-
-
- | 151 |
- HB_024_HD |
- HD |
- NA |
- 3272_VC_H_2186 |
-
-
- | 152 |
- HB_027_HD |
- HD |
- M |
- 3356_VC_H_2439 |
-
-
- | 153 |
- HB_028_HD |
- HD |
- F |
- 3394_PF_H_2104 |
-
-
- | 154 |
- HB_031_HD |
- HD |
- M |
- 3430_VC_H_1990 |
-
-
- | 155 |
- HB_032_HD |
- HD |
- NA |
- 3444_PF_H_2208 |
-
-
- | 156 |
- HB_034_HD |
- HD |
- F |
- 3482_VC_H_1987 |
-
-
- | 157 |
- HB_036_HD |
- HD |
- M |
- 3576_VC_H_1984 |
-
-
- | 158 |
- HB_037_HD |
- HD |
- F |
- 3579_VC_H_1983 |
-
-
- | 159 |
- HB_038_HD |
- HD |
- F |
- 3584_VC_H_2183 |
-
-
- | 160 |
- HB_039_HD |
- HD |
- NA |
- 3635_VC_H_2182 |
-
-
- | 161 |
- HB_041_HD |
- HD |
- F |
- 3695_CR_H_2267 |
-
-
- | 162 |
- HB_042_HD |
- HD |
- M |
- 3697_VC_H_1982 |
-
-
- | 163 |
- HB_043_HD |
- HD |
- NA |
- 3703_VC_H_2180 |
-
-
- | 164 |
- HB_044_HD |
- HD |
- NA |
- 3723_VC_H_2179 |
-
-
- | 165 |
- HB_046_HD |
- HD |
- F |
- 3735_VC_H_1981 |
-
-
- | 166 |
- HB_050_HD |
- HD |
- M |
- 3820_PF_H_2207 |
-
-
- | 167 |
- HB_051_HD |
- HD |
- F |
- 3849_CR_H_2262 |
-
-
- | 168 |
- HB_054_HD |
- HD |
- M |
- 3884_VC_H_2175 |
-
-
- | 169 |
- HB_056_HD |
- HD |
- NA |
- 4012_VC_H_2174 |
-
-
- | 170 |
- HB_057_HD |
- HD |
- NA |
- 4013_VC_H_2173 |
-
-
- | 171 |
- HB_059_HD |
- HD |
- NA |
- 4066_VC_H_2172 |
-
-
- | 172 |
- HB_060_HD |
- HD |
- NA |
- 4094_VC_H_2171 |
-
-
- | 173 |
- HB_061_HD |
- HD |
- F |
- 4116_VC_H_2170 |
-
-
- | 174 |
- HB_062_HD |
- HD |
- NA |
- 4121_VC_H_2169 |
-
-
- | 175 |
- HB_063_HD |
- HD |
- NA |
- 4215_VC_H_2167 |
-
-
- | 176 |
- HB_065_HD |
- HD |
- M |
- 4340_PF_H_2091 |
-
-
- | 177 |
- HB_066_HD |
- HD |
- F |
- 4344_VC_H_1977 |
-
-
- | 178 |
- HB_067_HD |
- HD |
- M |
- 4346_VC_H_2165 |
-
-
- | 179 |
- HB_069_HD |
- HD |
- F |
- 4356_VC_H_2164 |
-
-
- | 180 |
- HB_070_HD |
- HD |
- NA |
- 4386_CR_H_2249 |
-
-
- | 181 |
- HB_072_HD |
- HD |
- NA |
- 4404_VC_H_2161 |
-
-
- | 182 |
- HB_073_HD |
- HD |
- F |
- 4411_VC_H_1975 |
-
-
- | 183 |
- HB_074_HD |
- HD |
- NA |
- 4430_VC_H_2465 |
-
-
- | 184 |
- HB_075_HD |
- HD |
- M |
- 4470_VC_H_1974 |
-
-
- | 185 |
- HB_076_HD |
- HD |
- F |
- 4497_CR_H_1860 |
-
-
- | 186 |
- HB_077_HD |
- HD |
- M |
- 4509_CR_H_2244 |
-
-
- | 187 |
- HB_079_HD |
- HD |
- M |
- 4631_VC_H_1971 |
-
-
- | 188 |
- HB_080_HD |
- HD |
- F |
- 4653_PF_H_2083 |
-
-
- | 189 |
- HB_081_HD |
- HD |
- NA |
- 4678_CR_H_2242 |
-
-
- | 190 |
- HB_084_HD |
- HD |
- M |
- 4718_VC_H_2125 |
-
-
- | 191 |
- HB_090_HD |
- HD |
- NA |
- 4740_CR_H_2474 |
-
-
- | 192 |
- HB_094_HD |
- HD |
- NA |
- 4754_CR_H_2476 |
-
-
- | 193 |
- HB_098_HD |
- HD |
- NA |
- 4780_VC_H_2151 |
-
-
- | 194 |
- HB_101_HD |
- HD |
- F |
- 4809_VC_H_2148 |
-
-
- | 195 |
- HB_105_HD |
- HD |
- NA |
- 4819_CR_H_2238 |
-
-
- | 196 |
- HB_106_HD |
- HD |
- F |
- 4822_VC_H_1969 |
-
-
- | 197 |
- HB_108_HD |
- HD |
- M |
- 4826_VC_H_1968 |
-
-
- | 198 |
- HB_109_HD |
- HD |
- M |
- 4828_VC_H_2124 |
-
-
- | 199 |
- HB_115_HD |
- HD |
- NA |
- 4855_CR_H_2235 |
-
-
- | 200 |
- HB_121_HD |
- HD |
- F |
- 4902_VC_H_1967 |
-
-
- | 201 |
- HB_129_HD |
- HD |
- NA |
- 4938_VC_H_1966 |
-
-
- | 202 |
- HB_141_HD |
- HD |
- F |
- 4996_PF_H_2076 |
-
-
- | 203 |
- HB_152_HD |
- HD |
- NA |
- 5034_CR_H_2233 |
-
-
- | 204 |
- HB_153_HD |
- HD |
- M |
- 5043_VC_H_1960 |
-
-
- | 205 |
- HB_159_HD |
- HD |
- M |
- 5062_VC_H_1959 |
-
-
- | 206 |
- HB_172_HD |
- HD |
- F |
- 5114_PF_H_2070 |
-
-
- | 207 |
- HB_175_HD |
- HD |
- M |
- 5127_PF_H_2068 |
-
-
- | 208 |
- HB_180_HD |
- HD |
- M |
- 5148_VC_H_1944 |
-
-
- | 209 |
- HB_185_HD |
- HD |
- F |
- 5167_CR_H_2231 |
-
-
- | 210 |
- HB_188_HD |
- HD |
- F |
- 5172_VC_H_1951 |
-
-
- | 211 |
- HB_191_HD |
- HD |
- M |
- 5180_VC_H_1949 |
-
-
- | 212 |
- HB_196_HD |
- HD |
- NA |
- 5199_PF_H_2202 |
-
-
- | 213 |
- HB_203_HD |
- HD |
- F |
- 5228_PF_H_2059 |
-
-
- | 214 |
- HB_207_HD |
- HD |
- NA |
- 5248_PF_H_2201 |
-
-
- | 215 |
- HB_228_HD |
- HD |
- F |
- 5299_CR_H_2228 |
-
-
- | 216 |
- HB_233_HD |
- HD |
- M |
- 5312_VC_H_1938 |
-
-
- | 217 |
- HB_235_HD |
- HD |
- F |
- 5316_VC_H_1937 |
-
-
- | 218 |
- HB_242_HD |
- HD |
- F |
- 5328_PF_H_2048 |
-
-
- | 219 |
- HB_266_HD |
- HD |
- M |
- 5387_VC_H_1928 |
-
-
- | 220 |
- HB_271_HD |
- HD |
- M |
- 5394_PF_H_2039 |
-
-
- | 221 |
- HB_272_HD |
- HD |
- F |
- 5396_VC_H_1925 |
-
-
- | 222 |
- HB_279_HD |
- HD |
- F |
- 5409_VC_H_1924 |
-
-
- | 223 |
- HB_294_HD |
- HD |
- M |
- 5448_VC_H_1921 |
-
-
- | 224 |
- HB_301_HD |
- HD |
- NA |
- 5464_VC_H_1919 |
-
-
- | 225 |
- HB_304_HD |
- HD |
- F |
- 5471_VC_H_1918 |
-
-
- | 226 |
- HB_321_HD |
- HD |
- NA |
- 5522_PF_H_2199 |
-
-
- | 227 |
- HB_361_HD |
- HD |
- F |
- 5622_VC_H_2121 |
-
-
- | 228 |
- HB_370_HD |
- HD |
- M |
- 5645_VC_H_1904 |
-
-
- | 229 |
- HB_371_HD |
- HD |
- F |
- 5648_PF_H_2016 |
-
-
- | 230 |
- HB_384_HD |
- HD |
- F |
- 5688_PF_H_2012 |
-
-
- | 231 |
- HB_390_HD |
- HD |
- M |
- 5704_PF_H_2009 |
-
-
- | 232 |
- HB_393_HD |
- HD |
- F |
- 5709_VC_H_1895 |
-
-
- | 233 |
- HB_402_HD |
- HD |
- F |
- 5732_PF_H_2007 |
-
-
- | 234 |
- HB_405_HD |
- HD |
- NA |
- 5742_PF_H_2006 |
-
-
- | 235 |
- HB_407_HD |
- HD |
- M |
- 5745_PF_H_2005 |
-
-
- | 236 |
- HB_408_HD |
- HD |
- M |
- 5747_VC_H_1891 |
-
-
- | 237 |
- HB_415_HD |
- HD |
- NA |
- 5777_PF_H_1551 |
-
-
- | 238 |
- HB_417_HD |
- HD |
- M |
- 5784_PF_H_1554 |
-
-
- | 239 |
- HB_424_HD |
- HD |
- M |
- 5804_VC_H_1558 |
-
-
- | 240 |
- HB_444_HD |
- HD |
- M |
- 5856_VC_H_1567 |
-
-
- | 241 |
- HB_457_HD |
- HD |
- M |
- 5896_VC_H_1570 |
-
-
- | 242 |
- HB_466_HD |
- HD |
- M |
- 5910_PF_H_1572 |
-
-
- | 243 |
- HB_478_HD |
- HD |
- M |
- 5941_CR_H_1583 |
-
-
- | 244 |
- HB_487_HD |
- HD |
- F |
- 5964_VC_H_1597 |
-
-
- | 245 |
- HB_511_HD |
- HD |
- M |
- 6019_PF_H_2198 |
-
-
- | 246 |
- HB_513_HD |
- HD |
- F |
- 6024_VC_H_1612 |
-
-
- | 247 |
- HB_515_HD |
- HD |
- F |
- 6028_CR_H_1613 |
-
-
- | 248 |
- HB_518_HD |
- HD |
- M |
- 6033_VC_H_1618 |
-
-
- | 249 |
- HB_522_HD |
- HD |
- M |
- 6037_PF_H_1626 |
-
-
- | 250 |
- HB_527_HD |
- HD |
- F |
- 6047_VC_H_1639 |
-
-
- | 251 |
- HB_528_HD |
- HD |
- M |
- 6051_PF_H_1641 |
-
-
- | 252 |
- HB_530_HD |
- HD |
- M |
- 6054_VC_H_1648 |
-
-
- | 253 |
- HB_537_HD |
- HD |
- F |
- 6071_PF_H_1653 |
-
-
- | 254 |
- HB_549_HD |
- HD |
- M |
- 6119_CR_H_1670 |
-
-
- | 255 |
- HB_593_HD |
- HD |
- NA |
- 6219_CR_H_2567 |
-
-
- | 256 |
- HB_610_HD |
- HD |
- NA |
- 6275_PF_H_1692 |
-
-
- | 257 |
- HB_616_HD |
- HD |
- F |
- 6284_CR_H_1694 |
-
-
- | 258 |
- HB_626_HD |
- HD |
- M |
- 6315_VC_H_1702 |
-
-
- | 259 |
- HB_639_HD |
- HD |
- F |
- 6344_CR_H_1703 |
-
-
- | 260 |
- HB_649_HD |
- HD |
- F |
- 6382_CR_H_1709 |
-
-
- | 261 |
- HB_661_HD |
- HD |
- M |
- 6408_VC_H_1714 |
-
-
- | 262 |
- HB_682_HD |
- HD |
- M |
- 6467_PF_H_1725 |
-
-
- | 263 |
- HB_683_HD |
- HD |
- M |
- 6472_VC_H_1729 |
-
-
- | 264 |
- HB_691_HD |
- HD |
- F |
- 6493_VC_H_1732 |
-
-
- | 265 |
- HB_692_HD |
- HD |
- M |
- 6495_CR_H_1733 |
-
-
- | 266 |
- HB_707_HD |
- HD |
- M |
- 6535_PF_H_1737 |
-
-
- | 267 |
- HB_709_HD |
- HD |
- F |
- 6539_CR_H_1739 |
-
-
- | 268 |
- HB_725_HD |
- HD |
- M |
- 6572_PF_H_1746 |
-
-
- | 269 |
- HB_732_HD |
- HD |
- F |
- 6584_VC_H_1750 |
-
-
- | 270 |
- HB_734_HD |
- HD |
- F |
- 6587_CR_H_1751 |
-
-
- | 271 |
- HB_748_HD |
- HD |
- NA |
- 6615_VC_H_2315 |
-
-
- | 272 |
- HB_750_HD |
- HD |
- NA |
- 6628_PF_H_2326 |
-
-
- | 273 |
- HB_758_HD |
- HD |
- NA |
- 6643_VC_H_2602 |
-
-
- | 274 |
- HB_760_HD |
- HD |
- M |
- 6646_PF_H_1761 |
-
-
- | 275 |
- HB_762_HD |
- HD |
- M |
- 6650_VC_H_1765 |
-
-
- | 276 |
- HB_766_HD |
- HD |
- M |
- 6658_VC_H_1768 |
-
-
- | 277 |
- HB_768_HD |
- HD |
- NA |
- 6663_VC_H_1771 |
-
-
- | 278 |
- HB_769_HD |
- HD |
- M |
- 6666_VC_H_1774 |
-
-
- | 279 |
- HB_774_HD |
- HD |
- NA |
- 6689_PF_H_2344 |
-
-
- | 280 |
- HB_778_HD |
- HD |
- NA |
- 6696_PF_H_2356 |
-
-
- | 281 |
- HB_780_HD |
- HD |
- NA |
- 6704_PF_H_2362 |
-
-
- | 282 |
- HB_790_HD |
- HD |
- NA |
- 6788_PF_H_2389 |
-
-
- | 283 |
- HB_800_HD |
- HD |
- NA |
- 6807_PF_H_2419 |
-
-
- | 284 |
- HB_802_HD |
- HD |
- NA |
- 6811_PF_H_2425 |
-
-
- | 285 |
- HB_045_AD |
- AD |
- NA |
- 3734_CR_A_0122 |
-
-
- | 286 |
- HB_048_AD |
- AD |
- NA |
- 3791_CR_A_0128 |
-
-
- | 287 |
- HB_053_AD |
- AD |
- NA |
- 3877_CR_A_0134 |
-
-
- | 288 |
- HB_055_AD |
- AD |
- NA |
- 3893_VC_A_0142 |
-
-
- | 289 |
- HB_068_AD |
- AD |
- NA |
- 4349_VC_A_0148 |
-
-
- | 290 |
- HB_082_AD |
- AD |
- NA |
- 4712_CR_A_0309 |
-
-
- | 291 |
- HB_085_AD |
- AD |
- NA |
- 4726_VC_A_0311 |
-
-
- | 292 |
- HB_087_AD |
- AD |
- NA |
- 4730_CR_A_0315 |
-
-
- | 293 |
- HB_089_AD |
- AD |
- NA |
- 4733_VC_A_0320 |
-
-
- | 294 |
- HB_093_AD |
- AD |
- NA |
- 4749_VC_A_0323 |
-
-
- | 295 |
- HB_095_AD |
- AD |
- NA |
- 4759_CR_A_0327 |
-
-
- | 296 |
- HB_097_AD |
- AD |
- NA |
- 4773_CR_A_0866 |
-
-
- | 297 |
- HB_099_AD |
- AD |
- NA |
- 4785_VC_A_0332 |
-
-
- | 298 |
- HB_100_AD |
- AD |
- NA |
- 4795_VC_A_0335 |
-
-
- | 299 |
- HB_103_AD |
- AD |
- NA |
- 4811_VC_A_0341 |
-
-
- | 300 |
- HB_104_AD |
- AD |
- NA |
- 4813_CR_A_0345 |
-
-
- | 301 |
- HB_112_AD |
- AD |
- NA |
- 4842_VC_A_0870 |
-
-
- | 302 |
- HB_113_AD |
- AD |
- NA |
- 4850_CR_A_0351 |
-
-
- | 303 |
- HB_114_AD |
- AD |
- NA |
- 4852_CR_A_0354 |
-
-
- | 304 |
- HB_117_AD |
- AD |
- NA |
- 4868_VC_A_0874 |
-
-
- | 305 |
- HB_122_AD |
- AD |
- NA |
- 4904_CR_A_1132 |
-
-
- | 306 |
- HB_123_AD |
- AD |
- NA |
- 4905_VC_A_0884 |
-
-
- | 307 |
- HB_124_AD |
- AD |
- NA |
- 4916_VC_A_0886 |
-
-
- | 308 |
- HB_125_AD |
- AD |
- NA |
- 4917_CR_A_0360 |
-
-
- | 309 |
- HB_126_AD |
- AD |
- NA |
- 4921_VC_A_0362 |
-
-
- | 310 |
- HB_128_AD |
- AD |
- NA |
- 4936_CR_A_0369 |
-
-
- | 311 |
- HB_130_AD |
- AD |
- NA |
- 4939_VC_A_0888 |
-
-
- | 312 |
- HB_131_AD |
- AD |
- NA |
- 4944_CR_A_0889 |
-
-
- | 313 |
- HB_132_AD |
- AD |
- NA |
- 4946_CR_A_0372 |
-
-
- | 314 |
- HB_134_AD |
- AD |
- NA |
- 4951_CR_A_0891 |
-
-
- | 315 |
- HB_135_AD |
- AD |
- NA |
- 4953_VC_A_0893 |
-
-
- | 316 |
- HB_136_AD |
- AD |
- NA |
- 4965_VC_A_0160 |
-
-
- | 317 |
- HB_137_AD |
- AD |
- NA |
- 4966_VC_A_0374 |
-
-
- | 318 |
- HB_138_AD |
- AD |
- NA |
- 4969_VC_A_0895 |
-
-
- | 319 |
- HB_140_AD |
- AD |
- NA |
- 4993_CR_A_0896 |
-
-
- | 320 |
- HB_146_AD |
- AD |
- NA |
- 5018_CR_A_0384 |
-
-
- | 321 |
- HB_148_AD |
- AD |
- NA |
- 5022_VC_A_0386 |
-
-
- | 322 |
- HB_150_AD |
- AD |
- NA |
- 5031_VC_A_0392 |
-
-
- | 323 |
- HB_151_AD |
- AD |
- NA |
- 5033_CR_A_0396 |
-
-
- | 324 |
- HB_154_AD |
- AD |
- NA |
- 5048_VC_A_1321 |
-
-
- | 325 |
- HB_155_AD |
- AD |
- NA |
- 5056_VC_A_0398 |
-
-
- | 326 |
- HB_156_AD |
- AD |
- NA |
- 5057_VC_A_0163 |
-
-
- | 327 |
- HB_157_AD |
- AD |
- NA |
- 5059_VC_A_0401 |
-
-
- | 328 |
- HB_158_AD |
- AD |
- NA |
- 5061_PF_A_2612 |
-
-
- | 329 |
- HB_160_AD |
- AD |
- NA |
- 5064_PF_A_2615 |
-
-
- | 330 |
- HB_165_AD |
- AD |
- NA |
- 5092_CR_A_0899 |
-
-
- | 331 |
- HB_168_AD |
- AD |
- NA |
- 5097_VC_A_0407 |
-
-
- | 332 |
- HB_170_AD |
- AD |
- NA |
- 5101_VC_A_0410 |
-
-
- | 333 |
- HB_174_AD |
- AD |
- NA |
- 5124_PF_A_1343 |
-
-
- | 334 |
- HB_179_AD |
- AD |
- NA |
- 5145_VC_A_1351 |
-
-
- | 335 |
- HB_181_AD |
- AD |
- NA |
- 5152_CR_A_0414 |
-
-
- | 336 |
- HB_184_AD |
- AD |
- NA |
- 5166_VC_A_1354 |
-
-
- | 337 |
- HB_194_AD |
- AD |
- NA |
- 5193_VC_A_1360 |
-
-
- | 338 |
- HB_197_AD |
- AD |
- NA |
- 5202_CR_A_1368 |
-
-
- | 339 |
- HB_199_AD |
- AD |
- NA |
- 5205_VC_A_0166 |
-
-
- | 340 |
- HB_200_AD |
- AD |
- NA |
- 5210_VC_A_0905 |
-
-
- | 341 |
- HB_205_AD |
- AD |
- NA |
- 5235_VC_A_0419 |
-
-
- | 342 |
- HB_208_AD |
- AD |
- NA |
- 5249_VC_A_0422 |
-
-
- | 343 |
- HB_209_AD |
- AD |
- NA |
- 5252_VC_A_0907 |
-
-
- | 344 |
- HB_211_AD |
- AD |
- NA |
- 5257_VC_A_0169 |
-
-
- | 345 |
- HB_216_AD |
- AD |
- NA |
- 5272_VC_A_0425 |
-
-
- | 346 |
- HB_219_AD |
- AD |
- NA |
- 5279_CR_A_0147 |
-
-
- | 347 |
- HB_221_AD |
- AD |
- NA |
- 5283_VC_A_0145 |
-
-
- | 348 |
- HB_222_AD |
- AD |
- NA |
- 5285_VC_A_0141 |
-
-
- | 349 |
- HB_224_AD |
- AD |
- NA |
- 5288_VC_A_0428 |
-
-
- | 350 |
- HB_230_AD |
- AD |
- NA |
- 5301_VC_A_0174 |
-
-
- | 351 |
- HB_231_AD |
- AD |
- NA |
- 5305_VC_A_1384 |
-
-
- | 352 |
- HB_232_AD |
- AD |
- NA |
- 5310_CR_A_0176 |
-
-
- | 353 |
- HB_234_AD |
- AD |
- NA |
- 5313_PF_A_2618 |
-
-
- | 354 |
- HB_236_AD |
- AD |
- NA |
- 5317_PF_A_2624 |
-
-
- | 355 |
- HB_238_AD |
- AD |
- NA |
- 5322_CR_A_2632 |
-
-
- | 356 |
- HB_240_AD |
- AD |
- NA |
- 5325_VC_A_0137 |
-
-
- | 357 |
- HB_244_AD |
- AD |
- NA |
- 5337_VC_A_1387 |
-
-
- | 358 |
- HB_245_AD |
- AD |
- NA |
- 5339_VC_A_0181 |
-
-
- | 359 |
- HB_250_AD |
- AD |
- NA |
- 5346_VC_A_1393 |
-
-
- | 360 |
- HB_251_AD |
- AD |
- NA |
- 5350_VC_A_0184 |
-
-
- | 361 |
- HB_252_AD |
- AD |
- NA |
- 5355_VC_A_0133 |
-
-
- | 362 |
- HB_253_AD |
- AD |
- NA |
- 5359_CR_A_1395 |
-
-
- | 363 |
- HB_258_AD |
- AD |
- NA |
- 5370_PF_A_1400 |
-
-
- | 364 |
- HB_259_AD |
- AD |
- NA |
- 5371_PF_A_2636 |
-
-
- | 365 |
- HB_260_AD |
- AD |
- NA |
- 5375_VC_A_0188 |
-
-
- | 366 |
- HB_263_AD |
- AD |
- NA |
- 5381_VC_A_0022 |
-
-
- | 367 |
- HB_265_AD |
- AD |
- NA |
- 5385_VC_A_1402 |
-
-
- | 368 |
- HB_267_AD |
- AD |
- NA |
- 5389_VC_A_0928 |
-
-
- | 369 |
- HB_268_AD |
- AD |
- NA |
- 5390_CR_A_0151 |
-
-
- | 370 |
- HB_273_AD |
- AD |
- NA |
- 5400_PF_A_2645 |
-
-
- | 371 |
- HB_274_AD |
- AD |
- NA |
- 5401_VC_A_0931 |
-
-
- | 372 |
- HB_275_AD |
- AD |
- NA |
- 5404_PF_A_2648 |
-
-
- | 373 |
- HB_276_AD |
- AD |
- NA |
- 5406_VC_A_0933 |
-
-
- | 374 |
- HB_277_AD |
- AD |
- NA |
- 5407_PF_A_2651 |
-
-
- | 375 |
- HB_280_AD |
- AD |
- NA |
- 5412_VC_A_0935 |
-
-
- | 376 |
- HB_281_AD |
- AD |
- NA |
- 5413_PF_A_2657 |
-
-
- | 377 |
- HB_283_AD |
- AD |
- NA |
- 5419_VC_A_0937 |
-
-
- | 378 |
- HB_284_AD |
- AD |
- NA |
- 5420_VC_A_0939 |
-
-
- | 379 |
- HB_285_AD |
- AD |
- NA |
- 5421_CR_A_0432 |
-
-
- | 380 |
- HB_286_AD |
- AD |
- NA |
- 5423_PF_A_2660 |
-
-
- | 381 |
- HB_288_AD |
- AD |
- NA |
- 5425_PF_A_2666 |
-
-
- | 382 |
- HB_289_AD |
- AD |
- NA |
- 5426_VC_A_1405 |
-
-
- | 383 |
- HB_290_AD |
- AD |
- NA |
- 5433_VC_A_0434 |
-
-
- | 384 |
- HB_296_AD |
- AD |
- NA |
- 5456_PF_A_2675 |
-
-
- | 385 |
- HB_299_AD |
- AD |
- NA |
- 5461_VC_A_0192 |
-
-
- | 386 |
- HB_302_AD |
- AD |
- NA |
- 5465_PF_A_2678 |
-
-
- | 387 |
- HB_303_AD |
- AD |
- NA |
- 5469_VC_A_1417 |
-
-
- | 388 |
- HB_305_AD |
- AD |
- NA |
- 5479_PF_A_1421 |
-
-
- | 389 |
- HB_306_AD |
- AD |
- NA |
- 5480_VC_A_0437 |
-
-
- | 390 |
- HB_307_AD |
- AD |
- NA |
- 5482_VC_A_0028 |
-
-
- | 391 |
- HB_308_AD |
- AD |
- NA |
- 5483_VC_A_0941 |
-
-
- | 392 |
- HB_309_AD |
- AD |
- NA |
- 5487_CR_A_0441 |
-
-
- | 393 |
- HB_310_AD |
- AD |
- NA |
- 5488_CR_A_0194 |
-
-
- | 394 |
- HB_312_AD |
- AD |
- NA |
- 5500_VC_A_0198 |
-
-
- | 395 |
- HB_313_AD |
- AD |
- NA |
- 5502_PF_A_2684 |
-
-
- | 396 |
- HB_315_AD |
- AD |
- NA |
- 5513_PF_A_2687 |
-
-
- | 397 |
- HB_316_AD |
- AD |
- NA |
- 5516_PF_A_2690 |
-
-
- | 398 |
- HB_317_AD |
- AD |
- NA |
- 5517_PF_A_2693 |
-
-
- | 399 |
- HB_318_AD |
- AD |
- NA |
- 5518_CR_A_0030 |
-
-
- | 400 |
- HB_319_AD |
- AD |
- NA |
- 5519_CR_A_2695 |
-
-
- | 401 |
- HB_320_AD |
- AD |
- NA |
- 5520_PF_A_2699 |
-
-
- | 402 |
- HB_322_AD |
- AD |
- NA |
- 5527_VC_A_0945 |
-
-
- | 403 |
- HB_325_AD |
- AD |
- NA |
- 5532_PF_A_2702 |
-
-
- | 404 |
- HB_328_AD |
- AD |
- NA |
- 5541_PF_A_2705 |
-
-
- | 405 |
- HB_330_AD |
- AD |
- NA |
- 5544_VC_A_0201 |
-
-
- | 406 |
- HB_334_AD |
- AD |
- NA |
- 5554_VC_A_0452 |
-
-
- | 407 |
- HB_335_AD |
- AD |
- NA |
- 5557_VC_A_0950 |
-
-
- | 408 |
- HB_337_AD |
- AD |
- NA |
- 5560_VC_A_0204 |
-
-
- | 409 |
- HB_342_AD |
- AD |
- NA |
- 5571_PF_A_1430 |
-
-
- | 410 |
- HB_345_AD |
- AD |
- NA |
- 5583_PF_A_2708 |
-
-
- | 411 |
- HB_347_AD |
- AD |
- NA |
- 5589_PF_A_2714 |
-
-
- | 412 |
- HB_349_AD |
- AD |
- NA |
- 5592_PF_A_2717 |
-
-
- | 413 |
- HB_352_AD |
- AD |
- NA |
- 5604_VC_A_0037 |
-
-
- | 414 |
- HB_353_AD |
- AD |
- NA |
- 5607_PF_A_2723 |
-
-
- | 415 |
- HB_356_AD |
- AD |
- NA |
- 5615_VC_A_0041 |
-
-
- | 416 |
- HB_357_AD |
- AD |
- NA |
- 5616_CR_A_0127 |
-
-
- | 417 |
- HB_358_AD |
- AD |
- NA |
- 5617_CR_A_0456 |
-
-
- | 418 |
- HB_359_AD |
- AD |
- NA |
- 5618_CR_A_0044 |
-
-
- | 419 |
- HB_362_AD |
- AD |
- NA |
- 5625_CR_A_2495 |
-
-
- | 420 |
- HB_363_AD |
- AD |
- NA |
- 5626_CR_A_2498 |
-
-
- | 421 |
- HB_364_AD |
- AD |
- NA |
- 5629_CR_A_0390 |
-
-
- | 422 |
- HB_369_AD |
- AD |
- NA |
- 5643_VC_A_1143 |
-
-
- | 423 |
- HB_373_AD |
- AD |
- NA |
- 5654_VC_A_0047 |
-
-
- | 424 |
- HB_375_AD |
- AD |
- NA |
- 5660_CR_A_0462 |
-
-
- | 425 |
- HB_376_AD |
- AD |
- NA |
- 5661_VC_A_0464 |
-
-
- | 426 |
- HB_377_AD |
- AD |
- NA |
- 5667_VC_A_2509 |
-
-
- | 427 |
- HB_378_AD |
- AD |
- NA |
- 5668_VC_A_1438 |
-
-
- | 428 |
- HB_383_AD |
- AD |
- NA |
- 5686_CR_A_2728 |
-
-
- | 429 |
- HB_386_AD |
- AD |
- NA |
- 5695_VC_A_0953 |
-
-
- | 430 |
- HB_389_AD |
- AD |
- NA |
- 5700_VC_A_2514 |
-
-
- | 431 |
- HB_391_AD |
- AD |
- NA |
- 5705_CR_A_0474 |
-
-
- | 432 |
- HB_392_AD |
- AD |
- NA |
- 5706_VC_A_0476 |
-
-
- | 433 |
- HB_394_AD |
- AD |
- NA |
- 5713_VC_A_0479 |
-
-
- | 434 |
- HB_397_AD |
- AD |
- NA |
- 5721_CR_A_0210 |
-
-
- | 435 |
- HB_404_AD |
- AD |
- NA |
- 5735_CR_A_0489 |
-
-
- | 436 |
- HB_406_AD |
- AD |
- NA |
- 5744_CR_A_0960 |
-
-
- | 437 |
- HB_409_AD |
- AD |
- NA |
- 5749_CR_A_0159 |
-
-
- | 438 |
- HB_410_AD |
- AD |
- NA |
- 5751_CR_A_2518 |
-
-
- | 439 |
- HB_411_AD |
- AD |
- NA |
- 5755_CR_A_2731 |
-
-
- | 440 |
- HB_413_AD |
- AD |
- NA |
- 5766_VC_A_0214 |
-
-
- | 441 |
- HB_419_AD |
- AD |
- NA |
- 5790_VC_A_0217 |
-
-
- | 442 |
- HB_420_AD |
- AD |
- NA |
- 5796_CR_A_0964 |
-
-
- | 443 |
- HB_428_AD |
- AD |
- NA |
- 5811_CR_A_2524 |
-
-
- | 444 |
- HB_429_AD |
- AD |
- NA |
- 5819_CR_A_2527 |
-
-
- | 445 |
- HB_430_AD |
- AD |
- NA |
- 5822_CR_A_2530 |
-
-
- | 446 |
- HB_434_AD |
- AD |
- NA |
- 5828_CR_A_2533 |
-
-
- | 447 |
- HB_435_AD |
- AD |
- NA |
- 5831_CR_A_0222 |
-
-
- | 448 |
- HB_437_AD |
- AD |
- NA |
- 5839_CR_A_2539 |
-
-
- | 449 |
- HB_438_AD |
- AD |
- NA |
- 5843_CR_A_0227 |
-
-
- | 450 |
- HB_439_AD |
- AD |
- NA |
- 5845_CR_A_0230 |
-
-
- | 451 |
- HB_441_AD |
- AD |
- NA |
- 5849_CR_A_0233 |
-
-
- | 452 |
- HB_442_AD |
- AD |
- NA |
- 5850_CR_A_0495 |
-
-
- | 453 |
- HB_445_AD |
- AD |
- NA |
- 5858_CR_A_0969 |
-
-
- | 454 |
- HB_448_AD |
- AD |
- NA |
- 5864_CR_A_0974 |
-
-
- | 455 |
- HB_451_AD |
- AD |
- NA |
- 5871_CR_A_2542 |
-
-
- | 456 |
- HB_454_AD |
- AD |
- NA |
- 5879_CR_A_2545 |
-
-
- | 457 |
- HB_455_AD |
- AD |
- NA |
- 5887_CR_A_0976_Bis |
-
-
- | 458 |
- HB_459_AD |
- AD |
- NA |
- 5898_CR_A_2548 |
-
-
- | 459 |
- HB_460_AD |
- AD |
- NA |
- 5900_VC_A_0237 |
-
-
- | 460 |
- HB_461_AD |
- AD |
- NA |
- 5901_CR_A_0239 |
-
-
- | 461 |
- HB_469_AD |
- AD |
- NA |
- 5914_CR_A_2554 |
-
-
- | 462 |
- HB_471_AD |
- AD |
- NA |
- 5922_VC_A_0246 |
-
-
- | 463 |
- HB_473_AD |
- AD |
- NA |
- 5927_CR_A_2560 |
-
-
- | 464 |
- HB_474_AD |
- AD |
- NA |
- 5933_VC_A_1071 |
-
-
- | 465 |
- HB_477_AD |
- AD |
- NA |
- 5939_CR_A_1151 |
-
-
- | 466 |
- HB_479_AD |
- AD |
- NA |
- 5945_VC_A_0983 |
-
-
- | 467 |
- HB_484_AD |
- AD |
- NA |
- 5956_CR_A_0123 |
-
-
- | 468 |
- HB_489_AD |
- AD |
- NA |
- 5968_VC_A_1075 |
-
-
- | 469 |
- HB_491_AD |
- AD |
- NA |
- 5971_CR_A_0119 |
-
-
- | 470 |
- HB_492_AD |
- AD |
- NA |
- 5972_VC_A_0251 |
-
-
- | 471 |
- HB_494_AD |
- AD |
- NA |
- 5979_CR_A_0115 |
-
-
- | 472 |
- HB_498_AD |
- AD |
- NA |
- 5988_VC_A_0503 |
-
-
- | 473 |
- HB_502_AD |
- AD |
- NA |
- 5994_PF_A_1605 |
-
-
- | 474 |
- HB_503_AD |
- AD |
- NA |
- 5995_CR_A_2563 |
-
-
- | 475 |
- HB_510_AD |
- AD |
- NA |
- 6017_CR_A_0048 |
-
-
- | 476 |
- HB_514_AD |
- AD |
- NA |
- 6025_VC_A_0506 |
-
-
- | 477 |
- HB_517_AD |
- AD |
- NA |
- 6031_VC_A_0258 |
-
-
- | 478 |
- HB_520_AD |
- AD |
- NA |
- 6035_VC_A_1621 |
-
-
- | 479 |
- HB_523_AD |
- AD |
- NA |
- 6038_VC_A_0261 |
-
-
- | 480 |
- HB_524_AD |
- AD |
- NA |
- 6042_VC_A_1156 |
-
-
- | 481 |
- HB_525_AD |
- AD |
- NA |
- 6044_VC_A_0264 |
-
-
- | 482 |
- HB_531_AD |
- AD |
- NA |
- 6056_CR_A_0999 |
-
-
- | 483 |
- HB_533_AD |
- AD |
- NA |
- 6061_PF_A_1650 |
-
-
- | 484 |
- HB_534_AD |
- AD |
- NA |
- 6066_VC_A_0270 |
-
-
- | 485 |
- HB_535_AD |
- AD |
- NA |
- 6067_PF_A_1452 |
-
-
- | 486 |
- HB_536_AD |
- AD |
- NA |
- 6068_VC_A_0273 |
-
-
- | 487 |
- HB_545_AD |
- AD |
- NA |
- 6102_CR_A_1661 |
-
-
- | 488 |
- HB_546_AD |
- AD |
- NA |
- 6107_CR_A_0055 |
-
-
- | 489 |
- HB_550_AD |
- AD |
- NA |
- 6120_VC_A_0058 |
-
-
- | 490 |
- HB_552_AD |
- AD |
- NA |
- 6126_VC_A_1675 |
-
-
- | 491 |
- HB_553_AD |
- AD |
- NA |
- 6129_PF_A_0274 |
-
-
- | 492 |
- HB_554_AD |
- AD |
- NA |
- 6130_VC_A_1678 |
-
-
- | 493 |
- HB_555_AD |
- AD |
- NA |
- 6131_CR_A_0510 |
-
-
- | 494 |
- HB_556_AD |
- AD |
- NA |
- 6132_CR_A_0513 |
-
-
- | 495 |
- HB_558_AD |
- AD |
- NA |
- 6137_VC_A_1681 |
-
-
- | 496 |
- HB_564_AD |
- AD |
- NA |
- 6153_VC_A_1465 |
-
-
- | 497 |
- HB_565_AD |
- AD |
- NA |
- 6154_VC_A_1468 |
-
-
- | 498 |
- HB_566_AD |
- AD |
- NA |
- 6157_VC_A_0062 |
-
-
- | 499 |
- HB_568_AD |
- AD |
- NA |
- 6164_CR_A_1005 |
-
-
- | 500 |
- HB_571_AD |
- AD |
- NA |
- 6171_CR_A_0065 |
-
-
- | 501 |
- HB_573_AD |
- AD |
- NA |
- 6174_VC_A_0068 |
-
-
- | 502 |
- HB_576_AD |
- AD |
- NA |
- 6180_CR_A_0281 |
-
-
- | 503 |
- HB_583_AD |
- AD |
- NA |
- 6194_VC_A_0071 |
-
-
- | 504 |
- HB_585_AD |
- AD |
- NA |
- 6198_VC_A_0073 |
-
-
- | 505 |
- HB_590_AD |
- AD |
- NA |
- 6215_VC_A_0518 |
-
-
- | 506 |
- HB_591_AD |
- AD |
- NA |
- 6216_VC_A_1476 |
-
-
- | 507 |
- HB_592_AD |
- AD |
- NA |
- 6218_CR_A_0522 |
-
-
- | 508 |
- HB_594_AD |
- AD |
- NA |
- 6223_VC_A_0288 |
-
-
- | 509 |
- HB_596_AD |
- AD |
- NA |
- 6226_CR_A_0076 |
-
-
- | 510 |
- HB_597_AD |
- AD |
- NA |
- 6227_VC_A_0080 |
-
-
- | 511 |
- HB_598_AD |
- AD |
- NA |
- 6231_VC_A_1479 |
-
-
- | 512 |
- HB_605_AD |
- AD |
- NA |
- 6261_VC_A_0084 |
-
-
- | 513 |
- HB_608_AD |
- AD |
- NA |
- 6268_CR_A_0525 |
-
-
- | 514 |
- HB_611_AD |
- AD |
- NA |
- 6279_VC_A_0089 |
-
-
- | 515 |
- HB_612_AD |
- AD |
- NA |
- 6280_VC_A_0091 |
-
-
- | 516 |
- HB_613_AD |
- AD |
- NA |
- 6281_CR_A_0528 |
-
-
- | 517 |
- HB_621_AD |
- AD |
- NA |
- 6308_VC_A_1503 |
-
-
- | 518 |
- HB_623_AD |
- AD |
- NA |
- 6311_CR_A_0531 |
-
-
- | 519 |
- HB_624_AD |
- AD |
- NA |
- 6312_CR_A_0534 |
-
-
- | 520 |
- HB_630_AD |
- AD |
- NA |
- 6324_PF_A_1514 |
-
-
- | 521 |
- HB_633_AD |
- AD |
- NA |
- 6332_VC_A_1518 |
-
-
- | 522 |
- HB_634_AD |
- AD |
- NA |
- 6335_VC_A_0536 |
-
-
- | 523 |
- HB_635_AD |
- AD |
- NA |
- 6336_CR_A_0290 |
-
-
- | 524 |
- HB_636_AD |
- AD |
- NA |
- 6338_VC_A_0539 |
-
-
- | 525 |
- HB_642_AD |
- AD |
- NA |
- 6358_VC_A_0545 |
-
-
- | 526 |
- HB_652_AD |
- AD |
- NA |
- 6387_VC_A_0093 |
-
-
- | 527 |
- HB_657_AD |
- AD |
- NA |
- 6394_VC_A_0551 |
-
-
- | 528 |
- HB_664_AD |
- AD |
- NA |
- 6416_VC_A_1095 |
-
-
- | 529 |
- HB_666_AD |
- AD |
- NA |
- 6422_CR_A_0555 |
-
-
- | 530 |
- HB_669_AD |
- AD |
- NA |
- 6431_VC_A_0294 |
-
-
- | 531 |
- HB_674_AD |
- AD |
- NA |
- 6449_VC_A_1183 |
-
-
- | 532 |
- HB_680_AD |
- AD |
- NA |
- 6458_CR_A_2570 |
-
-
- | 533 |
- HB_685_AD |
- AD |
- NA |
- 6481_VC_A_0560 |
-
-
- | 534 |
- HB_690_AD |
- AD |
- NA |
- 6489_CR_A_0100 |
-
-
- | 535 |
- HB_696_AD |
- AD |
- NA |
- 6511_VC_A_1119 |
-
-
- | 536 |
- HB_698_AD |
- AD |
- NA |
- 6515_CR_A_0564 |
-
-
- | 537 |
- HB_699_AD |
- AD |
- NA |
- 6518_VC_A_0103 |
-
-
- | 538 |
- HB_703_AD |
- AD |
- NA |
- 6523_VC_A_0107 |
-
-
- | 539 |
- HB_704_AD |
- AD |
- NA |
- 6530_VC_A_0112 |
-
-
- | 540 |
- HB_706_AD |
- AD |
- NA |
- 6534_VC_A_0306 |
-
-
- | 541 |
- HB_712_AD |
- AD |
- NA |
- 6546_PF_A_1194 |
-
-
- | 542 |
- HB_713_AD |
- AD |
- NA |
- 6548_PF_A_1541 |
-
-
- | 543 |
- HB_715_AD |
- AD |
- NA |
- 6550_VC_A_1201 |
-
-
- | 544 |
- HB_718_AD |
- AD |
- NA |
- 6554_PF_A_1203 |
-
-
- | 545 |
- HB_720_AD |
- AD |
- NA |
- 6559_PF_A_2287 |
-
-
- | 546 |
- HB_722_AD |
- AD |
- NA |
- 6561_CR_A_2582 |
-
-
- | 547 |
- HB_723_AD |
- AD |
- NA |
- 6562_PF_A_2290 |
-
-
- | 548 |
- HB_724_AD |
- AD |
- NA |
- 6564_CR_A_2585 |
-
-
- | 549 |
- HB_727_AD |
- AD |
- NA |
- 6575_CR_A_2298 |
-
-
- | 550 |
- HB_728_AD |
- AD |
- NA |
- 6577_PF_A_2299 |
-
-
- | 551 |
- HB_729_AD |
- AD |
- NA |
- 6578_PF_A_2302 |
-
-
- | 552 |
- HB_731_AD |
- AD |
- NA |
- 6582_VC_A_1207 |
-
-
- | 553 |
- HB_733_AD |
- AD |
- NA |
- 6585_VC_A_1210 |
-
-
- | 554 |
- HB_736_AD |
- AD |
- NA |
- 6590_PF_A_1215 |
-
-
- | 555 |
- HB_743_AD |
- AD |
- NA |
- 6603_PF_A_1448 |
-
-
- | 556 |
- HB_745_AD |
- AD |
- NA |
- 6610_PF_A_1227 |
-
-
- | 557 |
- HB_746_AD |
- AD |
- NA |
- 6612_PF_A_2308 |
-
-
- | 558 |
- HB_749_AD |
- AD |
- NA |
- 6617_VC_A_2587 |
-
-
- | 559 |
- HB_751_AD |
- AD |
- NA |
- 6629_VC_A_2330 |
-
-
- | 560 |
- HB_752_AD |
- AD |
- NA |
- 6630_VC_A_2590 |
-
-
- | 561 |
- HB_753_AD |
- AD |
- NA |
- 6632_PF_A_2332 |
-
-
- | 562 |
- HB_754_AD |
- AD |
- NA |
- 6637_VC_A_2596 |
-
-
- | 563 |
- HB_755_AD |
- AD |
- NA |
- 6638_VC_A_2599 |
-
-
- | 564 |
- HB_756_AD |
- AD |
- NA |
- 6639_VC_A_2336 |
-
-
- | 565 |
- HB_757_AD |
- AD |
- NA |
- 6641_PF_A_2338 |
-
-
- | 566 |
- HB_763_AD |
- AD |
- NA |
- 6654_VC_A_1237 |
-
-
- | 567 |
- HB_773_AD |
- AD |
- NA |
- 6681_VC_A_1252 |
-
-
- | 568 |
- HB_775_AD |
- AD |
- NA |
- 6693_VC_A_2348 |
-
-
- | 569 |
- HB_776_AD |
- AD |
- NA |
- 6694_VC_A_2351 |
-
-
- | 570 |
- HB_777_AD |
- AD |
- NA |
- 6695_PF_A_2353 |
-
-
- | 571 |
- HB_779_AD |
- AD |
- NA |
- 6699_PF_A_2359 |
-
-
- | 572 |
- HB_781_AD |
- AD |
- NA |
- 6708_VC_A_2366 |
-
-
- | 573 |
- HB_782_AD |
- AD |
- NA |
- 6776_PF_A_2607 |
-
-
- | 574 |
- HB_783_AD |
- AD |
- NA |
- 6778_PF_A_2368 |
-
-
- | 575 |
- HB_784_AD |
- AD |
- NA |
- 6779_PF_A_2371 |
-
-
- | 576 |
- HB_785_AD |
- AD |
- NA |
- 6780_PF_A_2374 |
-
-
- | 577 |
- HB_786_AD |
- AD |
- NA |
- 6782_PF_A_2377 |
-
-
- | 578 |
- HB_787_AD |
- AD |
- NA |
- 6784_PF_A_2380 |
-
-
- | 579 |
- HB_788_AD |
- AD |
- NA |
- 6785_CR_A_2385 |
-
-
- | 580 |
- HB_789_AD |
- AD |
- NA |
- 6787_CR_A_2388 |
-
-
- | 581 |
- HB_791_AD |
- AD |
- NA |
- 6790_PF_A_2392 |
-
-
- | 582 |
- HB_792_AD |
- AD |
- NA |
- 6791_PF_A_2395 |
-
-
- | 583 |
- HB_793_AD |
- AD |
- NA |
- 6793_PF_A_2398 |
-
-
- | 584 |
- HB_794_AD |
- AD |
- NA |
- 6794_PF_A_2401 |
-
-
- | 585 |
- HB_795_AD |
- AD |
- NA |
- 6797_PF_A_2404 |
-
-
- | 586 |
- HB_796_AD |
- AD |
- NA |
- 6798_PF_A_2407 |
-
-
- | 587 |
- HB_797_AD |
- AD |
- NA |
- 6799_VC_A_2411 |
-
-
- | 588 |
- HB_798_AD |
- AD |
- NA |
- 6801_VC_A_2414 |
-
-
- | 589 |
- HB_799_AD |
- AD |
- NA |
- 6803_VC_A_2417 |
-
-
- | 590 |
- HB_801_AD |
- AD |
- NA |
- 6809_PF_A_2422 |
-
-
- | 591 |
- HB_803_AD |
- AD |
- NA |
- 6818_CR_A_2430 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HBTRC-MLVC_N_0611/notes.rtf b/general/datasets/HBTRC-MLVC_N_0611/notes.rtf
deleted file mode 100644
index ff90e34..0000000
--- a/general/datasets/HBTRC-MLVC_N_0611/notes.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Species: Human
-Tissue: Brain visual cortex,Brain cerebellum,Brain prefrontal cortex
-Disease: Neurological Disease
-Investigator: Francine Benes/ Eric Schadt
-Institution: Harvard Brain Tissue Resource Center/ Merck Research Laboratories
-Approximate Number Subjects: 803
diff --git a/general/datasets/HBTRC-MLVC_N_0611/summary.rtf b/general/datasets/HBTRC-MLVC_N_0611/summary.rtf
deleted file mode 100644
index 5cde3bf..0000000
--- a/general/datasets/HBTRC-MLVC_N_0611/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This study aims at identifying functional variation in the human genome (especially as it pertains to brain expressed RNAs) and elucidate its relationship to disease and drug response. The ~800 individuals in this dataset are composed of approximately 400 Alzheimers disease (AD) cases, 230 Huntington's Disease (HD) and 170 controls (N) matched for age, gender, and post mortem interval (PMI). The tissue specimens for this study were provided by Harvard Brain Tissue Resource Center (HBTRC). Three brain regions (cerebellum, visual cortex, and dorsolateral prefrontal cortex) from the same individuals were profiled on a custom-made Agilent 44K microarray of 39,280 DNA probes uniquely targeting 37,585 known and predicted genes, including splice variants, miRNAs and high-confidence non-coding RNA sequences. The individuals were genotyped on two different platforms, the Illumina HumanHap650Y array and a custom Perlegen 300K array (a focused panel for detection of singleton SNPs). Clinical outcomes available include age at onset, age at death, Braak scores (AD), Vonsattel scores (HD), Regional brain enlargement/atrophy.
diff --git a/general/datasets/HC_M2CB_1005_M/acknowledgment.rtf b/general/datasets/HC_M2CB_1005_M/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2CB_1005_M/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2CB_1005_M/cases.rtf b/general/datasets/HC_M2CB_1005_M/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2CB_1005_M/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2CB_1005_M/experiment-design.rtf b/general/datasets/HC_M2CB_1005_M/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2CB_1005_M/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2CB_1005_M/notes.rtf b/general/datasets/HC_M2CB_1005_M/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2CB_1005_M/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2CB_1005_M/platform.rtf b/general/datasets/HC_M2CB_1005_M/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2CB_1005_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2CB_1005_M/processing.rtf b/general/datasets/HC_M2CB_1005_M/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2CB_1005_M/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2CB_1005_M/summary.rtf b/general/datasets/HC_M2CB_1005_M/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2CB_1005_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2CB_1005_M/tissue.rtf b/general/datasets/HC_M2CB_1005_M/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2CB_1005_M/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2CB_1005_P/acknowledgment.rtf b/general/datasets/HC_M2CB_1005_P/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2CB_1005_P/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2CB_1005_P/cases.rtf b/general/datasets/HC_M2CB_1005_P/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2CB_1005_P/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2CB_1005_P/experiment-design.rtf b/general/datasets/HC_M2CB_1005_P/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2CB_1005_P/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2CB_1005_P/notes.rtf b/general/datasets/HC_M2CB_1005_P/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2CB_1005_P/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2CB_1005_P/platform.rtf b/general/datasets/HC_M2CB_1005_P/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2CB_1005_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2CB_1005_P/processing.rtf b/general/datasets/HC_M2CB_1005_P/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2CB_1005_P/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2CB_1005_P/summary.rtf b/general/datasets/HC_M2CB_1005_P/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2CB_1005_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2CB_1005_P/tissue.rtf b/general/datasets/HC_M2CB_1005_P/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2CB_1005_P/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2CB_1005_R/acknowledgment.rtf b/general/datasets/HC_M2CB_1005_R/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2CB_1005_R/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2CB_1005_R/cases.rtf b/general/datasets/HC_M2CB_1005_R/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2CB_1005_R/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2CB_1005_R/experiment-design.rtf b/general/datasets/HC_M2CB_1005_R/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2CB_1005_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2CB_1005_R/notes.rtf b/general/datasets/HC_M2CB_1005_R/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2CB_1005_R/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2CB_1005_R/platform.rtf b/general/datasets/HC_M2CB_1005_R/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2CB_1005_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2CB_1005_R/processing.rtf b/general/datasets/HC_M2CB_1005_R/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2CB_1005_R/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2CB_1005_R/summary.rtf b/general/datasets/HC_M2CB_1005_R/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2CB_1005_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2CB_1005_R/tissue.rtf b/general/datasets/HC_M2CB_1005_R/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2CB_1005_R/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2CB_1205_P/acknowledgment.rtf b/general/datasets/HC_M2CB_1205_P/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2CB_1205_P/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2CB_1205_P/cases.rtf b/general/datasets/HC_M2CB_1205_P/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2CB_1205_P/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2CB_1205_P/experiment-design.rtf b/general/datasets/HC_M2CB_1205_P/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2CB_1205_P/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2CB_1205_P/notes.rtf b/general/datasets/HC_M2CB_1205_P/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2CB_1205_P/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2CB_1205_P/platform.rtf b/general/datasets/HC_M2CB_1205_P/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2CB_1205_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2CB_1205_P/processing.rtf b/general/datasets/HC_M2CB_1205_P/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2CB_1205_P/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2CB_1205_P/summary.rtf b/general/datasets/HC_M2CB_1205_P/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2CB_1205_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2CB_1205_P/tissue.rtf b/general/datasets/HC_M2CB_1205_P/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2CB_1205_P/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2CB_1205_R/acknowledgment.rtf b/general/datasets/HC_M2CB_1205_R/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2CB_1205_R/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2CB_1205_R/cases.rtf b/general/datasets/HC_M2CB_1205_R/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2CB_1205_R/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2CB_1205_R/experiment-design.rtf b/general/datasets/HC_M2CB_1205_R/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2CB_1205_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2CB_1205_R/notes.rtf b/general/datasets/HC_M2CB_1205_R/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2CB_1205_R/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2CB_1205_R/platform.rtf b/general/datasets/HC_M2CB_1205_R/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2CB_1205_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2CB_1205_R/processing.rtf b/general/datasets/HC_M2CB_1205_R/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2CB_1205_R/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2CB_1205_R/summary.rtf b/general/datasets/HC_M2CB_1205_R/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2CB_1205_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2CB_1205_R/tissue.rtf b/general/datasets/HC_M2CB_1205_R/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2CB_1205_R/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2_0606_M/acknowledgment.rtf b/general/datasets/HC_M2_0606_M/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2_0606_M/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2_0606_M/cases.rtf b/general/datasets/HC_M2_0606_M/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2_0606_M/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_0606_M/experiment-design.rtf b/general/datasets/HC_M2_0606_M/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2_0606_M/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_0606_M/notes.rtf b/general/datasets/HC_M2_0606_M/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2_0606_M/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2_0606_M/platform.rtf b/general/datasets/HC_M2_0606_M/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2_0606_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_0606_M/processing.rtf b/general/datasets/HC_M2_0606_M/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2_0606_M/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_0606_M/summary.rtf b/general/datasets/HC_M2_0606_M/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2_0606_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2_0606_M/tissue.rtf b/general/datasets/HC_M2_0606_M/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2_0606_M/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2_0606_MDP/summary.rtf b/general/datasets/HC_M2_0606_MDP/summary.rtf
deleted file mode 100644
index c8593c7..0000000
--- a/general/datasets/HC_M2_0606_MDP/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 97, Name: Hippocampus Consortium M430v2 (Jun06)
\ No newline at end of file
diff --git a/general/datasets/HC_M2_0606_P/acknowledgment.rtf b/general/datasets/HC_M2_0606_P/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2_0606_P/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2_0606_P/cases.rtf b/general/datasets/HC_M2_0606_P/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2_0606_P/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_0606_P/experiment-design.rtf b/general/datasets/HC_M2_0606_P/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2_0606_P/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_0606_P/notes.rtf b/general/datasets/HC_M2_0606_P/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2_0606_P/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2_0606_P/platform.rtf b/general/datasets/HC_M2_0606_P/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2_0606_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_0606_P/processing.rtf b/general/datasets/HC_M2_0606_P/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2_0606_P/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_0606_P/summary.rtf b/general/datasets/HC_M2_0606_P/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2_0606_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2_0606_P/tissue.rtf b/general/datasets/HC_M2_0606_P/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2_0606_P/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2_0606_R/acknowledgment.rtf b/general/datasets/HC_M2_0606_R/acknowledgment.rtf
deleted file mode 100644
index 1481cd1..0000000
--- a/general/datasets/HC_M2_0606_R/acknowledgment.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
diff --git a/general/datasets/HC_M2_0606_R/cases.rtf b/general/datasets/HC_M2_0606_R/cases.rtf
deleted file mode 100644
index 15e6cda..0000000
--- a/general/datasets/HC_M2_0606_R/cases.rtf
+++ /dev/null
@@ -1,56 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondrial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_0606_R/experiment-design.rtf b/general/datasets/HC_M2_0606_R/experiment-design.rtf
deleted file mode 100644
index 356f1d2..0000000
--- a/general/datasets/HC_M2_0606_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_0606_R/notes.rtf b/general/datasets/HC_M2_0606_R/notes.rtf
deleted file mode 100644
index 9c11719..0000000
--- a/general/datasets/HC_M2_0606_R/notes.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-This study includes the following datasets:
-
-
- - Hippocampus Consortium M430v2 CXB (Oct05) MAS5
- - Hippocampus Consortium M430v2 CXB (Oct05) RMA
- - Hippocampus Consortium M430v2 CXB (Oct05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) PDNN
- - Hippocampus Consortium M430v2 CXB (Dec05) RMA
- - Hippocampus Consortium M430v2 (Jun06) RMA
- - Hippocampus Consortium M430v2 (Jun06) MAS5
- - Hippocampus Consortium M430v2 (Jun06) PDNN
-
diff --git a/general/datasets/HC_M2_0606_R/platform.rtf b/general/datasets/HC_M2_0606_R/platform.rtf
deleted file mode 100644
index 6c99bee..0000000
--- a/general/datasets/HC_M2_0606_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_0606_R/processing.rtf b/general/datasets/HC_M2_0606_R/processing.rtf
deleted file mode 100644
index 3698a7b..0000000
--- a/general/datasets/HC_M2_0606_R/processing.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very sensitive to the transformation method that is used. Using the PDNN transform, the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For example, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one would include the sample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the probe level (CEL) data after step 5 below. DataDesk allows the rapid detection of subsets of probes that are particularly sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - We performed a quantile normalization of the log base 2 values for all arrays using the same initial steps used by the RMA transform.
- - We computed the Z scores for each cell value.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
- - Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data from the CHP file: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_0606_R/summary.rtf b/general/datasets/HC_M2_0606_R/summary.rtf
deleted file mode 100644
index 1e86e54..0000000
--- a/general/datasets/HC_M2_0606_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-MOST HIGHLY RECOMMENDED DATA SET (Overall et al., 2009): The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
diff --git a/general/datasets/HC_M2_0606_R/tissue.rtf b/general/datasets/HC_M2_0606_R/tissue.rtf
deleted file mode 100644
index bcea7b0..0000000
--- a/general/datasets/HC_M2_0606_R/tissue.rtf
+++ /dev/null
@@ -1,3721 +0,0 @@
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST "B" Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.
-
-We finally purify RNA by using Na4OAc before running arrays. Here is the detailed method:
-
-Final RNA purification protocol
-
-
- - Add 1/10th volume of 3M Na4OAc , pH 5.2. If the sample was eluted with 100 µl nuclease-free water as suggested, this will be 10 µl of 3M Na4OAc.
- - Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2 hrs.
- - Centrifuge at speed of 13,000 rpm for 20 min at 4°C. Carefully remove and discard the supernatant.
- - Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8,600 rpm for 5 min, and remove the 75% ethanol. Wash again.
- - To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
- - Air dry the pellet.
- - Resuspend pellet in nuclease-free water.
-
-
-
-
-5. PROTOCOL: RNA/mRNA isolation by the RNA STAT-60 method includes the following steps:
-1. Homogenization RNA STAT-60TM (1 ml per 50-100 mg tissue, or 5-10 x 10-6 cells)
-2. RNA Extraction 1 vol. of homogenate +0.2 vol. of chloroform
-3. RNA Precipitation 0.5 vol. of isopropanol
-4. RNA Wash 75% ethanol
-
-Unless stated otherwise the procedure is carried out at room temperature.
-
-5.1 HOMOGENIZATION
-
-A. TISSUES: Homogenize tissues samples in the RNA STAT-60(1 ml/50-100mg tissue) in a glass-Teflon or Polytron homogenizer. Sample volume should not exceed 10% of the volume of the RNA STAT-60 used for homogenization.
-
-B. CELLS: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.
-
-5.2 RNA EXTRACTION: Following homogenization, store the homogenate for 5 min at room temp to permit the complete dissociation of nucleoprotein complexes. Next, add 0.2 ml of chloroform per 1 ml of the RNA STAT-60, cover the sample tightly, shake vigorously for 15 seconds and let it stay at room temperature for 2-3minutes. Centrifuge the homogenate at 12,000g (max) for 15 minutes at 4°C. Following centrifugation, the homogenate separates into two phases: a lower red phenol chloroform phase and the colorless upper aqueous phase. RNA remains exclusively in the aqueous phase whereas DNA and proteins are in the interferes and organic phase. The volume of the aqueous phase is about 60% of the volume of RNA STAT-60 used for homogenization.
-
-5.3 RNA PRECIPITATION: Transfer the aqueous phase to a fresh tube and mix with isopropanol. Add 0.5 ml of isopropanol per 1 ml of the RNA STAT-60 used for homogenization. Store samples at room temp for 5-10 minutes and centrifuge at 12,000g (max.) for 10 min at 4°C. RNA precipitate (often visible before centrifugation) forms a white pellet at the bottom of the tube.
-
-5.4 RNA WASH: Remove supernatant and wash the RNA pellet once with 75% ethanol by vortexing and subsequent centrifugation at 7,500g (max.) for 5 min at 4°C. Add at least 1 ml of 75% ethanol per 1 ml of the RNA STAT-60 used for the initial homogenization.
-
-At the end of the procedure, dry the RNA pellet briefly by air-drying or in a vacuum (5-10 min.). It is important not to let the RNA pellet dry completely as it will greatly decrease its solubility. Do not use the Speed-Vac for drying. Dissolve the RNA pellet in water or in 1 mm EDTA, pH 7, or 0.5% SDS solution. Vortex or pass the pellet a few times through a pipette tip. An incubation for 10-15 minutes at 55-60oC may be required to dissolve RNA samples. Diethylpyrocarbonate (DEPC) treated RNase-free solutions1 should be used for solubilization of RNA.
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: Our goal was to obtain a male sample pool and female sample pool from each isogenic group. While almost all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. All but 5 of 99 strains (BXD55, BXD86, BXD94, BALB/cByJ, and CAST/EiJ) are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-
-
-Sex Balance: Based on the expression of Xist, probe set 1427262_at, DBA/2J and KK/HlJ are represented only by female samples, BXD55, and BALB/cByJ are only represented by a single male sample, BXD74 is represented by two male samples, and BXD86, BXD94, and CAST/EiJ are possibly mixed sex samples. One of the BXD9 samples, array R1523, may be a mixed sex sample pool because the expression of Xist is intermediate.
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-COMPARISON with December 2005 Data Set: Both BXD14 arrays in the Dec05 data set were found to actually be from BXD23 cases. This error of strain identification has been corrected in the present data set. Four arrays in the Dec05 data set have been deleted because we judged them to be of poor quality (strain_sex_sample_firstreaction_group):
-
-
- - BXD21_F_1_1_G1
- - BXD23_M_1_1_G7
- - BXD36_M_1_1_G2
- - BXD36_F_1_1_G3
-
-
-In the Dec05 data set there are a total of 1986 transcripts with QTLs that have LRS scores above 50, whereas in the corrected June06 data sets there are a total of 2074 transcripts with QTLs above 50.
-
-Data Table 1:
-
-This table lists all arrays by file order (Index), tube/sample ID, age, sex, batch, and numbers of animals in each sample pool (pool size). The next columns (RMA outlier, scale factor, background average, present, absent, marginal, AFFY-b-ActinMur(3'/5'), AFFY-GapdhMur(3'/5')) are all Affymetrix QC data. Finally, source lists the source colony of the animals. (Final version, fully corrected, by Arthur Centeno, October 2008)
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool size |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 2 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 3 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M technical duplicate of above |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 4 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 5 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 6 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 7 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 8 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 9 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 10 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 14 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 15 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 16 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 17 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 18 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 19 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 20 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 21 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 22 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 23 |
- R1523H3 |
- BXD9 |
- 57 |
- MF (mixed) |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 24 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 25 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 26 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 27 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 28 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 29 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 30 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 31 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 32 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 33 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 34 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 35 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 36 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 37 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 38 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 39 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 40 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 41 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 42 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 43 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 44 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 45 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 46 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 47 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 48 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 49 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 50 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 51 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 52 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 54 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 55 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 56 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 57 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 58 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 59 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 60 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 61 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 62 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 63 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 64 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 65 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 66 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 67 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 68 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 69 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 70 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 71 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 72 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 74 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 75 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 76 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 77 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 78 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 80 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 81 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 82 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 83 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 84 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 85 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 86 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 87 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 88 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 89 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 90 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 91 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 92 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 93 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 94 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 95 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 96 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 97 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 98 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 99 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 100 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 101 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 102 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 103 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 104 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 105 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 106 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 107 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 108 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 109 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 110 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 111 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 112 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 113 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 114 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 115 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 116 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 117 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 118 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 119 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 120 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 121 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 122 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 123 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 124 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 125 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 126 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 127 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 128 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 129 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 130 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 131 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 132 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 133 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 134 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 135 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 136 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 137 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 138 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 139 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 140 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 141 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 142 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 143 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 144 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 145 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 146 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 147 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 148 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 149 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 150 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 152 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 153 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 154 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 155 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 156 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 157 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 158 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 159 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 160 |
- R2619H1 |
- CAST/EiJ |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 161 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 162 |
- R1687H3 |
- KK/HIJ |
- 72 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 163 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 164 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 165 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 166 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 167 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 168 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 169 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- M |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 170 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 171 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 172 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 173 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 174 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
- | 175 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 176 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 177 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 179 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 180 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 181 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 182 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 183 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 184 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 185 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 186 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 187 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 188 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 189 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 190 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 191 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 192 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 193 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 194 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 195 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 196 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 197 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 198 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 199 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 200 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 201 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HC_M2_1005_M/acknowledgment.rtf b/general/datasets/HC_M2_1005_M/acknowledgment.rtf
deleted file mode 100644
index 08c9160..0000000
--- a/general/datasets/HC_M2_1005_M/acknowledgment.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: NIH XXXX
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Yanhua Qu, Ph.D.
- Grant Support: NIH U01CA105417
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/HC_M2_1005_M/cases.rtf b/general/datasets/HC_M2_1005_M/cases.rtf
deleted file mode 100644
index 3e78bb4..0000000
--- a/general/datasets/HC_M2_1005_M/cases.rtf
+++ /dev/null
@@ -1,60 +0,0 @@
-This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).
-
-The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HIJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_1005_M/experiment-design.rtf b/general/datasets/HC_M2_1005_M/experiment-design.rtf
deleted file mode 100644
index 68713a4..0000000
--- a/general/datasets/HC_M2_1005_M/experiment-design.rtf
+++ /dev/null
@@ -1,3252 +0,0 @@
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays.Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-
- Data Table 1:
-
-
-This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool sizel |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 2 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 3 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 4 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 5 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 6 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 7 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 8 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 9 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 10 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 11 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 14 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 15 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 16 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 17 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 18 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 19 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 20 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 21 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 22 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 23 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 24 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 25 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 26 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 27 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 28 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 29 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 30 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 31 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 32 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 33 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 34 |
- R1347H2 |
- BXD21 |
- 64 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.881 |
- 61.49 |
- 0.494 |
- 0.486 |
- 0.019 |
- 0.92 |
- 1.22 |
- UMemphis |
-
-
- | 35 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 36 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 37 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 38 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 39 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 40 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 41 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 42 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 43 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 44 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 45 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 46 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 47 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 48 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 49 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 50 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 51 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 52 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 54 |
- R1469H1 |
- BXD36 |
- 83 |
- F |
- 3 |
- 3 |
- 0.02 |
- 3.473 |
- 49.9 |
- 0.494 |
- 0.486 |
- 0.02 |
- 1.11 |
- 0.76 |
- UMemphis |
-
-
- | 55 |
- R1363H1 |
- BXD36 |
- 77 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.184 |
- 48.19 |
- 0.538 |
- 0.443 |
- 0.02 |
- 1.28 |
- 0.77 |
- UMemphis |
-
-
- | 56 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 57 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 58 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 59 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 60 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 61 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 62 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 63 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 64 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 65 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 66 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 67 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 68 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 69 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 70 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 71 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 72 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 74 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 75 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 76 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 77 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 78 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 79 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 80 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 81 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 82 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 83 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 84 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 85 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 86 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 87 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 88 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 89 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 90 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 91 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 92 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 93 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 94 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 95 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 96 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 97 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 98 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 99 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 100 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 101 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 102 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 103 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 104 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 105 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 106 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 107 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 108 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 109 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 110 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 111 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 112 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 113 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 114 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 115 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 116 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 117 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 118 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 119 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 120 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 121 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 122 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 123 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 124 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 125 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 126 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 127 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 128 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 129 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 130 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 131 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 132 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 133 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 134 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 135 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 136 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 137 |
- R2619H1 |
- CAST/Ei |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 138 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 139 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 140 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 141 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 142 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 143 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 144 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 145 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
- | 146 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 147 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 148 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 149 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 150 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 152 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 153 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 154 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 155 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 156 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 157 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 158 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 159 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 160 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 161 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 162 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 163 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 164 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 165 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 166 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 167 |
- R1687H3 |
- KK/HIJ |
- 72 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 168 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 169 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 170 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 171 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 172 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 173 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 174 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 175 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 176 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 177 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 178 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/HC_M2_1005_M/notes.rtf b/general/datasets/HC_M2_1005_M/notes.rtf
deleted file mode 100644
index 4490ee3..0000000
--- a/general/datasets/HC_M2_1005_M/notes.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-This study includes the following datasets:
-
-
-Hippocampus Consortium M430v2 (Oct05) MAS5
-
-Hippocampus Consortium M430v2 (Oct05) RMA
-
-Hippocampus Consortium M430v2 (Oct05) PDNN
-
-Hippocampus Consortium M430v2 (Dec05) RMA
-
-Hippocampus Consortium M430v2 (Dec05) PDNN
-
-
-This text file originally generated prospectively by RWW on July 30 2005. Updated by RWW July 31, 2005.
diff --git a/general/datasets/HC_M2_1005_M/platform.rtf b/general/datasets/HC_M2_1005_M/platform.rtf
deleted file mode 100644
index af0948c..0000000
--- a/general/datasets/HC_M2_1005_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_1005_M/processing.rtf b/general/datasets/HC_M2_1005_M/processing.rtf
deleted file mode 100644
index df5513b..0000000
--- a/general/datasets/HC_M2_1005_M/processing.rtf
+++ /dev/null
@@ -1,40 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very senstive to the transformation method that is used. Using the PDNN transform the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For examploe, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one whould include the ssample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. <0L>
-
-
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_1005_M/summary.rtf b/general/datasets/HC_M2_1005_M/summary.rtf
deleted file mode 100644
index 9b7c1d6..0000000
--- a/general/datasets/HC_M2_1005_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-PRELIMINARY: The October 2005 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of approximately 99 genetically diverse strains of mice including 68 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of 16 diverse inbred strains, and 2 reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial for memory formation, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3, and parts of the subiculum) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section. Samples were processed using a total of 206 Affymetrix Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0 or M430v2), of which 179 passed stringent quality control and error checking. This particular data set was processed using the MAS5 protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_1005_M/tissue.rtf b/general/datasets/HC_M2_1005_M/tissue.rtf
deleted file mode 100644
index 2bb700d..0000000
--- a/general/datasets/HC_M2_1005_M/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thanks Muriel Davission for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below).
-
diff --git a/general/datasets/HC_M2_1005_P/acknowledgment.rtf b/general/datasets/HC_M2_1005_P/acknowledgment.rtf
deleted file mode 100644
index 08c9160..0000000
--- a/general/datasets/HC_M2_1005_P/acknowledgment.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: NIH XXXX
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Yanhua Qu, Ph.D.
- Grant Support: NIH U01CA105417
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/HC_M2_1005_P/cases.rtf b/general/datasets/HC_M2_1005_P/cases.rtf
deleted file mode 100644
index 3e78bb4..0000000
--- a/general/datasets/HC_M2_1005_P/cases.rtf
+++ /dev/null
@@ -1,60 +0,0 @@
-This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).
-
-The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HIJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_1005_P/experiment-design.rtf b/general/datasets/HC_M2_1005_P/experiment-design.rtf
deleted file mode 100644
index 68713a4..0000000
--- a/general/datasets/HC_M2_1005_P/experiment-design.rtf
+++ /dev/null
@@ -1,3252 +0,0 @@
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays.Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-
- Data Table 1:
-
-
-This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool sizel |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 2 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 3 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 4 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 5 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 6 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 7 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 8 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 9 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 10 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 11 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 14 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 15 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 16 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 17 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 18 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 19 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 20 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 21 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 22 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 23 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 24 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 25 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 26 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 27 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 28 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 29 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 30 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 31 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 32 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 33 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 34 |
- R1347H2 |
- BXD21 |
- 64 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.881 |
- 61.49 |
- 0.494 |
- 0.486 |
- 0.019 |
- 0.92 |
- 1.22 |
- UMemphis |
-
-
- | 35 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 36 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 37 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 38 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 39 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 40 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 41 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 42 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 43 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 44 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 45 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 46 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 47 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 48 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 49 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 50 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 51 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 52 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 54 |
- R1469H1 |
- BXD36 |
- 83 |
- F |
- 3 |
- 3 |
- 0.02 |
- 3.473 |
- 49.9 |
- 0.494 |
- 0.486 |
- 0.02 |
- 1.11 |
- 0.76 |
- UMemphis |
-
-
- | 55 |
- R1363H1 |
- BXD36 |
- 77 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.184 |
- 48.19 |
- 0.538 |
- 0.443 |
- 0.02 |
- 1.28 |
- 0.77 |
- UMemphis |
-
-
- | 56 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 57 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 58 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 59 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 60 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 61 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 62 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 63 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 64 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 65 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 66 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 67 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 68 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 69 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 70 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 71 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 72 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 74 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 75 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 76 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 77 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 78 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 79 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 80 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 81 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 82 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 83 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 84 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 85 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 86 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 87 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 88 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 89 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 90 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 91 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 92 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 93 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 94 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 95 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 96 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 97 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 98 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 99 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 100 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 101 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 102 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 103 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 104 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 105 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 106 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 107 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 108 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 109 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 110 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 111 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 112 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 113 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 114 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 115 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 116 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 117 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 118 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 119 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 120 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 121 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 122 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 123 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 124 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 125 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 126 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 127 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 128 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 129 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 130 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 131 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 132 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 133 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 134 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 135 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 136 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 137 |
- R2619H1 |
- CAST/Ei |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 138 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 139 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 140 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 141 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 142 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 143 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 144 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 145 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
- | 146 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 147 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 148 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 149 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 150 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 152 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 153 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 154 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 155 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 156 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 157 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 158 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 159 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 160 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 161 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 162 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 163 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 164 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 165 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 166 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 167 |
- R1687H3 |
- KK/HIJ |
- 72 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 168 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 169 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 170 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 171 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 172 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 173 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 174 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 175 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 176 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 177 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 178 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/HC_M2_1005_P/notes.rtf b/general/datasets/HC_M2_1005_P/notes.rtf
deleted file mode 100644
index 4490ee3..0000000
--- a/general/datasets/HC_M2_1005_P/notes.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-This study includes the following datasets:
-
-
-Hippocampus Consortium M430v2 (Oct05) MAS5
-
-Hippocampus Consortium M430v2 (Oct05) RMA
-
-Hippocampus Consortium M430v2 (Oct05) PDNN
-
-Hippocampus Consortium M430v2 (Dec05) RMA
-
-Hippocampus Consortium M430v2 (Dec05) PDNN
-
-
-This text file originally generated prospectively by RWW on July 30 2005. Updated by RWW July 31, 2005.
diff --git a/general/datasets/HC_M2_1005_P/platform.rtf b/general/datasets/HC_M2_1005_P/platform.rtf
deleted file mode 100644
index af0948c..0000000
--- a/general/datasets/HC_M2_1005_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_1005_P/processing.rtf b/general/datasets/HC_M2_1005_P/processing.rtf
deleted file mode 100644
index df5513b..0000000
--- a/general/datasets/HC_M2_1005_P/processing.rtf
+++ /dev/null
@@ -1,40 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very senstive to the transformation method that is used. Using the PDNN transform the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For examploe, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one whould include the ssample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. <0L>
-
-
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_1005_P/summary.rtf b/general/datasets/HC_M2_1005_P/summary.rtf
deleted file mode 100644
index 9b7c1d6..0000000
--- a/general/datasets/HC_M2_1005_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-PRELIMINARY: The October 2005 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of approximately 99 genetically diverse strains of mice including 68 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of 16 diverse inbred strains, and 2 reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial for memory formation, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3, and parts of the subiculum) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section. Samples were processed using a total of 206 Affymetrix Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0 or M430v2), of which 179 passed stringent quality control and error checking. This particular data set was processed using the MAS5 protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_1005_P/tissue.rtf b/general/datasets/HC_M2_1005_P/tissue.rtf
deleted file mode 100644
index 2bb700d..0000000
--- a/general/datasets/HC_M2_1005_P/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thanks Muriel Davission for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below).
-
diff --git a/general/datasets/HC_M2_1005_R/acknowledgment.rtf b/general/datasets/HC_M2_1005_R/acknowledgment.rtf
deleted file mode 100644
index 08c9160..0000000
--- a/general/datasets/HC_M2_1005_R/acknowledgment.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: NIH XXXX
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Yanhua Qu, Ph.D.
- Grant Support: NIH U01CA105417
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/HC_M2_1005_R/cases.rtf b/general/datasets/HC_M2_1005_R/cases.rtf
deleted file mode 100644
index 3e78bb4..0000000
--- a/general/datasets/HC_M2_1005_R/cases.rtf
+++ /dev/null
@@ -1,60 +0,0 @@
-This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).
-
-The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HIJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_1005_R/experiment-design.rtf b/general/datasets/HC_M2_1005_R/experiment-design.rtf
deleted file mode 100644
index 68713a4..0000000
--- a/general/datasets/HC_M2_1005_R/experiment-design.rtf
+++ /dev/null
@@ -1,3252 +0,0 @@
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays.Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-
- Data Table 1:
-
-
-This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool sizel |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 2 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 3 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 4 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 5 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 6 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 7 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 8 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 9 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 10 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 11 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 14 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 15 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 16 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 17 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 18 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 19 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 20 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 21 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 22 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 23 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 24 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 25 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 26 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 27 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 28 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 29 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 30 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 31 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 32 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 33 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 34 |
- R1347H2 |
- BXD21 |
- 64 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.881 |
- 61.49 |
- 0.494 |
- 0.486 |
- 0.019 |
- 0.92 |
- 1.22 |
- UMemphis |
-
-
- | 35 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 36 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 37 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 38 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 39 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 40 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 41 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 42 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 43 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 44 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 45 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 46 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 47 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 48 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 49 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 50 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 51 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 52 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 54 |
- R1469H1 |
- BXD36 |
- 83 |
- F |
- 3 |
- 3 |
- 0.02 |
- 3.473 |
- 49.9 |
- 0.494 |
- 0.486 |
- 0.02 |
- 1.11 |
- 0.76 |
- UMemphis |
-
-
- | 55 |
- R1363H1 |
- BXD36 |
- 77 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.184 |
- 48.19 |
- 0.538 |
- 0.443 |
- 0.02 |
- 1.28 |
- 0.77 |
- UMemphis |
-
-
- | 56 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 57 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 58 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 59 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 60 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 61 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 62 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 63 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 64 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 65 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 66 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 67 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 68 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 69 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 70 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 71 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 72 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 74 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 75 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 76 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 77 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 78 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 79 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 80 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 81 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 82 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 83 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 84 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 85 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 86 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 87 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 88 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 89 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 90 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 91 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 92 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 93 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 94 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 95 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 96 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 97 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 98 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 99 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 100 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 101 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 102 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 103 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 104 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 105 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 106 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 107 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 108 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 109 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 110 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 111 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 112 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 113 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 114 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 115 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 116 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 117 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 118 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 119 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 120 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 121 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 122 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 123 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 124 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 125 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 126 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 127 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 128 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 129 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 130 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 131 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 132 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 133 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 134 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 135 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 136 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 137 |
- R2619H1 |
- CAST/Ei |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 138 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 139 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 140 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 141 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 142 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 143 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 144 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 145 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
- | 146 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 147 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 148 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 149 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 150 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 152 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 153 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 154 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 155 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 156 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 157 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 158 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 159 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 160 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 161 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 162 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 163 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 164 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 165 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 166 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 167 |
- R1687H3 |
- KK/HIJ |
- 72 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 168 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 169 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 170 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 171 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 172 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 173 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 174 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 175 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 176 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 177 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 178 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/HC_M2_1005_R/notes.rtf b/general/datasets/HC_M2_1005_R/notes.rtf
deleted file mode 100644
index 4490ee3..0000000
--- a/general/datasets/HC_M2_1005_R/notes.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-This study includes the following datasets:
-
-
-Hippocampus Consortium M430v2 (Oct05) MAS5
-
-Hippocampus Consortium M430v2 (Oct05) RMA
-
-Hippocampus Consortium M430v2 (Oct05) PDNN
-
-Hippocampus Consortium M430v2 (Dec05) RMA
-
-Hippocampus Consortium M430v2 (Dec05) PDNN
-
-
-This text file originally generated prospectively by RWW on July 30 2005. Updated by RWW July 31, 2005.
diff --git a/general/datasets/HC_M2_1005_R/platform.rtf b/general/datasets/HC_M2_1005_R/platform.rtf
deleted file mode 100644
index af0948c..0000000
--- a/general/datasets/HC_M2_1005_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_1005_R/processing.rtf b/general/datasets/HC_M2_1005_R/processing.rtf
deleted file mode 100644
index df5513b..0000000
--- a/general/datasets/HC_M2_1005_R/processing.rtf
+++ /dev/null
@@ -1,40 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very senstive to the transformation method that is used. Using the PDNN transform the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For examploe, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one whould include the ssample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. <0L>
-
-
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_1005_R/summary.rtf b/general/datasets/HC_M2_1005_R/summary.rtf
deleted file mode 100644
index 9b7c1d6..0000000
--- a/general/datasets/HC_M2_1005_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-PRELIMINARY: The October 2005 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of approximately 99 genetically diverse strains of mice including 68 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of 16 diverse inbred strains, and 2 reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial for memory formation, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3, and parts of the subiculum) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section. Samples were processed using a total of 206 Affymetrix Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0 or M430v2), of which 179 passed stringent quality control and error checking. This particular data set was processed using the MAS5 protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_1005_R/tissue.rtf b/general/datasets/HC_M2_1005_R/tissue.rtf
deleted file mode 100644
index 2bb700d..0000000
--- a/general/datasets/HC_M2_1005_R/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thanks Muriel Davission for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below).
-
diff --git a/general/datasets/HC_M2_1205_P/acknowledgment.rtf b/general/datasets/HC_M2_1205_P/acknowledgment.rtf
deleted file mode 100644
index 08c9160..0000000
--- a/general/datasets/HC_M2_1205_P/acknowledgment.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: NIH XXXX
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Yanhua Qu, Ph.D.
- Grant Support: NIH U01CA105417
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/HC_M2_1205_P/cases.rtf b/general/datasets/HC_M2_1205_P/cases.rtf
deleted file mode 100644
index 3e78bb4..0000000
--- a/general/datasets/HC_M2_1205_P/cases.rtf
+++ /dev/null
@@ -1,60 +0,0 @@
-This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).
-
-The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HIJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_1205_P/experiment-design.rtf b/general/datasets/HC_M2_1205_P/experiment-design.rtf
deleted file mode 100644
index 68713a4..0000000
--- a/general/datasets/HC_M2_1205_P/experiment-design.rtf
+++ /dev/null
@@ -1,3252 +0,0 @@
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays.Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-
- Data Table 1:
-
-
-This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool sizel |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 2 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 3 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 4 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 5 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 6 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 7 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 8 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 9 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 10 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 11 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 14 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 15 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 16 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 17 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 18 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 19 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 20 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 21 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 22 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 23 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 24 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 25 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 26 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 27 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 28 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 29 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 30 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 31 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 32 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 33 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 34 |
- R1347H2 |
- BXD21 |
- 64 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.881 |
- 61.49 |
- 0.494 |
- 0.486 |
- 0.019 |
- 0.92 |
- 1.22 |
- UMemphis |
-
-
- | 35 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 36 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 37 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 38 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 39 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 40 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 41 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 42 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 43 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 44 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 45 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 46 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 47 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 48 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 49 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 50 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 51 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 52 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 54 |
- R1469H1 |
- BXD36 |
- 83 |
- F |
- 3 |
- 3 |
- 0.02 |
- 3.473 |
- 49.9 |
- 0.494 |
- 0.486 |
- 0.02 |
- 1.11 |
- 0.76 |
- UMemphis |
-
-
- | 55 |
- R1363H1 |
- BXD36 |
- 77 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.184 |
- 48.19 |
- 0.538 |
- 0.443 |
- 0.02 |
- 1.28 |
- 0.77 |
- UMemphis |
-
-
- | 56 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 57 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 58 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 59 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 60 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 61 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 62 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 63 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 64 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 65 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 66 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 67 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 68 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 69 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 70 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 71 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 72 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 74 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 75 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 76 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 77 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 78 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 79 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 80 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 81 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 82 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 83 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 84 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 85 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 86 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 87 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 88 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 89 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 90 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 91 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 92 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 93 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 94 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 95 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 96 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 97 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 98 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 99 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 100 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 101 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 102 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 103 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 104 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 105 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 106 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 107 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 108 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 109 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 110 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 111 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 112 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 113 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 114 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 115 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 116 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 117 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 118 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 119 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 120 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 121 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 122 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 123 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 124 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 125 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 126 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 127 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 128 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 129 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 130 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 131 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 132 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 133 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 134 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 135 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 136 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 137 |
- R2619H1 |
- CAST/Ei |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 138 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 139 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 140 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 141 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 142 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 143 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 144 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 145 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
- | 146 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 147 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 148 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 149 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 150 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 152 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 153 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 154 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 155 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 156 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 157 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 158 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 159 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 160 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 161 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 162 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 163 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 164 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 165 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 166 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 167 |
- R1687H3 |
- KK/HIJ |
- 72 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 168 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 169 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 170 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 171 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 172 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 173 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 174 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 175 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 176 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 177 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 178 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/HC_M2_1205_P/notes.rtf b/general/datasets/HC_M2_1205_P/notes.rtf
deleted file mode 100644
index 4490ee3..0000000
--- a/general/datasets/HC_M2_1205_P/notes.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-This study includes the following datasets:
-
-
-Hippocampus Consortium M430v2 (Oct05) MAS5
-
-Hippocampus Consortium M430v2 (Oct05) RMA
-
-Hippocampus Consortium M430v2 (Oct05) PDNN
-
-Hippocampus Consortium M430v2 (Dec05) RMA
-
-Hippocampus Consortium M430v2 (Dec05) PDNN
-
-
-This text file originally generated prospectively by RWW on July 30 2005. Updated by RWW July 31, 2005.
diff --git a/general/datasets/HC_M2_1205_P/platform.rtf b/general/datasets/HC_M2_1205_P/platform.rtf
deleted file mode 100644
index af0948c..0000000
--- a/general/datasets/HC_M2_1205_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_1205_P/processing.rtf b/general/datasets/HC_M2_1205_P/processing.rtf
deleted file mode 100644
index df5513b..0000000
--- a/general/datasets/HC_M2_1205_P/processing.rtf
+++ /dev/null
@@ -1,40 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very senstive to the transformation method that is used. Using the PDNN transform the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For examploe, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one whould include the ssample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. <0L>
-
-
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_1205_P/summary.rtf b/general/datasets/HC_M2_1205_P/summary.rtf
deleted file mode 100644
index 9b7c1d6..0000000
--- a/general/datasets/HC_M2_1205_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-PRELIMINARY: The October 2005 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of approximately 99 genetically diverse strains of mice including 68 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of 16 diverse inbred strains, and 2 reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial for memory formation, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3, and parts of the subiculum) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section. Samples were processed using a total of 206 Affymetrix Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0 or M430v2), of which 179 passed stringent quality control and error checking. This particular data set was processed using the MAS5 protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_1205_P/tissue.rtf b/general/datasets/HC_M2_1205_P/tissue.rtf
deleted file mode 100644
index 2bb700d..0000000
--- a/general/datasets/HC_M2_1205_P/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thanks Muriel Davission for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below).
-
diff --git a/general/datasets/HC_M2_1205_R/acknowledgment.rtf b/general/datasets/HC_M2_1205_R/acknowledgment.rtf
deleted file mode 100644
index 08c9160..0000000
--- a/general/datasets/HC_M2_1205_R/acknowledgment.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integratie Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: NIH XXXX
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Yanhua Qu, Ph.D.
- Grant Support: NIH U01CA105417
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/HC_M2_1205_R/cases.rtf b/general/datasets/HC_M2_1205_R/cases.rtf
deleted file mode 100644
index 3e78bb4..0000000
--- a/general/datasets/HC_M2_1205_R/cases.rtf
+++ /dev/null
@@ -1,60 +0,0 @@
-This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).
-
-The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-The CXB is the first and oldest set of recombinant inbred strains. Over 500 classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (Hld),characterized by Nowakowski and colleagues (1984). All of the CXBs have been recently genotyped at 13,377 SNPs.
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HIJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HILtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HC_M2_1205_R/experiment-design.rtf b/general/datasets/HC_M2_1205_R/experiment-design.rtf
deleted file mode 100644
index 68713a4..0000000
--- a/general/datasets/HC_M2_1205_R/experiment-design.rtf
+++ /dev/null
@@ -1,3252 +0,0 @@
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 99 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquotes R1291H3 and R1291H4).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays.Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
-
- Data Table 1:
-
-
-This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool sizel |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 2 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 3 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 4 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 5 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 6 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 7 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 8 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 9 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 10 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 11 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 12 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 13 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 14 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 15 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 16 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 17 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 18 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 19 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 20 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 21 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 22 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 23 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 24 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 25 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 26 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 27 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 28 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 29 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 30 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 31 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 32 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 33 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 34 |
- R1347H2 |
- BXD21 |
- 64 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.881 |
- 61.49 |
- 0.494 |
- 0.486 |
- 0.019 |
- 0.92 |
- 1.22 |
- UMemphis |
-
-
- | 35 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 36 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 37 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 38 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 39 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 40 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 41 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 42 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 43 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 44 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 45 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 46 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 47 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 48 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 49 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 50 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 51 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 52 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 53 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 54 |
- R1469H1 |
- BXD36 |
- 83 |
- F |
- 3 |
- 3 |
- 0.02 |
- 3.473 |
- 49.9 |
- 0.494 |
- 0.486 |
- 0.02 |
- 1.11 |
- 0.76 |
- UMemphis |
-
-
- | 55 |
- R1363H1 |
- BXD36 |
- 77 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.184 |
- 48.19 |
- 0.538 |
- 0.443 |
- 0.02 |
- 1.28 |
- 0.77 |
- UMemphis |
-
-
- | 56 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 57 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 58 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 59 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 60 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 61 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 62 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 63 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 64 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 65 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 66 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 67 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 68 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 69 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 70 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 71 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 72 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 73 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 74 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 75 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 76 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 77 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 78 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 79 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 80 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 81 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 82 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 83 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 84 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 85 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 86 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 87 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 88 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 89 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 90 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 91 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 92 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 93 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 94 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 95 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 96 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 97 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 98 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 99 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 100 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 101 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 102 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 103 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 104 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 105 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 106 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 107 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 108 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 109 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 110 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 111 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 112 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 113 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 114 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 115 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 116 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 117 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 118 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 119 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 120 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 121 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 122 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 123 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 124 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 125 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 126 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 127 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 128 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 129 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 130 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 131 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 132 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 133 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 134 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 135 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 136 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 137 |
- R2619H1 |
- CAST/Ei |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 138 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 139 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 140 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 141 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 142 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 143 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 144 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 145 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
- | 146 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 147 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 148 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 149 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 150 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 151 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 152 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 153 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 154 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 155 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 156 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 157 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 158 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 159 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 160 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 161 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 162 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 163 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 164 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 165 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 166 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 167 |
- R1687H3 |
- KK/HIJ |
- 72 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 168 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 169 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 170 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 171 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 172 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 173 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 174 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 175 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 176 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 177 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 178 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/HC_M2_1205_R/notes.rtf b/general/datasets/HC_M2_1205_R/notes.rtf
deleted file mode 100644
index 4490ee3..0000000
--- a/general/datasets/HC_M2_1205_R/notes.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-This study includes the following datasets:
-
-
-Hippocampus Consortium M430v2 (Oct05) MAS5
-
-Hippocampus Consortium M430v2 (Oct05) RMA
-
-Hippocampus Consortium M430v2 (Oct05) PDNN
-
-Hippocampus Consortium M430v2 (Dec05) RMA
-
-Hippocampus Consortium M430v2 (Dec05) PDNN
-
-
-This text file originally generated prospectively by RWW on July 30 2005. Updated by RWW July 31, 2005.
diff --git a/general/datasets/HC_M2_1205_R/platform.rtf b/general/datasets/HC_M2_1205_R/platform.rtf
deleted file mode 100644
index af0948c..0000000
--- a/general/datasets/HC_M2_1205_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
diff --git a/general/datasets/HC_M2_1205_R/processing.rtf b/general/datasets/HC_M2_1205_R/processing.rtf
deleted file mode 100644
index df5513b..0000000
--- a/general/datasets/HC_M2_1205_R/processing.rtf
+++ /dev/null
@@ -1,40 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very senstive to the transformation method that is used. Using the PDNN transform the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For examploe, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one whould include the ssample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. <0L>
-
-
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
diff --git a/general/datasets/HC_M2_1205_R/summary.rtf b/general/datasets/HC_M2_1205_R/summary.rtf
deleted file mode 100644
index 9b7c1d6..0000000
--- a/general/datasets/HC_M2_1205_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-PRELIMINARY: The October 2005 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of approximately 99 genetically diverse strains of mice including 68 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of 16 diverse inbred strains, and 2 reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial for memory formation, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3, and parts of the subiculum) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section. Samples were processed using a total of 206 Affymetrix Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0 or M430v2), of which 179 passed stringent quality control and error checking. This particular data set was processed using the MAS5 protocol. To simplify comparisons among transforms, MAS5 values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_1205_R/tissue.rtf b/general/datasets/HC_M2_1205_R/tissue.rtf
deleted file mode 100644
index 2bb700d..0000000
--- a/general/datasets/HC_M2_1205_R/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thanks Muriel Davission for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below).
-
diff --git a/general/datasets/HC_M2_1206_R/acknowledgment.rtf b/general/datasets/HC_M2_1206_R/acknowledgment.rtf
deleted file mode 100644
index aa6285a..0000000
--- a/general/datasets/HC_M2_1206_R/acknowledgment.rtf
+++ /dev/null
@@ -1,61 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Consortium. All of us thank Muriel Davisson, Cathy Lutz, and colleagues at the Jackson Laboratory for making it possible for us to add all of the CXB strains, and one or more samples from KK/HIJ, WSB/Ei, NZO/HILtJ, LG/J, CAST/Ei, PWD/PhJ, and PWK/PhJ to this study. We thank Yan Cui at UTHSC for allowing us to use his Linux cluster to align all M430 2.0 probes and probe sets to the mouse genome. We thank Hui-Chen Hsu and John Mountz for providing us BXD tissue samples, as well as many strains of BXD stock. We thanks Douglas Matthews (UMem in Table 1) and John Boughter (JBo in Table 1) for sharing BXD stock with us. Members of the Hippocampus Consortium thank the following sources for financial support of this effort:
-
-
- - David C. Airey, Ph.D.
- Grant Support: Vanderbilt Institute for Integrative Genomics
- Department of Pharmacology
- david.airey at vanderbilt.edu
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Fred H. Gage, Ph.D.
- Grant Support: Lookout Foundation
- - Dan Goldowitz, Ph.D.
- Grant Support: NIAAA INIA AA013503
- University of Tennessee Health Science Center
- Dept. Anatomy and Neurobiology
- email: dgold@nb.utmem.edu
- - Shirlean Goodwin, Ph.D.
- Grant Support: NIAAA INIA U01AA013515
- - Gerd Kempermann, M.D.
- Grant Support: The Volkswagen Foundation Grant on Permissive and Persistent Factors in Neurogenesis in the Adult Central Nervous System
- Humboldt-Universitat Berlin
- Universitatsklinikum Charite
- email: gerd.kempermann at mdc-berlin.de
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Richard S. Nowakowski, Ph.D.
- Grant Support: R01 NS049445-01
- - Yanhua Qu, Ph.D.
- Grant Support: NIH U01CA105417
- - Glenn D. Rosen, Ph.D.
- Grant Support: NIH P20
- - Leonard C. Schalkwyk, Ph.D.
- Grant Support: MRC Career Establishment Grant G0000170
- Social, Genetic and Developmental Psychiatry
- Institute of Psychiatry,Kings College London
- PO82, De Crespigny Park London SE5 8AF
- L.Schalkwyk@iop.kcl.ac.uk
- - Guus Smit, Ph.D.
- Dutch NeuroBsik Mouse Phenomics Consortium
- Center for Neurogenomics & Cognitive Research
- Vrije Universiteit Amsterdam, The Netherlands
- e-mail: guus.smit at falw.vu.nl
- Grant Support: BSIK 03053
- - Thomas Sutter, Ph.D.
- Grant Support: INIA U01 AA13515 and the W. Harry Feinstone Center for Genome Research
- - Stephen Whatley, Ph.D.
- Grant Support: XXXX
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
diff --git a/general/datasets/HC_M2_1206_R/cases.rtf b/general/datasets/HC_M2_1206_R/cases.rtf
deleted file mode 100644
index 28305bf..0000000
--- a/general/datasets/HC_M2_1206_R/cases.rtf
+++ /dev/null
@@ -1,3791 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1 and D2B6F1
- F1 hybrids generated by crossing C57BL/6J with DBA/2J
-
-
-We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
-
-
-
-This table lists all arrays by order of processing (Run), Sample ID, Strain, Sex, Age, number of animals in each sample pool (Pool), F generation number when less than 30 (GenN, and the Source of animals. SampleID is the ID number of the pooled RNA sample with a H1 through H3 suffix to indicate the actual hippocampal RNA aliquot used to prepare cRNA. Grp is the sequential group processing number (1 - 6).
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- batch ID |
- pool sizel |
- RMA outlier |
- scale factor |
- back ground average |
- present |
- absent |
- marginal |
- AFFX-b-ActinMur (3'/5') |
- AFFX-GapdhMur (3'/5') |
- source |
-
-
- | 1 |
- R2028H2 |
- 129S1/SvImJ |
- 66 |
- F |
- 5 |
- 3 |
- 0.1 |
- 4.362 |
- 64.49 |
- 0.497 |
- 0.484 |
- 0.019 |
- 2.78 |
- 1.13 |
- JAX |
-
-
- | 2 |
- R2029H2 |
- 129S1/SvImJ |
- 66 |
- M |
- 6 |
- 3 |
- 0.04 |
- 5.208 |
- 41.21 |
- 0.49 |
- 0.49 |
- 0.02 |
- 1.62 |
- 0.95 |
- JAX |
-
-
- | 3 |
- R2670H1 |
- A/J |
- 65 |
- F |
- 7 |
- 3 |
- 0.04 |
- 3.951 |
- 46.8 |
- 0.498 |
- 0.485 |
- 0.017 |
- 1.32 |
- 0.75 |
- UTM RW |
-
-
- | 4 |
- R2030H1 |
- A/J |
- 57 |
- M |
- 5 |
- 2 |
- 0.06 |
- 3.307 |
- 45.16 |
- 0.527 |
- 0.454 |
- 0.018 |
- 1.63 |
- 0.99 |
- UTM RW |
-
-
- | 5 |
- R2032H3 |
- AKR/J |
- 66 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.054 |
- 61.03 |
- 0.51 |
- 0.471 |
- 0.018 |
- 1.46 |
- 0.79 |
- JAX |
-
-
- | 6 |
- R2454H1 |
- AKR/J |
- 66 |
- M |
- 6 |
- 4 |
- 0.11 |
- 2.892 |
- 58.55 |
- 0.474 |
- 0.507 |
- 0.019 |
- 1.99 |
- 0.78 |
- JAX |
-
-
- | 7 |
- R1289H2 |
- B6D2F1 |
- 64 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.406 |
- 53.84 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.61 |
- 0.96 |
- UTM RW |
-
-
- | 8 |
- R1291H3 |
- B6D2F1 |
- 66 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.524 |
- 48.54 |
- 0.487 |
- 0.494 |
- 0.019 |
- 1.21 |
- 1.52 |
- UTM RW |
-
-
- | 9 |
- R1291H4 |
- B6D2F1 |
- 66 |
- M |
- 6 |
- 3 |
- 0.08 |
- 3.891 |
- 46.69 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.9 |
- 0.89 |
- UTM RW |
-
-
- | 10 |
- R1675H1 |
- BALB/cByJ |
- 83 |
- M |
- 7 |
- 3 |
- 0.03 |
- 3.405 |
- 48.13 |
- 0.509 |
- 0.474 |
- 0.018 |
- 1.13 |
- 0.78 |
- JAX |
-
-
- | 11 |
- R2036H3 |
- BALB/cJ |
- 51 |
- F |
- 5 |
- 3 |
- 0.12 |
- 2.611 |
- 56.29 |
- 0.518 |
- 0.466 |
- 0.017 |
- 3.3 |
- 1.23 |
- UTM RW |
-
-
- | 12 |
- R2053H1 |
- BALB/cJ |
- 55 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.505 |
- 63.27 |
- 0.499 |
- 0.483 |
- 0.018 |
- 3.1 |
- 1.34 |
- UTM RW |
-
-
- | 13 |
- R2037H2 |
- BALB/cJ |
- 51 |
- M |
- 6 |
- 4 |
- 0.01 |
- 2.546 |
- 58.13 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.26 |
- 0.77 |
- UTM RW |
-
-
- | 14 |
- R1507H1 |
- BXD1 |
- 58 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.056 |
- 60.17 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.15 |
- 0.76 |
- Glenn |
-
-
- | 15 |
- R1542H1 |
- BXD1 |
- 59 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.792 |
- 80.56 |
- 0.492 |
- 0.489 |
- 0.018 |
- 1.57 |
- 0.79 |
- Glenn |
-
-
- | 16 |
- R1520H1 |
- BXD2 |
- 56 |
- F |
- 4 |
- 4 |
- 0.09 |
- 1.715 |
- 71.62 |
- 0.515 |
- 0.467 |
- 0.018 |
- 2.36 |
- 1.6 |
- Glenn |
-
-
- | 17 |
- R1516H1 |
- BXD2 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 2.231 |
- 64.86 |
- 0.508 |
- 0.474 |
- 0.019 |
- 1.3 |
- 1.53 |
- Glenn |
-
-
- | 18 |
- R1593H2 |
- BXD5 |
- 60 |
- F |
- 1 |
- 4 |
- 0 |
- 1.913 |
- 59.96 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.98 |
- 1.44 |
- Glenn |
-
-
- | 19 |
- R1692H1 |
- BXD5 |
- 60 |
- M |
- 3 |
- 2 |
- 0.07 |
- 3.764 |
- 72.74 |
- 0.465 |
- 0.516 |
- 0.02 |
- 1.15 |
- 0.74 |
- Glenn |
-
-
- | 20 |
- R1539H2 |
- BXD6 |
- 59 |
- F |
- 1 |
- 4 |
- 0 |
- 2.488 |
- 54.97 |
- 0.518 |
- 0.463 |
- 0.018 |
- 1.08 |
- 1.33 |
- Glenn |
-
-
- | 21 |
- R1538H1 |
- BXD6 |
- 59 |
- M |
- 4 |
- 3 |
- 0.01 |
- 2.585 |
- 50.27 |
- 0.505 |
- 0.475 |
- 0.02 |
- 1.46 |
- 0.79 |
- Glenn |
-
-
- | 22 |
- R1518H1 |
- BXD8 |
- 56 |
- F |
- 1 |
- 3 |
- 0 |
- 2.92 |
- 54.84 |
- 0.515 |
- 0.465 |
- 0.02 |
- 1.32 |
- 1.24 |
- Glenn |
-
-
- | 23 |
- R1548H1 |
- BXD8 |
- 59 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.132 |
- 59.37 |
- 0.504 |
- 0.477 |
- 0.019 |
- 2.16 |
- 1.54 |
- Glenn |
-
-
- | 24 |
- R1350H2 |
- BXD9 |
- 86 |
- F |
- 1 |
- 3 |
- 0.05 |
- 2.771 |
- 60.62 |
- 0.5 |
- 0.482 |
- 0.018 |
- 1.01 |
- 1.28 |
- UMemphis |
-
-
- | 25 |
- R1523H3 |
- BXD9 |
- 57 |
- M |
- 7 |
- 3 |
- 0.14 |
- 3.9 |
- 78.36 |
- 0.435 |
- 0.547 |
- 0.018 |
- 1.36 |
- 0.77 |
- UTM RW |
-
-
- | 26 |
- R1531H1 |
- BXD11 |
- 56 |
- F |
- 6 |
- 3 |
- 0.06 |
- 2.229 |
- 56.36 |
- 0.505 |
- 0.475 |
- 0.02 |
- 2.23 |
- 1.02 |
- Glenn |
-
-
- | 27 |
- R1367H1 |
- BXD11 |
- 56 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.11 |
- 78.78 |
- 0.503 |
- 0.477 |
- 0.02 |
- 1.07 |
- 1.27 |
- Glenn |
-
-
- | 28 |
- R1530H1 |
- BXD12 |
- 58 |
- F |
- 1 |
- 3 |
- 0 |
- 3.227 |
- 53.77 |
- 0.505 |
- 0.477 |
- 0.018 |
- 0.95 |
- 1.4 |
- Glenn |
-
-
- | 29 |
- R2674H1 |
- BXD12 |
- 59 |
- M |
- 7 |
- 3 |
- 0.03 |
- 1.924 |
- 83.44 |
- 0.519 |
- 0.464 |
- 0.018 |
- 1.21 |
- 0.78 |
- Glenn |
-
-
- | 30 |
- R1529H1 |
- BXD13 |
- 58 |
- F |
- 6 |
- 3 |
- 0.05 |
- 2.55 |
- 59.05 |
- 0.497 |
- 0.485 |
- 0.018 |
- 2 |
- 1.54 |
- Glenn |
-
-
- | 31 |
- R1662H2 |
- BXD13 |
- 60 |
- M |
- 1 |
- 3 |
- 0.03 |
- 4.603 |
- 45.81 |
- 0.509 |
- 0.472 |
- 0.019 |
- 1.3 |
- 0.82 |
- Glenn |
-
-
- | 32 |
- R1304H2 |
- BXD14 |
- 72 |
- F |
- 7 |
- 3 |
- 0.03 |
- 3.946 |
- 61.87 |
- 0.484 |
- 0.498 |
- 0.018 |
- 1.22 |
- 0.77 |
- UTM RW |
-
-
- | 33 |
- R1278H2 |
- BXD14 |
- 55 |
- M |
- 7 |
- 3 |
- 0.06 |
- 4.75 |
- 67.52 |
- 0.449 |
- 0.532 |
- 0.019 |
- 1.1 |
- 0.73 |
- UTM RW |
-
-
- | 34 |
- R1524H1 |
- BXD15 |
- 60 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.961 |
- 50.93 |
- 0.497 |
- 0.484 |
- 0.019 |
- 1.74 |
- 0.91 |
- Glenn |
-
-
- | 35 |
- R1515H1 |
- BXD15 |
- 61 |
- M |
- 1 |
- 3 |
- 0.01 |
- 3.316 |
- 57.05 |
- 0.503 |
- 0.478 |
- 0.019 |
- 1.32 |
- 1.21 |
- Glenn |
-
-
- | 36 |
- R1661H1 |
- BXD16 |
- 61 |
- F |
- 1 |
- 3 |
- 0.01 |
- 2.778 |
- 59.81 |
- 0.516 |
- 0.466 |
- 0.019 |
- 1.39 |
- 1.2 |
- Glenn |
-
-
- | 37 |
- R1594H1 |
- BXD16 |
- 61 |
- M |
- 4 |
- 3 |
- 0.03 |
- 2.634 |
- 53.66 |
- 0.504 |
- 0.478 |
- 0.018 |
- 1.96 |
- 1.51 |
- Glenn |
-
-
- | 38 |
- R2666H1 |
- BXD19 |
- 60 |
- F |
- 7 |
- 3 |
- 0.02 |
- 2.498 |
- 76.2 |
- 0.495 |
- 0.486 |
- 0.019 |
- 1.41 |
- 0.77 |
- Glenn |
-
-
- | 39 |
- R1471H1 |
- BXD19 |
- 157 |
- M |
- 1 |
- 3 |
- 0.02 |
- 3.165 |
- 43.34 |
- 0.519 |
- 0.462 |
- 0.018 |
- 1.01 |
- 1.29 |
- UTM JB |
-
-
- | 40 |
- R1573H1 |
- BXD20 |
- 59 |
- F |
- 1 |
- 3 |
- 0.02 |
- 3.749 |
- 52.7 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.01 |
- 1.27 |
- Glenn |
-
-
- | 41 |
- R2507H1 |
- BXD20 |
- 60 |
- M |
- 6 |
- 3 |
- 0.06 |
- 3.568 |
- 57 |
- 0.472 |
- 0.508 |
- 0.02 |
- 1.29 |
- 0.76 |
- Glenn |
-
-
- | 42 |
- R1347H2 |
- BXD21 |
- 64 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.881 |
- 61.49 |
- 0.494 |
- 0.486 |
- 0.019 |
- 0.92 |
- 1.22 |
- UMemphis |
-
-
- | 43 |
- R2668H1 |
- BXD21 |
- 60 |
- M |
- 7 |
- 4 |
- 0.07 |
- 2.605 |
- 44.9 |
- 0.535 |
- 0.449 |
- 0.017 |
- 1.54 |
- 0.76 |
- Glenn |
-
-
- | 44 |
- R1337H2 |
- BXD21 |
- 102 |
- F |
- 2 |
- 4 |
- 0 |
- 2.673 |
- 58.05 |
- 0.492 |
- 0.489 |
- 0.019 |
- 1.4 |
- 0.76 |
- UAB |
-
-
- | 45 |
- R1848H3 |
- BXD22 |
- 196 |
- F |
- 6 |
- 4 |
- 0.02 |
- 2.943 |
- 51.7 |
- 0.494 |
- 0.485 |
- 0.021 |
- 2.2 |
- 0.78 |
- UAB |
-
-
- | 46 |
- R1525H1 |
- BXD22 |
- 59 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.248 |
- 55.76 |
- 0.548 |
- 0.433 |
- 0.018 |
- 1.26 |
- 0.74 |
- Glenn |
-
-
- | 47 |
- R1280H2 |
- BXD23 |
- 56 |
- F |
- 1 |
- 3 |
- 0.01 |
- 3.187 |
- 54.63 |
- 0.458 |
- 0.523 |
- 0.019 |
- 0.96 |
- 1.2 |
- UTM RW |
-
-
- | 48 |
- R1537H1 |
- BXD23 |
- 58 |
- F |
- 5 |
- 3 |
- 0.1 |
- 3.719 |
- 67.54 |
- 0.468 |
- 0.513 |
- 0.019 |
- 1.51 |
- 0.96 |
- Glenn |
-
-
- | 49 |
- R1244H2 |
- BXD23 |
- 65 |
- M |
- 7 |
- 3 |
- 0.05 |
- 1.257 |
- 81.93 |
- 0.565 |
- 0.417 |
- 0.018 |
- 1.24 |
- 0.74 |
- Glenn |
-
-
- | 50 |
- R1343H2 |
- BXD24 |
- 71 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.083 |
- 65.07 |
- 0.506 |
- 0.474 |
- 0.019 |
- 1.46 |
- 0.75 |
- UMemphis |
-
-
- | 51 |
- R1517H1 |
- BXD24 |
- 57 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.471 |
- 53.66 |
- 0.504 |
- 0.476 |
- 0.019 |
- 1.28 |
- 0.78 |
- Glenn |
-
-
- | 52 |
- R1366H1 |
- BXD27 |
- 60 |
- F |
- 2 |
- 4 |
- 0 |
- 2.26 |
- 48.46 |
- 0.518 |
- 0.463 |
- 0.019 |
- 1.29 |
- 0.77 |
- Glenn |
-
-
- | 53 |
- R1849H1 |
- BXD27 |
- 70 |
- M |
- 5 |
- 3 |
- 0.06 |
- 8.801 |
- 38.34 |
- 0.468 |
- 0.512 |
- 0.019 |
- 2.42 |
- 1.08 |
- UAB |
-
-
- | 54 |
- R1353H1 |
- BXD28 |
- 79 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.22 |
- 76.22 |
- 0.48 |
- 0.5 |
- 0.02 |
- 1.33 |
- 0.78 |
- UMemphis |
-
-
- | 55 |
- R2332H1 |
- BXD28 |
- 60 |
- M |
- 2 |
- 3 |
- 0.01 |
- 3.217 |
- 63.68 |
- 0.491 |
- 0.49 |
- 0.019 |
- 1.37 |
- 0.79 |
- Glenn |
-
-
- | 56 |
- R1532H1 |
- BXD29 |
- 57 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.122 |
- 59.18 |
- 0.524 |
- 0.456 |
- 0.019 |
- 1.17 |
- 0.76 |
- Glenn |
-
-
- | 57 |
- R1356H1 |
- BXD29 |
- 76 |
- M |
- 5 |
- 3 |
- 0.01 |
- 4.033 |
- 47.67 |
- 0.52 |
- 0.463 |
- 0.017 |
- 1.17 |
- 0.78 |
- UMemphis |
-
-
- | 58 |
- R1240H2 |
- BXD31 |
- 61 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.335 |
- 65.17 |
- 0.507 |
- 0.474 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 59 |
- R1526H2 |
- BXD31 |
- 57 |
- F |
- 7 |
- 4 |
- 0.1 |
- 7.267 |
- 89.54 |
- 0.435 |
- 0.547 |
- 0.017 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 60 |
- R2675H1 |
- BXD32 |
- 57 |
- F |
- 7 |
- 3 |
- 0.03 |
- 2.268 |
- 78.01 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.22 |
- 0.78 |
- Glenn |
-
-
- | 61 |
- R1508H2 |
- BXD32 |
- 58 |
- M |
- 2 |
- 4 |
- 0.01 |
- 1.917 |
- 67.78 |
- 0.539 |
- 0.442 |
- 0.019 |
- 1.28 |
- 0.73 |
- Glenn |
-
-
- | 62 |
- R1345H3 |
- BXD33 |
- 65 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.098 |
- 63.14 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.27 |
- 0.73 |
- UMemphis |
-
-
- | 63 |
- R1581H1 |
- BXD33 |
- 59 |
- M |
- 3 |
- 3 |
- 0.01 |
- 3.229 |
- 53.16 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.19 |
- 0.78 |
- Glenn |
-
-
- | 64 |
- R1527H1 |
- BXD34 |
- 59 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.3 |
- 58.92 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.24 |
- 0.76 |
- Glenn |
-
-
- | 65 |
- R1339H3 |
- BXD34 |
- 74 |
- M |
- 5 |
- 3 |
- 0.12 |
- 2.888 |
- 53.49 |
- 0.506 |
- 0.476 |
- 0.018 |
- 2.39 |
- 1.35 |
- UMemphis |
-
-
- | 66 |
- R1469H1 |
- BXD36 |
- 83 |
- F |
- 3 |
- 3 |
- 0.02 |
- 3.473 |
- 49.9 |
- 0.494 |
- 0.486 |
- 0.02 |
- 1.11 |
- 0.76 |
- UMemphis |
-
-
- | 67 |
- R1363H1 |
- BXD36 |
- 77 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.184 |
- 48.19 |
- 0.538 |
- 0.443 |
- 0.02 |
- 1.28 |
- 0.77 |
- UMemphis |
-
-
- | 68 |
- R1855H1 |
- BXD38 |
- 55 |
- F |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 54.54 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.39 |
- 0.75 |
- Glenn |
-
-
- | 69 |
- R1510H1 |
- BXD38 |
- 59 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.186 |
- 68.06 |
- 0.521 |
- 0.46 |
- 0.019 |
- 1.26 |
- 0.79 |
- Glenn |
-
-
- | 70 |
- R1528H2 |
- BXD39 |
- 59 |
- F |
- 2 |
- 3 |
- 0.03 |
- 4.717 |
- 38.3 |
- 0.511 |
- 0.47 |
- 0.02 |
- 1.12 |
- 0.75 |
- Glenn |
-
-
- | 71 |
- R1514H1 |
- BXD39 |
- 59 |
- M |
- 3 |
- 3 |
- 0.03 |
- 3.992 |
- 56.06 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.43 |
- 0.81 |
- Glenn |
-
-
- | 72 |
- R1522H1 |
- BXD40 |
- 59 |
- F |
- 4 |
- 4 |
- 0 |
- 2.631 |
- 67.16 |
- 0.49 |
- 0.491 |
- 0.018 |
- 1.56 |
- 0.77 |
- Glenn |
-
-
- | 73 |
- R1359H1 |
- BXD40 |
- 73 |
- M |
- 2 |
- 3 |
- 0.09 |
- 7.458 |
- 39.86 |
- 0.451 |
- 0.527 |
- 0.021 |
- 1.28 |
- 0.74 |
- UMemphis |
-
-
- | 74 |
- R1541H2 |
- BXD42 |
- 58 |
- F |
- 7 |
- 3 |
- 0.07 |
- 6.784 |
- 52.12 |
- 0.483 |
- 0.499 |
- 0.017 |
- 1.13 |
- 0.66 |
- Glenn |
-
-
- | 75 |
- R1540H1 |
- BXD42 |
- 58 |
- M |
- 7 |
- 4 |
- 0.03 |
- 2.423 |
- 75.14 |
- 0.492 |
- 0.488 |
- 0.02 |
- 1.48 |
- 0.78 |
- Glenn |
-
-
- | 76 |
- R1334H2 |
- BXD43 |
- 59 |
- F |
- 1 |
- 3 |
- 0 |
- 2.672 |
- 54.36 |
- 0.492 |
- 0.491 |
- 0.017 |
- 1.2 |
- 2.06 |
- UTM RW |
-
-
- | 77 |
- R1303H1 |
- BXD43 |
- 63 |
- M |
- 3 |
- 4 |
- 0.02 |
- 3.497 |
- 51.9 |
- 0.486 |
- 0.495 |
- 0.019 |
- 1.15 |
- 0.8 |
- UTM RW |
-
-
- | 78 |
- R1326H1 |
- BXD44 |
- 65 |
- F |
- 3 |
- 4 |
- 0 |
- 3.412 |
- 53.96 |
- 0.496 |
- 0.485 |
- 0.018 |
- 1.35 |
- 0.78 |
- UTM RW |
-
-
- | 79 |
- R1577H2 |
- BXD44 |
- 56 |
- M |
- 1 |
- 3 |
- 0.02 |
- 2.159 |
- 67.52 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.18 |
- 1.71 |
- UTM RW |
-
-
- | 80 |
- R1403H2 |
- BXD45 |
- 63 |
- F |
- 7 |
- 2 |
- 0.03 |
- 3.146 |
- 44.5 |
- 0.524 |
- 0.457 |
- 0.018 |
- 1.41 |
- 0.78 |
- Glenn |
-
-
- | 81 |
- R1472H1 |
- BXD45 |
- 65 |
- M |
- 7 |
- 4 |
- 0.04 |
- 1.651 |
- 73.31 |
- 0.543 |
- 0.44 |
- 0.018 |
- 1.63 |
- 0.74 |
- UTM RW |
-
-
- | 82 |
- R1316H1 |
- BXD48 |
- 58 |
- F |
- 4 |
- 3 |
- 0 |
- 2.445 |
- 68.59 |
- 0.515 |
- 0.467 |
- 0.019 |
- 1.16 |
- 0.73 |
- UTM RW |
-
-
- | 83 |
- R1575H3 |
- BXD48 |
- 65 |
- M |
- 3 |
- 4 |
- 0.05 |
- 4.577 |
- 55.78 |
- 0.466 |
- 0.514 |
- 0.019 |
- 1.59 |
- 0.9 |
- UTM RW |
-
-
- | 84 |
- R2521H1 |
- BXD50 |
- 63 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.109 |
- 57.28 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.23 |
- 0.78 |
- UTM RW |
-
-
- | 85 |
- R1944H2 |
- BXD50 |
- 81 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.546 |
- 63.39 |
- 0.495 |
- 0.485 |
- 0.02 |
- 0.9 |
- 1.57 |
- UTM RW |
-
-
- | 86 |
- R2331H1 |
- BXD51 |
- 66 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.534 |
- 44.42 |
- 0.501 |
- 0.481 |
- 0.017 |
- 1.2 |
- 0.9 |
- UTM RW |
-
-
- | 87 |
- R1582H1 |
- BXD51 |
- 71 |
- M |
- 6 |
- 4 |
- 0.03 |
- 2.92 |
- 47.87 |
- 0.489 |
- 0.491 |
- 0.02 |
- 1.36 |
- 0.75 |
- UTM RW |
-
-
- | 88 |
- R2680H1 |
- BXD55 |
- 65 |
- M |
- 7 |
- 3 |
- 0.07 |
- 1.707 |
- 79.75 |
- 0.503 |
- 0.48 |
- 0.017 |
- 1.91 |
- 1.05 |
- UTM RW |
-
-
- | 89 |
- R1331H1 |
- BXD60 |
- 60 |
- F |
- 4 |
- 3 |
- 0.01 |
- 2.867 |
- 50.33 |
- 0.492 |
- 0.487 |
- 0.021 |
- 1.34 |
- 0.78 |
- UTM RW |
-
-
- | 90 |
- R1281H2 |
- BXD60 |
- 59 |
- M |
- 1 |
- 3 |
- 0 |
- 2.39 |
- 58.44 |
- 0.511 |
- 0.469 |
- 0.02 |
- 0.94 |
- 1.2 |
- UTM RW |
-
-
- | 91 |
- R2667H1 |
- BXD61 |
- 70 |
- F |
- 7 |
- 4 |
- 0.03 |
- 3.36 |
- 59.04 |
- 0.495 |
- 0.488 |
- 0.018 |
- 1.16 |
- 0.76 |
- UTM RW |
-
-
- | 92 |
- R1856H2 |
- BXD61 |
- 94 |
- M |
- 1 |
- 2 |
- 0 |
- 3.502 |
- 49.6 |
- 0.501 |
- 0.48 |
- 0.019 |
- 0.96 |
- 1.3 |
- UTM RW |
-
-
- | 93 |
- R1246H1 |
- BXD62 |
- 54 |
- F |
- 1 |
- 4 |
- 0.02 |
- 3.405 |
- 51.47 |
- 0.511 |
- 0.471 |
- 0.018 |
- 1.14 |
- 1.34 |
- UTM RW |
-
-
- | 94 |
- R1585H2 |
- BXD62 |
- 64 |
- M |
- 6 |
- 4 |
- 0.01 |
- 3.156 |
- 55.77 |
- 0.518 |
- 0.464 |
- 0.018 |
- 1.43 |
- 0.82 |
- UTM RW |
-
-
- | 95 |
- R1945H1 |
- BXD63 |
- 107 |
- F |
- 1 |
- 3 |
- 0.02 |
- 2.811 |
- 52.65 |
- 0.522 |
- 0.459 |
- 0.019 |
- 1.05 |
- 1.36 |
- UTM RW |
-
-
- | 96 |
- R2093H3 |
- BXD63 |
- 70 |
- M |
- 6 |
- 3 |
- 0.02 |
- 3.894 |
- 42.85 |
- 0.503 |
- 0.477 |
- 0.019 |
- 1.29 |
- 1.01 |
- UTM RW |
-
-
- | 97 |
- R2062H2 |
- BXD64 |
- 65 |
- F |
- 1 |
- 3 |
- 0.05 |
- 3.795 |
- 78.48 |
- 0.513 |
- 0.468 |
- 0.019 |
- 0.98 |
- 1.43 |
- UTM RW |
-
-
- | 98 |
- R2061H1 |
- BXD64 |
- 87 |
- M |
- 3 |
- 4 |
- 0.01 |
- 3.536 |
- 61.57 |
- 0.477 |
- 0.504 |
- 0.019 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 99 |
- R2054H2 |
- BXD65 |
- 55 |
- F |
- 1 |
- 2 |
- 0.03 |
- 3.159 |
- 80.96 |
- 0.48 |
- 0.502 |
- 0.018 |
- 1.09 |
- 1.24 |
- UTM RW |
-
-
- | 100 |
- R2056H2 |
- BXD65 |
- 89 |
- M |
- 6 |
- 2 |
- 0 |
- 2.836 |
- 59.6 |
- 0.504 |
- 0.477 |
- 0.019 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 101 |
- R1941H2 |
- BXD66 |
- 78 |
- F |
- 1 |
- 4 |
- 0.01 |
- 2.734 |
- 50.93 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.18 |
- 1.29 |
- UTM RW |
-
-
- | 102 |
- R1949H2 |
- BXD66 |
- 96 |
- M |
- 4 |
- 2 |
- 0.04 |
- 2.828 |
- 51.27 |
- 0.474 |
- 0.508 |
- 0.019 |
- 2.05 |
- 1.12 |
- UTM RW |
-
-
- | 103 |
- R2060H1 |
- BXD67 |
- 54 |
- F |
- 6 |
- 3 |
- 0.01 |
- 2.561 |
- 43.88 |
- 0.502 |
- 0.479 |
- 0.02 |
- 1.7 |
- 0.84 |
- UTM RW |
-
-
- | 104 |
- R2052H1 |
- BXD67 |
- 61 |
- M |
- 1 |
- 4 |
- 0.01 |
- 3.161 |
- 43.23 |
- 0.521 |
- 0.46 |
- 0.018 |
- 1.09 |
- 1.31 |
- UTM RW |
-
-
- | 105 |
- R2074H1 |
- BXD68 |
- 60 |
- F |
- 5 |
- 3 |
- 0.02 |
- 6.528 |
- 49.62 |
- 0.479 |
- 0.502 |
- 0.019 |
- 1.48 |
- 0.83 |
- UTM RW |
-
-
- | 106 |
- R1928H1 |
- BXD68 |
- 72 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.404 |
- 48.28 |
- 0.521 |
- 0.459 |
- 0.02 |
- 1.3 |
- 0.74 |
- UTM RW |
-
-
- | 107 |
- R1439H3 |
- BXD69 |
- 60 |
- F |
- 2 |
- 3 |
- 0.02 |
- 2.463 |
- 59.14 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.31 |
- 0.78 |
- UTM RW |
-
-
- | 108 |
- R1559H1 |
- BXD69 |
- 64 |
- M |
- 3 |
- 3 |
- 0.03 |
- 2.987 |
- 67.74 |
- 0.486 |
- 0.496 |
- 0.017 |
- 1.38 |
- 0.8 |
- UTM RW |
-
-
- | 109 |
- R2134H1 |
- BXD70 |
- 64 |
- F |
- 5 |
- 2 |
- 0.02 |
- 2.148 |
- 58.64 |
- 0.532 |
- 0.45 |
- 0.019 |
- 1.4 |
- 0.85 |
- UTM RW |
-
-
- | 110 |
- R2063H1 |
- BXD70 |
- 55 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.481 |
- 55.32 |
- 0.513 |
- 0.469 |
- 0.018 |
- 1.28 |
- 0.71 |
- UTM RW |
-
-
- | 111 |
- R1277H1 |
- BXD73 |
- 60 |
- F |
- 4 |
- 2 |
- 0.01 |
- 2.576 |
- 62.45 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.35 |
- 0.79 |
- UTM RW |
-
-
- | 112 |
- R1443H2 |
- BXD73 |
- 76 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.312 |
- 64.34 |
- 0.499 |
- 0.481 |
- 0.02 |
- 1.48 |
- 0.77 |
- UTM RW |
-
-
- | 113 |
- R2055H2 |
- BXD74 |
- 79 |
- M |
- 2 |
- 3 |
- 0.01 |
- 2.576 |
- 56.84 |
- 0.509 |
- 0.473 |
- 0.018 |
- 1.46 |
- 0.88 |
- UTM RW |
-
-
- | 114 |
- R2316H1 |
- BXD74 |
- 193 |
- M |
- 5 |
- 2 |
- 0.01 |
- 3.457 |
- 55.35 |
- 0.508 |
- 0.471 |
- 0.02 |
- 1.17 |
- 0.78 |
- UTM RW |
-
-
- | 115 |
- R1871H1 |
- BXD75 |
- 61 |
- F |
- 2 |
- 3 |
- 0.04 |
- 1.723 |
- 56.4 |
- 0.53 |
- 0.451 |
- 0.019 |
- 1.3 |
- 0.76 |
- UTM RW |
-
-
- | 116 |
- R1844H2 |
- BXD75 |
- 90 |
- M |
- 3 |
- 4 |
- 0.01 |
- 1.934 |
- 56.23 |
- 0.52 |
- 0.461 |
- 0.019 |
- 1.62 |
- 0.86 |
- UTM RW |
-
-
- | 117 |
- R1948H2 |
- BXD76 |
- 81 |
- F |
- 2 |
- 3 |
- 0.01 |
- 1.507 |
- 68.85 |
- 0.553 |
- 0.428 |
- 0.02 |
- 1.3 |
- 0.75 |
- UTM RW |
-
-
- | 118 |
- R2094H1 |
- BXD76 |
- 61 |
- M |
- 5 |
- 4 |
- 0.01 |
- 3.299 |
- 42.69 |
- 0.519 |
- 0.462 |
- 0.019 |
- 1.39 |
- 0.88 |
- UTM RW |
-
-
- | 119 |
- R2262H1 |
- BXD77 |
- 62 |
- F |
- 3 |
- 4 |
- 0.02 |
- 4.317 |
- 47.16 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.32 |
- 0.74 |
- UTM RW |
-
-
- | 120 |
- R1423H1 |
- BXD77 |
- 62 |
- M |
- 2 |
- 3 |
- 0.02 |
- 3.071 |
- 54.15 |
- 0.51 |
- 0.471 |
- 0.019 |
- 1.26 |
- 0.74 |
- UTM RW |
-
-
- | 121 |
- R1947H1 |
- BXD79 |
- 108 |
- F |
- 2 |
- 2 |
- 0.01 |
- 2.599 |
- 51.52 |
- 0.524 |
- 0.457 |
- 0.019 |
- 1.35 |
- 0.74 |
- UTM RW |
-
-
- | 122 |
- R2092H1 |
- BXD79 |
- 86 |
- M |
- 5 |
- 4 |
- 0.06 |
- 3.735 |
- 42.25 |
- 0.514 |
- 0.468 |
- 0.018 |
- 2.94 |
- 1.06 |
- UTM RW |
-
-
- | 123 |
- R1880H1 |
- BXD80 |
- 68 |
- F |
- 5 |
- 3 |
- 0.06 |
- 4.855 |
- 42.22 |
- 0.501 |
- 0.481 |
- 0.018 |
- 2.17 |
- 1.36 |
- UTM RW |
-
-
- | 124 |
- R1881H2 |
- BXD80 |
- 68 |
- M |
- 2 |
- 3 |
- 0.02 |
- 2.073 |
- 48.93 |
- 0.524 |
- 0.458 |
- 0.019 |
- 1.34 |
- 0.83 |
- UTM RW |
-
-
- | 125 |
- R2075H1 |
- BXD83 |
- 60 |
- F |
- 2 |
- 3 |
- 0.01 |
- 2.454 |
- 55.1 |
- 0.502 |
- 0.48 |
- 0.018 |
- 1.27 |
- 0.77 |
- UTM RW |
-
-
- | 126 |
- R2076H2 |
- BXD83 |
- 60 |
- M |
- 6 |
- 3 |
- 0.03 |
- 2.624 |
- 55.65 |
- 0.495 |
- 0.488 |
- 0.018 |
- 2.21 |
- 0.94 |
- UTM RW |
-
-
- | 127 |
- R2077H2 |
- BXD84 |
- 62 |
- F |
- 6 |
- 2 |
- 0 |
- 2.1 |
- 71.87 |
- 0.522 |
- 0.459 |
- 0.018 |
- 1.68 |
- 0.81 |
- UTM RW |
-
-
- | 128 |
- R2135H3 |
- BXD84 |
- 75 |
- M |
- 2 |
- 2 |
- 0.01 |
- 2.467 |
- 64.46 |
- 0.505 |
- 0.476 |
- 0.019 |
- 1.2 |
- 0.74 |
- UTM RW |
-
-
- | 129 |
- R1473H1 |
- BXD85 |
- 79 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.384 |
- 55.34 |
- 0.478 |
- 0.502 |
- 0.02 |
- 1.24 |
- 0.77 |
- UTM RW |
-
-
- | 130 |
- R1474H1 |
- BXD85 |
- 57 |
- M |
- 1 |
- 3 |
- 0.01 |
- 2.831 |
- 55.24 |
- 0.522 |
- 0.461 |
- 0.018 |
- 1.04 |
- 1.29 |
- UTM RW |
-
-
- | 131 |
- R1597H1 |
- BXD85 |
- 86 |
- M |
- 4 |
- 4 |
- 0.09 |
- 2.028 |
- 53.95 |
- 0.487 |
- 0.492 |
- 0.021 |
- 1.28 |
- 0.83 |
- UTM RW |
-
-
- | 132 |
- R1415H1 |
- BXD86 |
- 77 |
- F |
- 4 |
- 3 |
- 0.02 |
- 2.525 |
- 53.16 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.66 |
- 0.91 |
- UTM RW |
-
-
- | 133 |
- R2669H2 |
- BXD87 |
- 63 |
- F |
- 7 |
- 3 |
- 0.07 |
- 2.61 |
- 57.59 |
- 0.513 |
- 0.47 |
- 0.018 |
- 1.6 |
- 0.91 |
- UTM RW |
-
-
- | 134 |
- R1710H1 |
- BXD87 |
- 84 |
- M |
- 2 |
- 4 |
- 0.01 |
- 2.697 |
- 56.4 |
- 0.512 |
- 0.469 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 135 |
- R1872H2 |
- BXD89 |
- 90 |
- F |
- 2 |
- 2 |
- 0.02 |
- 3.013 |
- 63.53 |
- 0.492 |
- 0.488 |
- 0.021 |
- 1.22 |
- 0.72 |
- UTM RW |
-
-
- | 136 |
- R1850H3 |
- BXD89 |
- 82 |
- M |
- 4 |
- 4 |
- 0.03 |
- 2.736 |
- 44.89 |
- 0.498 |
- 0.483 |
- 0.019 |
- 1.5 |
- 0.83 |
- UTM RW |
-
-
- | 137 |
- R2058H1 |
- BXD90 |
- 61 |
- F |
- 2 |
- 3 |
- 0.01 |
- 3.389 |
- 48.05 |
- 0.502 |
- 0.478 |
- 0.02 |
- 1.53 |
- 0.76 |
- UTM RW |
-
-
- | 138 |
- R1600H2 |
- BXD90 |
- 74 |
- M |
- 7 |
- 4 |
- 0.03 |
- 3.261 |
- 51.31 |
- 0.517 |
- 0.465 |
- 0.018 |
- 1.16 |
- 0.75 |
- Glenn |
-
-
- | 139 |
- R1301H2 |
- BXD92 |
- 58 |
- F |
- 2 |
- 3 |
- 0.02 |
- 3.543 |
- 41.97 |
- 0.522 |
- 0.46 |
- 0.018 |
- 1.5 |
- 0.79 |
- UTM RW |
-
-
- | 140 |
- R1309H1 |
- BXD92 |
- 59 |
- M |
- 4 |
- 3 |
- 0.05 |
- 1.655 |
- 66.34 |
- 0.498 |
- 0.481 |
- 0.021 |
- 1.52 |
- 0.82 |
- UTM RW |
-
-
- | 141 |
- R2057H1 |
- BXD93 |
- 92 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.033 |
- 44.41 |
- 0.509 |
- 0.471 |
- 0.02 |
- 1.22 |
- 0.78 |
- UTM RW |
-
-
- | 142 |
- R2059H1 |
- BXD93 |
- 58 |
- M |
- 1 |
- 3 |
- 0 |
- 3.058 |
- 60.29 |
- 0.493 |
- 0.488 |
- 0.019 |
- 1.18 |
- 1.37 |
- UTM RW |
-
-
- | 143 |
- R2313H1 |
- BXD94 |
- 59 |
- F |
- 3 |
- 3 |
- 0 |
- 3.091 |
- 59.45 |
- 0.487 |
- 0.495 |
- 0.018 |
- 1.34 |
- 0.73 |
- UTM RW |
-
-
- | 144 |
- R1915H1 |
- BXD96 |
- 65 |
- F |
- 5 |
- 2 |
- 0.04 |
- 5.145 |
- 46.19 |
- 0.502 |
- 0.481 |
- 0.017 |
- 1.37 |
- 0.74 |
- UTM RW |
-
-
- | 145 |
- R1846H2 |
- BXD96 |
- 63 |
- M |
- 1 |
- 3 |
- 0 |
- 3.159 |
- 55.85 |
- 0.487 |
- 0.493 |
- 0.02 |
- 0.92 |
- 1.26 |
- UTM RW |
-
-
- | 146 |
- R2648H1 |
- BXD97 |
- 74 |
- F |
- 7 |
- 4 |
- 0.02 |
- 1.664 |
- 82.08 |
- 0.518 |
- 0.464 |
- 0.019 |
- 1.4 |
- 0.78 |
- UTM RW |
-
-
- | 147 |
- R1927H2 |
- BXD97 |
- 67 |
- M |
- 1 |
- 3 |
- 0.04 |
- 2.622 |
- 57.81 |
- 0.539 |
- 0.444 |
- 0.017 |
- 1.45 |
- 1.32 |
- UTM RW |
-
-
- | 148 |
- R1942H1 |
- BXD98 |
- 62 |
- F |
- 5 |
- 3 |
- 0.04 |
- 3.104 |
- 48.42 |
- 0.528 |
- 0.454 |
- 0.019 |
- 2.22 |
- 1.08 |
- UTM RW |
-
-
- | 149 |
- R1943H2 |
- BXD98 |
- 62 |
- M |
- 3 |
- 3 |
- 0.02 |
- 4.04 |
- 56.85 |
- 0.484 |
- 0.497 |
- 0.019 |
- 1.18 |
- 0.76 |
- UTM RW |
-
-
- | 150 |
- R2197H1 |
- BXD99 |
- 70 |
- F |
- 3 |
- 3 |
- 0.02 |
- 4.288 |
- 51.75 |
- 0.49 |
- 0.492 |
- 0.018 |
- 1.35 |
- 0.81 |
- UTM RW |
-
-
- | 151 |
- R2315H1 |
- BXD99 |
- 84 |
- M |
- 5 |
- 2 |
- 0.03 |
- 6.036 |
- 43.05 |
- 0.484 |
- 0.497 |
- 0.018 |
- 1.7 |
- 0.96 |
- UTM RW |
-
-
- | 152 |
- R2038H3 |
- C3H/HeJ |
- 63 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.671 |
- 66.74 |
- 0.476 |
- 0.504 |
- 0.02 |
- 1.41 |
- 0.77 |
- UTM RW |
-
-
- | 153 |
- R2039H1 |
- C3H/HeJ |
- 63 |
- M |
- 5 |
- 3 |
- 0.1 |
- 3.384 |
- 44.15 |
- 0.528 |
- 0.454 |
- 0.017 |
- 2.16 |
- 0.88 |
- UTM RW |
-
-
- | 154 |
- R2137H1 |
- C57BL/6ByJ |
- 55 |
- F |
- 5 |
- 3 |
- 0.02 |
- 4.746 |
- 47.01 |
- 0.488 |
- 0.493 |
- 0.018 |
- 1.23 |
- 0.79 |
- JAX |
-
-
- | 155 |
- R2673H1 |
- C57BL/6ByJ |
- 55 |
- M |
- 7 |
- 3 |
- 0.08 |
- 1.842 |
- 67.69 |
- 0.514 |
- 0.469 |
- 0.017 |
- 1.75 |
- 0.78 |
- JAX |
-
-
- | 156 |
- R1361H1 |
- C57BL/6J |
- 69 |
- F |
- 6 |
- 4 |
- 0.01 |
- 3.058 |
- 51.87 |
- 0.477 |
- 0.503 |
- 0.02 |
- 1.67 |
- 0.76 |
- UTM RW |
-
-
- | 157 |
- R2041H2 |
- C57BL/6J |
- 65 |
- M |
- 1 |
- 4 |
- 0.04 |
- 3.341 |
- 49.26 |
- 0.527 |
- 0.456 |
- 0.018 |
- 1.14 |
- 1.45 |
- UTM RW |
-
-
- | 158 |
- R1449H2 |
- C57BL/6J |
- 71 |
- M |
- 5 |
- 3 |
- 0.09 |
- 3.592 |
- 44.32 |
- 0.47 |
- 0.51 |
- 0.02 |
- 1.68 |
- 0.77 |
- UTM DG |
-
-
- | 159 |
- R2619H1 |
- CAST/Ei |
- 64 |
- F |
- 5 |
- 3 |
- 0.14 |
- 4.077 |
- 51.87 |
- 0.455 |
- 0.528 |
- 0.018 |
- 2.74 |
- 1.2 |
- JAX |
-
-
- | 160 |
- R2116H1 |
- CXB1 |
- 55 |
- F |
- 3 |
- 3 |
- 0.07 |
- 5.792 |
- 51.59 |
- 0.459 |
- 0.521 |
- 0.02 |
- 1.17 |
- 0.8 |
- JAX |
-
-
- | 161 |
- R2096H1 |
- CXB1 |
- 55 |
- M |
- 4 |
- 2 |
- 0.01 |
- 3.435 |
- 53.78 |
- 0.495 |
- 0.485 |
- 0.02 |
- 1.22 |
- 0.79 |
- JAX |
-
-
- | 162 |
- R2124H1 |
- CXB10 |
- 53 |
- F |
- 4 |
- 2 |
- 0.11 |
- 4.867 |
- 39.88 |
- 0.451 |
- 0.528 |
- 0.02 |
- 1.55 |
- 0.8 |
- JAX |
-
-
- | 163 |
- R2671H1 |
- CXB10 |
- 53 |
- M |
- 7 |
- 3 |
- 0.09 |
- 2.348 |
- 71.45 |
- 0.488 |
- 0.494 |
- 0.018 |
- 2.2 |
- 1.14 |
- JAX |
-
-
- | 164 |
- R2125H1 |
- CXB11 |
- 58 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.256 |
- 54.95 |
- 0.461 |
- 0.519 |
- 0.02 |
- 1.46 |
- 0.77 |
- JAX |
-
-
- | 165 |
- R2128H1 |
- CXB11 |
- 58 |
- M |
- 4 |
- 2 |
- 0.06 |
- 4.986 |
- 54.13 |
- 0.465 |
- 0.515 |
- 0.02 |
- 1.11 |
- 0.83 |
- JAX |
-
-
- | 166 |
- R2126H1 |
- CXB12 |
- 47 |
- F |
- 4 |
- 3 |
- 0.11 |
- 3.935 |
- 54.11 |
- 0.469 |
- 0.511 |
- 0.021 |
- 1.5 |
- 0.79 |
- JAX |
-
-
- | 167 |
- R2109H1 |
- CXB12 |
- 47 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.518 |
- 49.26 |
- 0.488 |
- 0.492 |
- 0.02 |
- 1.23 |
- 0.77 |
- JAX |
-
-
- | 168 |
- R2672H1 |
- CXB13 |
- 49 |
- F |
- 7 |
- 3 |
- 0.03 |
- 1.722 |
- 79.52 |
- 0.516 |
- 0.465 |
- 0.019 |
- 1.64 |
- 0.75 |
- JAX |
-
-
- | 169 |
- R2110H1 |
- CXB13 |
- 56 |
- M |
- 4 |
- 3 |
- 0.21 |
- 3.478 |
- 48.08 |
- 0.461 |
- 0.517 |
- 0.022 |
- 1.21 |
- 0.78 |
- JAX |
-
-
- | 170 |
- R2117H2 |
- CXB2 |
- 62 |
- F |
- 4 |
- 2 |
- 0.04 |
- 3.39 |
- 45.97 |
- 0.533 |
- 0.45 |
- 0.017 |
- 2.05 |
- 0.89 |
- JAX |
-
-
- | 171 |
- R2098H1 |
- CXB2 |
- 68 |
- M |
- 3 |
- 3 |
- 0.02 |
- 2.572 |
- 54.22 |
- 0.496 |
- 0.485 |
- 0.019 |
- 1.38 |
- 0.86 |
- JAX |
-
-
- | 172 |
- R2118H1 |
- CXB3 |
- 47 |
- F |
- 3 |
- 3 |
- 0.03 |
- 3.646 |
- 63.16 |
- 0.478 |
- 0.503 |
- 0.019 |
- 1.22 |
- 0.77 |
- JAX |
-
-
- | 173 |
- R2100H1 |
- CXB3 |
- 47 |
- M |
- 4 |
- 3 |
- 0.02 |
- 5.76 |
- 51.38 |
- 0.48 |
- 0.503 |
- 0.017 |
- 1.24 |
- 0.81 |
- JAX |
-
-
- | 174 |
- R2119H1 |
- CXB4 |
- 58 |
- F |
- 4 |
- 3 |
- 0.02 |
- 3.897 |
- 49.21 |
- 0.488 |
- 0.494 |
- 0.018 |
- 1.31 |
- 0.79 |
- JAX |
-
-
- | 175 |
- R2101H1 |
- CXB4 |
- 58 |
- M |
- 3 |
- 3 |
- 0.13 |
- 7.372 |
- 53.77 |
- 0.433 |
- 0.548 |
- 0.019 |
- 1.2 |
- 0.97 |
- JAX |
-
-
- | 176 |
- R2505H1 |
- CXB5 |
- 80 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.83 |
- 49.6 |
- 0.499 |
- 0.48 |
- 0.02 |
- 1.33 |
- 0.76 |
- UTM RW |
-
-
- | 177 |
- R2131H1 |
- CXB5 |
- 42 |
- M |
- 4 |
- 3 |
- 0.1 |
- 5.577 |
- 51.15 |
- 0.434 |
- 0.547 |
- 0.019 |
- 1.7 |
- 0.89 |
- JAX |
-
-
- | 178 |
- R0129H2 |
- CXB5 |
- 70 |
- M |
- 3 |
- 3 |
- 0.07 |
- 4.829 |
- 45.42 |
- 0.488 |
- 0.493 |
- 0.019 |
- 1.23 |
- 0.83 |
- UTM RW |
-
-
- | 179 |
- R2676H1 |
- CXB6 |
- 47 |
- F |
- 7 |
- 2 |
- 0.05 |
- 2.146 |
- 62.51 |
- 0.507 |
- 0.475 |
- 0.018 |
- 1.52 |
- 0.78 |
- JAX |
-
-
- | 180 |
- R2102H1 |
- CXB6 |
- 49 |
- M |
- 4 |
- 3 |
- 0.07 |
- 5.148 |
- 51.63 |
- 0.453 |
- 0.529 |
- 0.018 |
- 1.43 |
- 0.87 |
- JAX |
-
-
- | 181 |
- R2121H1 |
- CXB7 |
- 63 |
- F |
- 4 |
- 2 |
- 0.06 |
- 4.904 |
- 48.71 |
- 0.464 |
- 0.517 |
- 0.019 |
- 1.19 |
- 0.92 |
- JAX |
-
-
- | 182 |
- R2104H2 |
- CXB7 |
- 58 |
- M |
- 3 |
- 2 |
- 0.06 |
- 3.389 |
- 48.79 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.74 |
- 1.48 |
- JAX |
-
-
- | 183 |
- R2122H1 |
- CXB8 |
- 54 |
- F |
- 3 |
- 3 |
- 0.04 |
- 4.128 |
- 59.77 |
- 0.451 |
- 0.529 |
- 0.02 |
- 1.12 |
- 0.76 |
- JAX |
-
-
- | 184 |
- R2105H1 |
- CXB8 |
- 41 |
- M |
- 4 |
- 3 |
- 0.16 |
- 3.146 |
- 61.04 |
- 0.451 |
- 0.53 |
- 0.019 |
- 1.34 |
- 0.84 |
- JAX |
-
-
- | 185 |
- R2123H1 |
- CXB9 |
- 54 |
- F |
- 3 |
- 3 |
- 0.08 |
- 5.708 |
- 55.94 |
- 0.438 |
- 0.543 |
- 0.019 |
- 1.32 |
- 0.78 |
- JAX |
-
-
- | 186 |
- R2106H1 |
- CXB9 |
- 54 |
- M |
- 4 |
- 3 |
- 0.06 |
- 5.868 |
- 46.55 |
- 0.469 |
- 0.512 |
- 0.019 |
- 1.18 |
- 0.82 |
- JAX |
-
-
- | 187 |
- R2045H2 |
- D2B6F1 |
- 65 |
- F |
- 1 |
- 2 |
- 0.01 |
- 4.403 |
- 47.99 |
- 0.497 |
- 0.485 |
- 0.018 |
- 1.09 |
- 1.53 |
- UTM RW |
-
-
- | 188 |
- R1595H2 |
- D2B6F1 |
- 63 |
- F |
- 5 |
- 3 |
- 0.06 |
- 2.579 |
- 58.49 |
- 0.506 |
- 0.475 |
- 0.019 |
- 2.49 |
- 1.21 |
- UTM RW |
-
-
- | 189 |
- R1551H1 |
- D2B6F1 |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 2.62 |
- 53.76 |
- 0.506 |
- 0.476 |
- 0.018 |
- 1.37 |
- 0.76 |
- UTM RW |
-
-
- | 190 |
- R1290H2 |
- DBA/2J |
- 63 |
- F |
- 7 |
- 2 |
- 0.04 |
- 2.576 |
- 59.6 |
- 0.513 |
- 0.468 |
- 0.018 |
- 1.3 |
- 0.78 |
- JAX |
-
-
- | 191 |
- R1468H1 |
- DBA/2J |
- 64 |
- F |
- 5 |
- 3 |
- 0.03 |
- 2.929 |
- 53.8 |
- 0.515 |
- 0.465 |
- 0.019 |
- 1.28 |
- 0.79 |
- UTM RW |
-
-
- | 192 |
- R1683H1 |
- KK/HIJ |
- 72 |
- F |
- 6 |
- 3 |
- 0.02 |
- 3.919 |
- 54.23 |
- 0.491 |
- 0.489 |
- 0.02 |
- 1.31 |
- 0.83 |
- JAX |
-
-
- | 193 |
- R1687H3 |
- KK/HIJ |
- 72 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.888 |
- 40.86 |
- 0.499 |
- 0.483 |
- 0.019 |
- 1.86 |
- 0.88 |
- JAX |
-
-
- | 194 |
- R2046H1 |
- LG/J |
- 63 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.822 |
- 59.18 |
- 0.514 |
- 0.468 |
- 0.018 |
- 1.68 |
- 0.8 |
- UTM RW |
-
-
- | 195 |
- R2047H2 |
- LG/J |
- 63 |
- M |
- 6 |
- 3 |
- 0.07 |
- 2.038 |
- 60.34 |
- 0.509 |
- 0.471 |
- 0.02 |
- 2.16 |
- 0.95 |
- UTM RW |
-
-
- | 196 |
- R2048H1 |
- NOD/LtJ |
- 77 |
- F |
- 6 |
- 2 |
- 0.14 |
- 4.045 |
- 50.21 |
- 0.489 |
- 0.49 |
- 0.021 |
- 2.89 |
- 0.95 |
- UTM RW |
-
-
- | 197 |
- R2049H3 |
- NOD/LtJ |
- 76 |
- M |
- 5 |
- 3 |
- 0.1 |
- 2.328 |
- 52.78 |
- 0.519 |
- 0.462 |
- 0.019 |
- 3.09 |
- 1.35 |
- UTM RW |
-
-
- | 198 |
- R2200H1 |
- NZO/HlLtJ |
- 62 |
- F |
- 5 |
- 2 |
- 0.03 |
- 2.648 |
- 54.29 |
- 0.543 |
- 0.438 |
- 0.019 |
- 1.27 |
- 0.8 |
- JAX |
-
-
- | 199 |
- R2350H1 |
- NZO/HlLtJ |
- 96 |
- M |
- 6 |
- 2 |
- 0.19 |
- 2.391 |
- 50.52 |
- 0.518 |
- 0.463 |
- 0.02 |
- 3.71 |
- 2.21 |
- JAX |
-
-
- | 200 |
- R2677H1 |
- PWD/PhJ |
- 65 |
- F |
- 7 |
- 2 |
- 0.12 |
- 2.764 |
- 65.49 |
- 0.462 |
- 0.52 |
- 0.018 |
- 1.89 |
- 1.16 |
- UTM RW |
-
-
- | 201 |
- R2051H3 |
- PWD/PhJ |
- 64 |
- M |
- 5 |
- 3 |
- 0.07 |
- 3.266 |
- 51.5 |
- 0.475 |
- 0.506 |
- 0.019 |
- 2.8 |
- 1.01 |
- UTM RW |
-
-
- | 202 |
- R2322H1 |
- PWK/PhJ |
- 63 |
- F |
- 5 |
- 2 |
- 0.09 |
- 2.94 |
- 54.91 |
- 0.511 |
- 0.47 |
- 0.019 |
- 2.32 |
- 1.02 |
- JAX |
-
-
- | 203 |
- R2349H1 |
- PWK/PhJ |
- 83 |
- M |
- 6 |
- 2 |
- 0.15 |
- 3.306 |
- 54.93 |
- 0.459 |
- 0.522 |
- 0.019 |
- 4.65 |
- 1.45 |
- JAX |
-
-
- | 204 |
- R2198H2 |
- WSB/EiJ |
- 58 |
- F |
- 6 |
- 1 |
- 0.02 |
- 2.922 |
- 57.97 |
- 0.502 |
- 0.479 |
- 0.019 |
- 1.44 |
- 0.76 |
- JAX |
-
-
- | 205 |
- R2199H1 |
- WSB/EiJ |
- 58 |
- M |
- 5 |
- 3 |
- 0.04 |
- 3.171 |
- 54.95 |
- 0.475 |
- 0.505 |
- 0.02 |
- 1.32 |
- 0.81 |
- JAX |
-
-
-
- |
-
-
-
-
-
-Downloading all data:
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/HC_M2_1206_R/experiment-design.rtf b/general/datasets/HC_M2_1206_R/experiment-design.rtf
deleted file mode 100644
index 23a857d..0000000
--- a/general/datasets/HC_M2_1206_R/experiment-design.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Sample Processing: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80 deg. C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. While all strains were orginally represented by matched male and female samples, not all data sets passed the final quality control steps. Seventy-seven of 97 strains are represented by pairs or (rarely) trios of arrays. The first and last samples are technical replicates of a B6D2F1 hippocampal pool (aliquots R1291H3 and R1291H4).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in six groups over a three month period (May 2005 to August 2005). Each group consists of 32 to 34 arrays. Sex, strain, and strain type (BXD, CXB, and MDP) were interleaved among groups to ensure reasonable balance and to minimize group-by-strain statistical confounds in group normalization. The two independent samples from a single strain were always run in different groups. All arrays were processed using a single protocol by a single operator, Shirlean Goodwin.
-
-All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4 deg C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.
-
diff --git a/general/datasets/HC_M2_1206_R/notes.rtf b/general/datasets/HC_M2_1206_R/notes.rtf
deleted file mode 100644
index f5f115c..0000000
--- a/general/datasets/HC_M2_1206_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW and Rupert Overall on January 30, 2007.
diff --git a/general/datasets/HC_M2_1206_R/platform.rtf b/general/datasets/HC_M2_1206_R/platform.rtf
deleted file mode 100644
index 4b34d93..0000000
--- a/general/datasets/HC_M2_1206_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 16,578 NCBI Reference Sequences. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The annotation used in this data set assigns probes to probe sets based on their alignment to Entrez GeneID sequences using the latest Mouse Genome assembly (Build 36, mm8).
-
diff --git a/general/datasets/HC_M2_1206_R/processing.rtf b/general/datasets/HC_M2_1206_R/processing.rtf
deleted file mode 100644
index bfc45d4..0000000
--- a/general/datasets/HC_M2_1206_R/processing.rtf
+++ /dev/null
@@ -1,41 +0,0 @@
-Harshlight was used to examine the image quality of the array (CEL files). Bad areas (bubbles, scratches, blemishes) of arrays were masked.
-First pass data quality control: Affymetrix GCOS provides useful array quality control data including:
-
-
- - The scale factor used to normalize mean probe intensity. This averaged 3.3 for the 179 arrays that passed and 6.2 for arrays that were excluded. The scale factor is not a particular critical parameter.
- - The average background level. Values averaged 54.8 units for the data sets that passed and 55.8 for data sets that were excluded. This factor is not important for quality control.
- - The percentage of probe sets that are associated with good signal ("present" calls). This averaged 50% for the 179 data sets that passed and 42% for those that failed. Values for passing data sets extended from 43% to 55%. This is a particularly important criterion.
- - The 3':5' signal ratios of actin and Gapdh. Values for passing data sets averaged 1.5 for actin and 1.0 for Gapdh. Values for excluded data sets averaged 12.9 for actin and 9.6 for Gapdh. This is a highly discriminative QC criterion, although one must keep in mind that only two transcripts are being tested. Sequence variation among strains (particularly wild derivative strains such as CAST/Ei) may affect these ratios.
-
-
-The second step in our post-processing QC involves a count of the number of probe sets in each array that are more than 2 standard deviations (z score units) from the mean across the entire 206 array data sets. This was the most important criterion used to eliminate "bad" data sets. All 206 arrays were processed togther using standard RMA and PDNN methods. The count and percentage of probe sets in each array that were beyond the 2 z theshold was computed. Using the RMA transform the average percentage of probe sets beyond the 2 z threshold for the 179 arrays that finally passed of QC procedure was 1.76% (median of 1.18%). In contrast the 2 z percentage was more than 10-fold higher (mean of 22.4% and median 20.2%) for those arrays that were excluded. This method is not very senstive to the transformation method that is used. Using the PDNN transform the average percent of probe sets exceeding was 1.31% for good arrays and was 22.6% for those that were excluded. In our opinion, this 2 z criterion is the most useful criterion for the final decision of whether or not to include arrays, although again, allowances need to be made for wild strains that one expects to be different from the majority of conventional inbred strains. For examploe, if a data set has excellent characteristics on all of the Affymetrix GCOS metrics listed above, but generates a high 2 z percentage, then one whould include the ssample if one can verify that there are no problems in sample and data set identification.
-
-The entire procedure can be reapplied once the initial outlier data sets have been eliminated to detect any remaining outlier data sets.
-
-DataDesk was used to examine the statistical quality of the of the probe level (CEL) data after step 5 below. DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes). We do not yet understand the technical origins of reaction classes. The number of probes that contribute to the definition of reaction classes is quite small (<10% of all probes). We have categorized all arrays in this data set into one of 5 reaction classes. These have then been treated as if they were separate batches. Probes in these data type "batches" have been aligned to a common mean as described below.
-
-Probe set data with custom CDF mapping: The original Affymetrix annotation often has multiple probe sets mapping to a single gene. Some of these redundancies represent alternative splicing products, while some reflect our changing knowledge of the mouse genome. This transformation uses an annotation generated by the Microarray Group at the University of Michigan where each probe has been checked against the latest mouse genome build (Build 36, mm8) and then collated into a new probe set based on its placement within a gene sequence in the Entrez Gene database. The following quote from their Brainarray website explains in more detail:
-
-Affymetrix GeneChips were based on the best UniGene clustering and genomic sequence information available at the time of chip design. Due to the significant increase in EST/cDNA/Genomic sequence information in the last couple of years, some oligonucleotide probes in these old designs can now be assigned to different genes/transcripts based on the current UniGene clustering and genome annotation. While Affymetrix's current annotation system maps each probe set to the latest UniGene build every couple of months, it does not deal with situations where a subset of oligonucleotide probes in a probe set may be assigned to another gene or more than one gene based on the current UniGene clustering and genome annotation. In addition, a significant portion of UniGene clusters can be represented by more than one oligonucleotide probe set on GeneChips but there is no standard approach to deal with signals from different probe sets representing the same gene. It will be highly desirable to have one probe set-one target relationship for the interpretation of the data.
-
-
- - CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
- - Probe level data from the CEL files were transformed with the RMA transform using the Mm74Bv2_Mm_ENTREZG_8 (Version 8) CDF mapping. Data transformation was done in Bioconductor using the
affy.justRMA() package and the Mm430_Mm_ENTREZG file as contained in the Bioconductor repository. This yields only one unique probeset for each Entrez GeneID.
- - We computed the Z scores for each array.
- - The arithmetic mean of the values for the set of microarrays for each strain was computed.
-
- - The Z scores were recomputed for each strain.
- - We multiplied all Z scores by 2.
- - We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.
-
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. XY plots of probe expression and signal variance were also examined. Probe level array data sets were organized into reaction groups. Arrays with probe data that were not homogeneous when compared to other arrays were flagged.
-
-Probe set level QC: The final normalized individual array data were evaluated for outliers. This involved counting the number of times that the probe set value for a particular array was beyond two standard deviations of the mean. This outlier analysis was carried out using the PDNN, RMA and MAS5 transforms and outliers across different levels of expression. Arrays that were associated with an average of more than 8% outlier probe sets across all transforms and at all expression levels were eliminated. In contrast, most other arrays generated fewer than 5% outliers.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
diff --git a/general/datasets/HC_M2_1206_R/summary.rtf b/general/datasets/HC_M2_1206_R/summary.rtf
deleted file mode 100644
index 60da981..0000000
--- a/general/datasets/HC_M2_1206_R/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-PRELIMINARY: The June 2006 Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a set of diverse inbred strains, and two reciprocal F1 hybrids.
-
-The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
-
-Samples were processed using a total of 205 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 179 passed stringent quality control and error checking . This particular data set was processed using the RMA protocol using a custom CDF. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/HC_M2_1206_R/tissue.rtf b/general/datasets/HC_M2_1206_R/tissue.rtf
deleted file mode 100644
index 2bb700d..0000000
--- a/general/datasets/HC_M2_1206_R/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thanks Muriel Davission for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria.
-
-A pool of dissected tissue typically from six hippocampi and three naive adults of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Two-hundred and one RNA samples were extracted at UTHSC by Zhiping Jia, four samples by Shuhua Qi (R2331H1, R2332H1, P2350H1, R2349H1), and one by Siming Shou (R0129H2).
-
-A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days; see Table 1 below).
-
diff --git a/general/datasets/HC_U_0303_M/acknowledgment.rtf b/general/datasets/HC_U_0303_M/acknowledgment.rtf
deleted file mode 100644
index e520fa9..0000000
--- a/general/datasets/HC_U_0303_M/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Cell and samples were generated by Leonid V. Bystrykh, Ellen Weersing, Bert Dontje, Gerald de Haan, Department of Stem Cell Biology, University of Groningen, the Netherlands. RNA amplification and array processing were carried out by Michael Cooke, John Hogenesch, Andrew Su, and colleagues at GNF.
-
-Data normalization and conversion for WebQTL were handled by Robert Williams, Kenneth Manly, Jintao Wang, and Yanhua Qu at UTHSC and Roswell Park Cancer Institute.
-
diff --git a/general/datasets/HC_U_0303_M/cases.rtf b/general/datasets/HC_U_0303_M/cases.rtf
deleted file mode 100644
index 03bd3fe..0000000
--- a/general/datasets/HC_U_0303_M/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-BXD recombinant inbred mice were purchased from The Jackson Laboratory and upon arrival were housed under clean conventional conditions in the Central Animal Facility of the University of Groningen, Netherlands. We used female mice between 3 and 6 months old.
-
-Stem cells (described below) were isolated from pooled bone marrow obtained from three BXD animals per strain. Pooled RNA samples were split in two aliquots and each sample was independently amplified and hybridized to the U74Av2 array (3 mice x 2 arrays).
-
diff --git a/general/datasets/HC_U_0303_M/experiment-design.rtf b/general/datasets/HC_U_0303_M/experiment-design.rtf
deleted file mode 100644
index 5b0ad70..0000000
--- a/general/datasets/HC_U_0303_M/experiment-design.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-About amplification and hybridization:
-
-Total RNA was quantified using RiboGreen and split into equal aliquots of approximately 10 ng, representing RNA from approximately 10,000 cells, and labeled using a total of three rounds of RNA amplification, exactly as described previously (Scherer et al. 2003). Labeled cRNA was fractionated and hybridized to the U74Av2 microarray following standard Affymetrix protocols.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/HC_U_0303_M/notes.rtf b/general/datasets/HC_U_0303_M/notes.rtf
deleted file mode 100644
index c9da172..0000000
--- a/general/datasets/HC_U_0303_M/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Information about this text file:
-
-
-This text file originally generated by GdH and RWW, March 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/HC_U_0303_M/processing.rtf b/general/datasets/HC_U_0303_M/processing.rtf
deleted file mode 100644
index 6de5cfc..0000000
--- a/general/datasets/HC_U_0303_M/processing.rtf
+++ /dev/null
@@ -1,30 +0,0 @@
-About data processing:
-
-Probe (cell) level data from the CEL file: These CEL values produced by MAS 5 are the 75% quantiles from a set of 36 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefore represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/HC_U_0303_M/summary.rtf b/general/datasets/HC_U_0303_M/summary.rtf
deleted file mode 100644
index f04a43e..0000000
--- a/general/datasets/HC_U_0303_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is now superceeded by the March 2004 RMA data set. The original March 2003 data freeze provides estimates of mRNA expression in hematopoietic stem cells (HSC) from adult female BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the Genomics Institute of the Norvartis Research Foundations (GNF) and by de Haan and colleagues at the University of Groningen. Samples from 22 strains were hybridized to 44 arrays in a single batch. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between data sets (HSC and other tissues), the MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units.
diff --git a/general/datasets/HC_U_0303_M/tissue.rtf b/general/datasets/HC_U_0303_M/tissue.rtf
deleted file mode 100644
index cde2ac6..0000000
--- a/general/datasets/HC_U_0303_M/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Bone marrow cells were flushed from the femurs and tibiae of three mice and pooled. After standard erythrocyte lysis nucleated cells were incubated with normal rat serum for 15 min at 4 degrees Celsius. Subsequently cells were stained with a panel of biotinylated lineage-specific antibodies (murine progenitor enrichment cocktail, containing anti-CD5, anti-CD45R, anti-CD11b, anti-TER119, anti-Gr-1, and anti-7-4, Stem Cell Technologies, Vancouver, Canada), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Cells were washed twice, and incubated for 30 minutes with streptavidin-PerCP (Pharmingen). After two washes cells were resuspended in PBS with 1% BSA, and purified using a MoFlo flow cytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PerCP-fluorescence intensity. Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. A small aliquot of each sample of purified cells was functionally tested for stem cell activity by directly depositing single cells in a cobblestone area forming cell assay. The remainder of the cells was immediately collected in RNA lysis buffer. Total RNA was isolated using StrataPrep Total RNA Microprep kit (Stratagene) as described by the manufacturer. RNA pellets were resolved in 500 microliters absolute ethanol, and sent on dry ice by courrier to GNF, La Jolla, CA.
-
diff --git a/general/datasets/HC_U_0304_R/acknowledgment.rtf b/general/datasets/HC_U_0304_R/acknowledgment.rtf
deleted file mode 100644
index e520fa9..0000000
--- a/general/datasets/HC_U_0304_R/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Cell and samples were generated by Leonid V. Bystrykh, Ellen Weersing, Bert Dontje, Gerald de Haan, Department of Stem Cell Biology, University of Groningen, the Netherlands. RNA amplification and array processing were carried out by Michael Cooke, John Hogenesch, Andrew Su, and colleagues at GNF.
-
-Data normalization and conversion for WebQTL were handled by Robert Williams, Kenneth Manly, Jintao Wang, and Yanhua Qu at UTHSC and Roswell Park Cancer Institute.
-
diff --git a/general/datasets/HC_U_0304_R/cases.rtf b/general/datasets/HC_U_0304_R/cases.rtf
deleted file mode 100644
index 03bd3fe..0000000
--- a/general/datasets/HC_U_0304_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-BXD recombinant inbred mice were purchased from The Jackson Laboratory and upon arrival were housed under clean conventional conditions in the Central Animal Facility of the University of Groningen, Netherlands. We used female mice between 3 and 6 months old.
-
-Stem cells (described below) were isolated from pooled bone marrow obtained from three BXD animals per strain. Pooled RNA samples were split in two aliquots and each sample was independently amplified and hybridized to the U74Av2 array (3 mice x 2 arrays).
-
diff --git a/general/datasets/HC_U_0304_R/experiment-design.rtf b/general/datasets/HC_U_0304_R/experiment-design.rtf
deleted file mode 100644
index 5b0ad70..0000000
--- a/general/datasets/HC_U_0304_R/experiment-design.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-About amplification and hybridization:
-
-Total RNA was quantified using RiboGreen and split into equal aliquots of approximately 10 ng, representing RNA from approximately 10,000 cells, and labeled using a total of three rounds of RNA amplification, exactly as described previously (Scherer et al. 2003). Labeled cRNA was fractionated and hybridized to the U74Av2 microarray following standard Affymetrix protocols.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/HC_U_0304_R/notes.rtf b/general/datasets/HC_U_0304_R/notes.rtf
deleted file mode 100644
index c9da172..0000000
--- a/general/datasets/HC_U_0304_R/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Information about this text file:
-
-
-This text file originally generated by GdH and RWW, March 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/HC_U_0304_R/processing.rtf b/general/datasets/HC_U_0304_R/processing.rtf
deleted file mode 100644
index 6de5cfc..0000000
--- a/general/datasets/HC_U_0304_R/processing.rtf
+++ /dev/null
@@ -1,30 +0,0 @@
-About data processing:
-
-Probe (cell) level data from the CEL file: These CEL values produced by MAS 5 are the 75% quantiles from a set of 36 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefore represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/HC_U_0304_R/summary.rtf b/general/datasets/HC_U_0304_R/summary.rtf
deleted file mode 100644
index f04a43e..0000000
--- a/general/datasets/HC_U_0304_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is now superceeded by the March 2004 RMA data set. The original March 2003 data freeze provides estimates of mRNA expression in hematopoietic stem cells (HSC) from adult female BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the Genomics Institute of the Norvartis Research Foundations (GNF) and by de Haan and colleagues at the University of Groningen. Samples from 22 strains were hybridized to 44 arrays in a single batch. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between data sets (HSC and other tissues), the MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units.
diff --git a/general/datasets/HC_U_0304_R/tissue.rtf b/general/datasets/HC_U_0304_R/tissue.rtf
deleted file mode 100644
index cde2ac6..0000000
--- a/general/datasets/HC_U_0304_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Bone marrow cells were flushed from the femurs and tibiae of three mice and pooled. After standard erythrocyte lysis nucleated cells were incubated with normal rat serum for 15 min at 4 degrees Celsius. Subsequently cells were stained with a panel of biotinylated lineage-specific antibodies (murine progenitor enrichment cocktail, containing anti-CD5, anti-CD45R, anti-CD11b, anti-TER119, anti-Gr-1, and anti-7-4, Stem Cell Technologies, Vancouver, Canada), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Cells were washed twice, and incubated for 30 minutes with streptavidin-PerCP (Pharmingen). After two washes cells were resuspended in PBS with 1% BSA, and purified using a MoFlo flow cytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PerCP-fluorescence intensity. Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. A small aliquot of each sample of purified cells was functionally tested for stem cell activity by directly depositing single cells in a cobblestone area forming cell assay. The remainder of the cells was immediately collected in RNA lysis buffer. Total RNA was isolated using StrataPrep Total RNA Microprep kit (Stratagene) as described by the manufacturer. RNA pellets were resolved in 500 microliters absolute ethanol, and sent on dry ice by courrier to GNF, La Jolla, CA.
-
diff --git a/general/datasets/HC_U_0903_M/acknowledgment.rtf b/general/datasets/HC_U_0903_M/acknowledgment.rtf
deleted file mode 100644
index e520fa9..0000000
--- a/general/datasets/HC_U_0903_M/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Cell and samples were generated by Leonid V. Bystrykh, Ellen Weersing, Bert Dontje, Gerald de Haan, Department of Stem Cell Biology, University of Groningen, the Netherlands. RNA amplification and array processing were carried out by Michael Cooke, John Hogenesch, Andrew Su, and colleagues at GNF.
-
-Data normalization and conversion for WebQTL were handled by Robert Williams, Kenneth Manly, Jintao Wang, and Yanhua Qu at UTHSC and Roswell Park Cancer Institute.
-
diff --git a/general/datasets/HC_U_0903_M/cases.rtf b/general/datasets/HC_U_0903_M/cases.rtf
deleted file mode 100644
index 03bd3fe..0000000
--- a/general/datasets/HC_U_0903_M/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-BXD recombinant inbred mice were purchased from The Jackson Laboratory and upon arrival were housed under clean conventional conditions in the Central Animal Facility of the University of Groningen, Netherlands. We used female mice between 3 and 6 months old.
-
-Stem cells (described below) were isolated from pooled bone marrow obtained from three BXD animals per strain. Pooled RNA samples were split in two aliquots and each sample was independently amplified and hybridized to the U74Av2 array (3 mice x 2 arrays).
-
diff --git a/general/datasets/HC_U_0903_M/experiment-design.rtf b/general/datasets/HC_U_0903_M/experiment-design.rtf
deleted file mode 100644
index 5b0ad70..0000000
--- a/general/datasets/HC_U_0903_M/experiment-design.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-About amplification and hybridization:
-
-Total RNA was quantified using RiboGreen and split into equal aliquots of approximately 10 ng, representing RNA from approximately 10,000 cells, and labeled using a total of three rounds of RNA amplification, exactly as described previously (Scherer et al. 2003). Labeled cRNA was fractionated and hybridized to the U74Av2 microarray following standard Affymetrix protocols.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see http://genome.ucsc.edu/). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/HC_U_0903_M/notes.rtf b/general/datasets/HC_U_0903_M/notes.rtf
deleted file mode 100644
index c9da172..0000000
--- a/general/datasets/HC_U_0903_M/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Information about this text file:
-
-
-This text file originally generated by GdH and RWW, March 2003. Updated by RWW, October 30, 2004.
-
diff --git a/general/datasets/HC_U_0903_M/processing.rtf b/general/datasets/HC_U_0903_M/processing.rtf
deleted file mode 100644
index 6de5cfc..0000000
--- a/general/datasets/HC_U_0903_M/processing.rtf
+++ /dev/null
@@ -1,30 +0,0 @@
-About data processing:
-
-Probe (cell) level data from the CEL file: These CEL values produced by MAS 5 are the 75% quantiles from a set of 36 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefore represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the array probe set names:
-
-
-Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:
-
-
- - f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
- - s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
- - g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
- - r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
- - i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
- - st (sense target): Designates a sense target; almost always generated in error.
-
-
-Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.
-
diff --git a/general/datasets/HC_U_0903_M/summary.rtf b/general/datasets/HC_U_0903_M/summary.rtf
deleted file mode 100644
index f04a43e..0000000
--- a/general/datasets/HC_U_0903_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is now superceeded by the March 2004 RMA data set. The original March 2003 data freeze provides estimates of mRNA expression in hematopoietic stem cells (HSC) from adult female BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the Genomics Institute of the Norvartis Research Foundations (GNF) and by de Haan and colleagues at the University of Groningen. Samples from 22 strains were hybridized to 44 arrays in a single batch. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between data sets (HSC and other tissues), the MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units.
diff --git a/general/datasets/HC_U_0903_M/tissue.rtf b/general/datasets/HC_U_0903_M/tissue.rtf
deleted file mode 100644
index cde2ac6..0000000
--- a/general/datasets/HC_U_0903_M/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Bone marrow cells were flushed from the femurs and tibiae of three mice and pooled. After standard erythrocyte lysis nucleated cells were incubated with normal rat serum for 15 min at 4 degrees Celsius. Subsequently cells were stained with a panel of biotinylated lineage-specific antibodies (murine progenitor enrichment cocktail, containing anti-CD5, anti-CD45R, anti-CD11b, anti-TER119, anti-Gr-1, and anti-7-4, Stem Cell Technologies, Vancouver, Canada), FITC-anti-Sca-1 and APC-anti-c-kit (Pharmingen). Cells were washed twice, and incubated for 30 minutes with streptavidin-PerCP (Pharmingen). After two washes cells were resuspended in PBS with 1% BSA, and purified using a MoFlo flow cytometer. The lineage-depleted bone marrow cell population was defined as the 5% cells showing least PerCP-fluorescence intensity. Stem cell yield across all BXD samples varied from 16,000 to 118,000 Lin-Sca-1+ c-kit+ cells. A small aliquot of each sample of purified cells was functionally tested for stem cell activity by directly depositing single cells in a cobblestone area forming cell assay. The remainder of the cells was immediately collected in RNA lysis buffer. Total RNA was isolated using StrataPrep Total RNA Microprep kit (Stratagene) as described by the manufacturer. RNA pellets were resolved in 500 microliters absolute ethanol, and sent on dry ice by courrier to GNF, La Jolla, CA.
-
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/acknowledgment.rtf b/general/datasets/HEIONCvsCRetILM6_0911/acknowledgment.rtf
deleted file mode 100644
index a41ff76..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/acknowledgment.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The HEI Retinal Database is supported by National Eye Institute Grants:
-
-
-
-
- - R01EY017841 (Dr. Eldon E. Geisert, PI)
-
-
- - P030EY13080 (NEI Vision Core Grant), and
-
-
- - A Unrestricted Grand from Research to Prevent Blindness (Dr. Barrett Haik, PI)
-
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/cases.rtf b/general/datasets/HEIONCvsCRetILM6_0911/cases.rtf
deleted file mode 100644
index b37d700..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/cases.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 48 and maximum age is 118 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J.
-
-BXD strains:
-
-
- - The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s.
- - In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset.
- - The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set.
-
-
-
-
-What Makes the G2 HEI Retina Database different from the HEI Retina Database Examination of Gfap expression across all of the strains in the HEI Retinal Dataset, reveals that some strains express very high levels of Gfap relative to others. For example, BXD24 expresses Gfap at a 9-fold higher level, than BXD22. It has been established that BXD24 acquired a mutation in Cep290 that results in early onset photoreceptor degeneration (Chang et al., 2006). This degeneration results in reactive gliosis throughout the retina. In addition to BXD24, other BXD strains expressed very high levels of Gfap including: BXD32, BXD49, BXD70, BXD83 and BXD89. For the G2 dataset all of these strains with potential reactive gliosis were removed from the dataset.
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/experiment-design.rtf b/general/datasets/HEIONCvsCRetILM6_0911/experiment-design.rtf
deleted file mode 100644
index 4fff707..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/experiment-design.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Expression profiling by array
-
-We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.
-
-All normalization was performed by William E. Orr in the HEI Vision Core Facility
-
-
- - Computed the log base 2 of each raw signal value
- - Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
- - Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/notes.rtf b/general/datasets/HEIONCvsCRetILM6_0911/notes.rtf
deleted file mode 100644
index 13ff99a..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/platform.rtf b/general/datasets/HEIONCvsCRetILM6_0911/platform.rtf
deleted file mode 100644
index 2c52707..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina MouseWG-6 v2.0 arrays: The Illumina Sentrix Mouse-6 BeadChip uses 50-nucleotide probes to interrogate approximately 46,000 sequences from the mouse transcriptome. For each array, the RNA was pooled from two retinas.
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/processing.rtf b/general/datasets/HEIONCvsCRetILM6_0911/processing.rtf
deleted file mode 100644
index 97cc2be..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/processing.rtf
+++ /dev/null
@@ -1,2654 +0,0 @@
-Values of all 45,281 probe sets in this data set range from a low of 6.25 (Rho GTPase activating protein 11A, Arhgap11a, probe ID ILMN_2747167) to a high of 18.08 (Ubiquitin B, Ubb, probe ID ILMN_2516699). This corresponds to 11.83 units or a 1 to 3641 dynamic range of expression (2^11.83). We normalized raw signal values using Beadstudio’s rank invariant normalization algorithm. BXD62 was the strain used as the control group
-
-
-
-Sample Processing: Drs. Natalie E. Freeman-Anderson and Justin P. Templeton extracted the retinas from the mice and Dr. Natalie Freeman-Anderson processed all samples in the HEI Vision Core Facility. The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX) listed above. The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system. The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA. The cRNA for each sample was then hybridized to an Illumina Sentrix® Mouse-6-V2 BeadChip (Illumina, San Diego, CA)
-
-
-
-
-
-Quality control analysis of the raw image data was performed using the Illumina BeadStudio software. MIAME standards were used for all microarray data. Rank invariant normalization with BeadStudio software was used to calculate the data. Once this data was collected, the data was globally normalized across all samples using the formula 2 (z-score of log2 [intensity]) + 8.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.
-
-Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice
-
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain |
- Age |
- Sex |
- Source of Animal |
-
-
- | 1 |
- 121608_11-C57BL/6JcFA |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 2 |
- 121608_12-C57BL/6JcFB |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 3 |
- KA7444-C57BL/6JcMC |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 4 |
- KA7444-C57BL/6JcMD |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 5 |
- 31209.05-DBA2JcFA |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 6 |
- 31209.05-DBA2JcFB |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 7 |
- 121608_13-DBA/2JcMA |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 8 |
- 121608_14-DBA/2JcMB |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 9 |
- KA7446-B6D2F1cFA |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 10 |
- KA7446-B6D2F1cFB |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 11 |
- KA7446-B6D2F1cMC |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 12 |
- KA7446-B6D2F1cMD |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 13 |
- KA7466-D2B6F1cFA |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 14 |
- KA7466-D2B6F1cFB |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 15 |
- KA7466-D2B6F1cMC |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 16 |
- KA7466-D2B6F1cMD |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 17 |
- 82609.13-1cFA |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 18 |
- 82609.14-1cFB |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 19 |
- KA7389-1cFA |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 20 |
- KA7389-1cFB |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 21 |
- KA7389-1cMC |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 22 |
- KA7389-1cMD |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 23 |
- KA7300-2cFA |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 24 |
- KA7300-2cFB |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 25 |
- 100909.01-2cMA |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 26 |
- 100909.02-2cMB |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 27 |
- KA6699-5cFA |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 28 |
- KA6699-5cFB |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 29 |
- KA6699-5cFC |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 30 |
- KA6699-5cFD |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 31 |
- 82609.09-5cMA |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 32 |
- 82609.1-5cMB |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 33 |
- KA6763-6cFA |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 34 |
- KA6763-6cFB |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 35 |
- 81209.06-6cMA |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 36 |
- 81209.07-6cMB |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 37 |
- 82609.07-8cFA |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 38 |
- 82609.08-8cFB |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 39 |
- JAX-8cMA |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 40 |
- JAX-8cMB |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 41 |
- KA7289-9cFA |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 42 |
- KA7289-9cFB |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 43 |
- KA7289-9cMC |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 44 |
- KA7289-9cMD |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 45 |
- JAX-11cFA |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 46 |
- JAX-11cFB |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 47 |
- JAX-11cMC |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 48 |
- JAX-11cMD |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 49 |
- 40209.07-12cFA |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 50 |
- 40209.08-12cFB |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 51 |
- 011309.01-12cMA |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 52 |
- 011309.02-12cMB |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 53 |
- KA7286-13cFA |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 54 |
- KA7286-13cFB |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 55 |
- KA7286-13cMC |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 56 |
- KA7286-13cMD |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 57 |
- KA7302-14cFA |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 58 |
- KA7302-14cFB |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 59 |
- 100909.05-14cMA |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 60 |
- 100909.06-14cMB |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 61 |
- KA7288-15cFA |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 62 |
- KA7288-15cFB |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 63 |
- KA7288-15cMC |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 64 |
- KA7288-15cMD |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 65 |
- 062509.01-16cFA |
- BXD16 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 66 |
- KA7267-16cMA |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 67 |
- KA7267-16cMB |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 68 |
- KA6686-18cFB |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 69 |
- KA6686-18cFC |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 70 |
- KA6686-18cME |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 71 |
- KA6686-18cMF |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 72 |
- KA6676-19cFB |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 73 |
- KA6676-19cFC |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 74 |
- KA6676-19cME |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 75 |
- KA6676-19cMF |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 76 |
- 060409.05-20cFA |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- 060409.06-20cFB |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 78 |
- 021909.03-20cMA |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 79 |
- 021909.04-20cMB |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 80 |
- 82609.02-21cFC |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 81 |
- 82609.03-21cFD |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 82 |
- 121709.01-21cMA |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 83 |
- 121709.02-21cMB |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 84 |
- 121709.03-22cFA |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 85 |
- 121709.04-22cFB |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 86 |
- 092308_03-22cMA |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 87 |
- 092308_04-22cMB |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 88 |
- 80409.01-24AcFA |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 89 |
- 080409_02_24AcFB |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 90 |
- 82609.26-24AcFC |
- BXD24A |
- 64 |
- F |
- UTHSC RW |
-
-
- | 91 |
- 81209.03-24AcMC |
- BXD24A |
- 62 |
- M |
- UTHSC RW |
-
-
- | 92 |
- KA6678-24cFA |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 93 |
- KA6678-24cFB |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 94 |
- KA6678-24cME |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 95 |
- KA6678-24cMF |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- 060409.07-27cFA |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 97 |
- 060409.08-27cFB |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 98 |
- 80409.03-27cMA |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 99 |
- 80409.04-27cMB |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 100 |
- JAX-28cFA |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 101 |
- JAX-28cFB |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 102 |
- JAX-28cMC |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 103 |
- JAX-28cMD |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 104 |
- 82609.11-29cFA |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 105 |
- 82609.12-29cFB |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 106 |
- 82609.04-29cMA |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 107 |
- 82609.05-29cMB |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 108 |
- JAX-31cMB |
- BXD 31 |
- 56 |
- M |
- JAX |
-
-
- | 109 |
- JAX-31cFC |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 110 |
- JAX-31cFD |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 111 |
- 011309.03-32cFA |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 112 |
- 011309.04-32cFB |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 113 |
- KA7318-32cFC |
- BXD32 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 114 |
- KA7319-32cMA |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 115 |
- KA7319-32cMB |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 116 |
- 100909.07-33cFA |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 117 |
- 100909.08-33cFB |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 118 |
- 022609.01-33cMA |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 119 |
- 022609.02-33cMB |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 120 |
- KA7416-34cFA |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 121 |
- KA7416-34cFB |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 122 |
- KA6321-34cMA |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 123 |
- KA6321-34cMB |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 124 |
- 060409.01-36cFA |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 125 |
- 060409.02-36cFB |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 126 |
- 060409.03-36cMC |
- BXD36 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 127 |
- KA6702-38cFA |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 128 |
- KA6702-38cFB |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 129 |
- 82609.24-38cFA |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 130 |
- 82609.25-38cFB |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 131 |
- 100909.03-38cMA |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 132 |
- 100909.04-38cMB |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 133 |
- 022609.05-39cFA |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 134 |
- 022609.06-39cFB |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 135 |
- 31209.01-39cMC |
- BXD39 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 136 |
- 92409.01-40cFA |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 137 |
- 92409.02-40cFB |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 138 |
- KA6173-40cMA |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 139 |
- KA6173-40cMB |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 140 |
- KA6173-40cMC |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 141 |
- 091809.01-42cFA |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 142 |
- 091809.02-42cFB |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 143 |
- 021909.01-42cFA |
- BXD42 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 144 |
- 011309.06-42cMA |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 145 |
- 011309.07-42cMB |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- 110408_02-43cFA |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 147 |
- 110408_03-43cFB |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 148 |
- KA6158-43cMA |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 149 |
- KA6158-43cMB |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 150 |
- 100308_01-44cFA |
- BXD44 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 151 |
- 102208_02-44cMD |
- BXD44 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 152 |
- 103009.03-45cFA |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 153 |
- 103009.04-45cFB |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 154 |
- 022609.03-45cFA |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 155 |
- 022609.04-45cFB |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 156 |
- 40309.05-45cMB |
- BXD45 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 157 |
- 40209.05-48cFB |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 158 |
- 40209.06-48cFC |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 159 |
- 81209.04-48cMA |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 160 |
- 81209.05-48cMB |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 161 |
- 81209.08-49cFA |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 162 |
- 81209.09-49cFB |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 163 |
- 40209.01-49cMA |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 164 |
- 40209.02-49cMB |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 165 |
- 40209.03-49cMC |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 166 |
- KA737850cFA |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 167 |
- KA737850cFB |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 168 |
- 121908_01-50cMA |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 169 |
- 121908_02-50cMB |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 170 |
- 111208_01-51cFA |
- BXD51 |
- 99 |
- F |
- UTHSC RW |
-
-
- | 171 |
- 102208_03-51cMA |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 172 |
- 102208_04-51cMB |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 173 |
- 090208_14-53BcFA |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 174 |
- 090208_15-53BcFB |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 175 |
- 090208_16-53BcMC |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 176 |
- 090208_17-53BcMD |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 177 |
- 111208_05-55cFB |
- BXD55 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 178 |
- KA6183-55cMA |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 179 |
- KA6183-55cMB |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 180 |
- KA7362-56cFB |
- BXD 56 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 181 |
- KA6088-56cMA |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 182 |
- KA6088-56cMB |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 183 |
- KA6088-56cMC |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 184 |
- 21810.01-60RFA |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 185 |
- 21810.02-60RFB |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 186 |
- 21810.02-60RFC |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 187 |
- SQ7325-60cMA |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 188 |
- SQ7325-60cMB |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 189 |
- 092308_10-61cFA |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 190 |
- 092308_11-61cFB |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 191 |
- 31909.01-61cMA |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 192 |
- 31909.02-61cMB |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 193 |
- KA7462-62cFA |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 194 |
- KA7462-62cFB |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 195 |
- KA5996-62cMA |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 196 |
- KA5996-62cMB |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 197 |
- KA5996-62cMC |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 198 |
- 090309.01-63cFA |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 199 |
- 090309.02-63cFB |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 200 |
- 110609.01-63cMA |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 201 |
- 110609.02-63cMB |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 202 |
- 091809.03-65cFA |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 203 |
- 091809.04-65cFB |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 204 |
- 103009.01-65cMA |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 205 |
- 103009.02-65cMB |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 206 |
- 110408_05-66cFB |
- BXD66 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 207 |
- KA7165-66cMA |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 208 |
- KA7165-66cMB |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 209 |
- 90809.01-67cMA |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 210 |
- 90809.02-67cMB |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 211 |
- 110609.03-67cFA |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 212 |
- 110609.04-67cFB |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 213 |
- 120408_01-68cFA |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 214 |
- 120408_02-68cFB |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 215 |
- SQ7205-68cMA |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 216 |
- SQ7205-68cMB |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 217 |
- KA6316-68cMA |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 218 |
- KA6316-68cMB |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 219 |
- KA6316-68cMC |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 220 |
- KA76-69cFA |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 221 |
- KA76-69cFB |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 222 |
- KA6074-69cMA |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 223 |
- KA6074-69cMB |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 224 |
- 121608_01-70cFA |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 225 |
- 121608_02-70cFB |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 226 |
- KA7394-70cMA |
- BXD70 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 227 |
- 81209.08-70cMA |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 228 |
- 81209.09-70cMB |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 229 |
- 052809.01-71cFA |
- BXD71 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 230 |
- 060409.09-71cMA |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 231 |
- 060409.10-71cMB |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 232 |
- 40809.01-73cFA |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 233 |
- 40809.02-73cFB |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 234 |
- 111708_01-73cFA |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 235 |
- 111708_01-73cFB |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 236 |
- KA6164-73cMB |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 237 |
- KA6164-73cMC |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 238 |
- 82609.22-74cFA |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 239 |
- 82609.23-74cFB |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 240 |
- 82609.20-74cMA |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 241 |
- 82609.21-74cMB |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 242 |
- KA733675cFA |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 243 |
- KA733675cFB |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 244 |
- KA38-75cMB |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 245 |
- KA38-75cMC |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 246 |
- 41509.01-77cFA |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 247 |
- 41509.02-77cFB |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 248 |
- 41509.03-77cMC |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 249 |
- 41509.04-77cMD |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 250 |
- 121608_03-80cFA |
- BXD80 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 251 |
- 121608_05-80cMC |
- BXD80 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 252 |
- KA23-80cMC |
- BXD80 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 253 |
- KA7305-81cFA |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 254 |
- KA7305-81cFB |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 255 |
- KA7305-81cMD |
- BXD81 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 256 |
- 060409.11-83cFA |
- BXD83 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 257 |
- KA24-83cFA |
- BXD83 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 258 |
- 121608_07-83cMA |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 259 |
- 121608_08-83cMB |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 260 |
- KA24-83cMD |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 261 |
- 090409.05-84cFA |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 262 |
- 090409.06-84cFB |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 263 |
- KA6203-84cMA |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 264 |
- KA6203-84cMB |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 265 |
- 40309.02-85cFD |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 266 |
- 40309.03-85cFE |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 267 |
- 32609.01-85cMA |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 268 |
- 32609.02-85cMB |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 269 |
- 41509.05-86cFA |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 270 |
- 41509.06-86cFB |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 271 |
- KA6101-86cMA |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 272 |
- KA6101-86cMC |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 273 |
- 070909.02-87cFA |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 274 |
- 070909.03-87cFB |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 275 |
- KA7407-87cMA |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 276 |
- KA7407-87cMB |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 277 |
- 102208_05-89cFA |
- BXD89 |
- 82 |
- F |
- UTHSC RW |
-
-
- | 278 |
- KA5974-89cMA |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 279 |
- KA5974-89cMB |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 280 |
- 102208_06-89cMC |
- BXD89 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 281 |
- 72309.01-90cFA |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 282 |
- 72309.02-90cFB |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 283 |
- 090409.03-90cMA |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 284 |
- 090409.04-90cMB |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 285 |
- KA6094-92cMA |
- BXD92 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 286 |
- 020609.01-95cFA |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 287 |
- 020609.02-95cFB |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 288 |
- KA6181-95cMA |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 289 |
- KA6181-95cMB |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 290 |
- 31209.03-96cFA |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 291 |
- 31209.04-96cFB |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 292 |
- KA7246-96cMA |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 293 |
- KA7246-96cMB |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 294 |
- 81209.10-97cFA |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 295 |
- 81209.11-97cFB |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 296 |
- 81209.1-97cMA |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 297 |
- 81209.11-97cMB |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 298 |
- SQ7520-98cFA |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 299 |
- SQ7520-98cFB |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 300 |
- SQ7520-98cMC |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 301 |
- SQ7520-98cMD |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 302 |
- 82609.17-99cFA |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 303 |
- 82609.18-99cFB |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 304 |
- 81409.01-99cMA |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 305 |
- 81409.02-99cMB |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 306 |
- 121608_09-100cFA |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 307 |
- 121608_10-100cFB |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 308 |
- KA6001-100cMA |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 309 |
- KA6001-100cMB |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 310 |
- 81209.12-101cFA |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 311 |
- 81209.13-101cFB |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 312 |
- KA7296-101cMA |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 313 |
- KA7296-101cMB |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 314 |
- 92409.03-102cFA |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 315 |
- 92409.04-102cFB |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 316 |
- KA7380-102cMA |
- BXD102 |
- 115 |
- M |
- UTHSC RW |
-
-
- | 317 |
- 43009.01-103cFA |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 318 |
- 43009.02-103cFB |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 319 |
- KA79-103cFA |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 320 |
- KA79-103cFB |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 321 |
- KA79-103cMC |
- BXD103 |
- 48 |
- M |
- UTHSC RW |
-
-
- | 322 |
- 82609.15-103cMA |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 323 |
- 82609.16-103cMB |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 324 |
- 102909.01-BALBCcFA |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 325 |
- 102909.02-BALBCcFB |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 326 |
- 102909.03-BALBCcMA |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
- | 327 |
- 102909.04-BALBCcMB |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/summary.rtf b/general/datasets/HEIONCvsCRetILM6_0911/summary.rtf
deleted file mode 100644
index 44e98a7..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/summary.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-
-This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork.
-
-HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified.
-
-COMMENT on FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set.
-
-The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as BXD24/TyJ-Cep290/J, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243).
-
-The data are now open and available for analysis.
-
-Please cite: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text PDF or HTML
-
-This is rank invariant expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.25 to 18.08 (11.83 units), a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.
-
-The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842.
-
-The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.
-
-
-
-
-Other Related Publications
-
-
-
-
-
- - Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (Link)
- - Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674
- - Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (Link)
- - Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90.(Link)
-
-
-
-
-
-
-
-Other Data Sets Users of these mouse retina data may also find the following complementary resources useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
-
diff --git a/general/datasets/HEIONCvsCRetILM6_0911/tissue.rtf b/general/datasets/HEIONCvsCRetILM6_0911/tissue.rtf
deleted file mode 100644
index 766ab59..0000000
--- a/general/datasets/HEIONCvsCRetILM6_0911/tissue.rtf
+++ /dev/null
@@ -1,32 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RNAlater at room temperature. Two retinas from one mouse were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.
-
-
-
-Dissecting and preparing eyes for RNA extraction
-
-
-
-Retinas for RNA extraction were placed in RNA STAT-60 (Tel-Test Inc.) and processed per manufacturer’s instructions (in brief form below). Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
-
-
- - Homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue via syringe)
- - Allow the homogenate to stand for 5-10 min at room temperature
- - Add 0.2 ml of chloroform per 1 ml RNA STAT-60
- - Mix the sample vigorously for 15 sec and let the sample incubate at room temperature for 5-10 min
- - Centrifuge at 12,000 g for 1 hr at 4°C
- - Transfer the aqueous phase to a clean centrifuge tube
- - Add 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - Vortex and incubate the sample at -20°C for 1 hr or overnight
- - Centrifuge at 12,000 g for 1 hr
- - Remove the supernatant and wash the RNA pellet with 75% ethanol
- - Remove ethanol, let air dry (5-10 min)
- - Dissolve the pellet in 50 μl of nuclease free water.
-
-
-
-
diff --git a/general/datasets/HLCF_0311/acknowledgment.rtf b/general/datasets/HLCF_0311/acknowledgment.rtf
deleted file mode 100644
index 119d5f3..0000000
--- a/general/datasets/HLCF_0311/acknowledgment.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6:e107. Full text
-
-Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY (2010) Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res. 20:1020-36.
-
-GEO Series GSE9588
-Genotype data for 228 individuals who satisfy privacy policy have been submitted to the NCBI dbGaP (http://www.ncbi.nlm.nih.gov/gap/) under accession no. phs000253.v1.p1.]
diff --git a/general/datasets/HLCF_0311/experiment-design.rtf b/general/datasets/HLCF_0311/experiment-design.rtf
deleted file mode 100644
index cae776a..0000000
--- a/general/datasets/HLCF_0311/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.
diff --git a/general/datasets/HLCF_0311/platform.rtf b/general/datasets/HLCF_0311/platform.rtf
deleted file mode 100644
index 6687600..0000000
--- a/general/datasets/HLCF_0311/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Rosetta/Merck Human 44k 1.1 microarray
diff --git a/general/datasets/HLCF_0311/summary.rtf b/general/datasets/HLCF_0311/summary.rtf
deleted file mode 100644
index d0282cd..0000000
--- a/general/datasets/HLCF_0311/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-The Human Liver Cohort (HLC) study aimed to characterize the genetic architecture of gene expression in human liver using genotyping, gene expression profiling, and enzyme activity measurements of Cytochrom P450. The HLC was assembled from a total of 780 liver samples screened. These liver samples were acquired from caucasian individuals from three independant tissue collection centers. DNA samples were genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays representing a total of 782,476 unique single nucleotide polymorphisms (SNPs). Only the genotype data from those samples which were collected postmortem are accessible in dbGap. These 228 samples represent a subset of the 427 samples included in the Human Liver Cohort Publication (Schadt, Molony et al. 2008). RNA samples were profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Each of the liver samples was processed into cytosol and microsomes using a standard differential centrifugation method. The activities of nine P450 enzymes (CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, and 3A4) in isolated microsomes from 398 HLC liver samples were measured in the microsome preparations using probe substrate metabolism assays expressed as nmol/min/mg protein. Each was measured with a single substrate except for the CYP3A4 activity that was measured using two substrates, midazolam and testosterone.
-
-To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs. The relatively large sample size of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue. A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases.
-
-Clincal data was requested, but not provided by submitter. Keywords: eQTL
diff --git a/general/datasets/HLCM_0311/acknowledgment.rtf b/general/datasets/HLCM_0311/acknowledgment.rtf
deleted file mode 100644
index 119d5f3..0000000
--- a/general/datasets/HLCM_0311/acknowledgment.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6:e107. Full text
-
-Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY (2010) Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res. 20:1020-36.
-
-GEO Series GSE9588
-Genotype data for 228 individuals who satisfy privacy policy have been submitted to the NCBI dbGaP (http://www.ncbi.nlm.nih.gov/gap/) under accession no. phs000253.v1.p1.]
diff --git a/general/datasets/HLCM_0311/experiment-design.rtf b/general/datasets/HLCM_0311/experiment-design.rtf
deleted file mode 100644
index cae776a..0000000
--- a/general/datasets/HLCM_0311/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.
diff --git a/general/datasets/HLCM_0311/platform.rtf b/general/datasets/HLCM_0311/platform.rtf
deleted file mode 100644
index 6687600..0000000
--- a/general/datasets/HLCM_0311/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Rosetta/Merck Human 44k 1.1 microarray
diff --git a/general/datasets/HLCM_0311/summary.rtf b/general/datasets/HLCM_0311/summary.rtf
deleted file mode 100644
index d0282cd..0000000
--- a/general/datasets/HLCM_0311/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-The Human Liver Cohort (HLC) study aimed to characterize the genetic architecture of gene expression in human liver using genotyping, gene expression profiling, and enzyme activity measurements of Cytochrom P450. The HLC was assembled from a total of 780 liver samples screened. These liver samples were acquired from caucasian individuals from three independant tissue collection centers. DNA samples were genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays representing a total of 782,476 unique single nucleotide polymorphisms (SNPs). Only the genotype data from those samples which were collected postmortem are accessible in dbGap. These 228 samples represent a subset of the 427 samples included in the Human Liver Cohort Publication (Schadt, Molony et al. 2008). RNA samples were profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Each of the liver samples was processed into cytosol and microsomes using a standard differential centrifugation method. The activities of nine P450 enzymes (CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, and 3A4) in isolated microsomes from 398 HLC liver samples were measured in the microsome preparations using probe substrate metabolism assays expressed as nmol/min/mg protein. Each was measured with a single substrate except for the CYP3A4 activity that was measured using two substrates, midazolam and testosterone.
-
-To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs. The relatively large sample size of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue. A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases.
-
-Clincal data was requested, but not provided by submitter. Keywords: eQTL
diff --git a/general/datasets/HLC_0311/acknowledgment.rtf b/general/datasets/HLC_0311/acknowledgment.rtf
deleted file mode 100644
index 119d5f3..0000000
--- a/general/datasets/HLC_0311/acknowledgment.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6:e107. Full text
-
-Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY (2010) Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res. 20:1020-36.
-
-GEO Series GSE9588
-Genotype data for 228 individuals who satisfy privacy policy have been submitted to the NCBI dbGaP (http://www.ncbi.nlm.nih.gov/gap/) under accession no. phs000253.v1.p1.]
diff --git a/general/datasets/HLC_0311/experiment-design.rtf b/general/datasets/HLC_0311/experiment-design.rtf
deleted file mode 100644
index cae776a..0000000
--- a/general/datasets/HLC_0311/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.
diff --git a/general/datasets/HLC_0311/platform.rtf b/general/datasets/HLC_0311/platform.rtf
deleted file mode 100644
index 6687600..0000000
--- a/general/datasets/HLC_0311/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Rosetta/Merck Human 44k 1.1 microarray
diff --git a/general/datasets/HLC_0311/summary.rtf b/general/datasets/HLC_0311/summary.rtf
deleted file mode 100644
index d0282cd..0000000
--- a/general/datasets/HLC_0311/summary.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-The Human Liver Cohort (HLC) study aimed to characterize the genetic architecture of gene expression in human liver using genotyping, gene expression profiling, and enzyme activity measurements of Cytochrom P450. The HLC was assembled from a total of 780 liver samples screened. These liver samples were acquired from caucasian individuals from three independant tissue collection centers. DNA samples were genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays representing a total of 782,476 unique single nucleotide polymorphisms (SNPs). Only the genotype data from those samples which were collected postmortem are accessible in dbGap. These 228 samples represent a subset of the 427 samples included in the Human Liver Cohort Publication (Schadt, Molony et al. 2008). RNA samples were profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Each of the liver samples was processed into cytosol and microsomes using a standard differential centrifugation method. The activities of nine P450 enzymes (CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, and 3A4) in isolated microsomes from 398 HLC liver samples were measured in the microsome preparations using probe substrate metabolism assays expressed as nmol/min/mg protein. Each was measured with a single substrate except for the CYP3A4 activity that was measured using two substrates, midazolam and testosterone.
-
-To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs. The relatively large sample size of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue. A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases.
-
-Clincal data was requested, but not provided by submitter. Keywords: eQTL
diff --git a/general/datasets/HQFNeoc_0208_RankInv/acknowledgment.rtf b/general/datasets/HQFNeoc_0208_RankInv/acknowledgment.rtf
deleted file mode 100644
index 3135d79..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/acknowledgment.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Data were generated with funds to RW Williams, Glenn D. Rosen, Weikuan Gu, and Lu Lu from the High Q Foundation. Informatics support also provided by NIH NIAAA INIA grants to RWW and LL.
-
-
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
-
diff --git a/general/datasets/HQFNeoc_0208_RankInv/cases.rtf b/general/datasets/HQFNeoc_0208_RankInv/cases.rtf
deleted file mode 100644
index a98a7ff..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/cases.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 25 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 20 inbred strains and an F1 hybrid (B6D2F1). These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1
- This F1 hybrid was generated by crossing C57BL/6J with DBA/2J.
-
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HQFNeoc_0208_RankInv/experiment-design.rtf b/general/datasets/HQFNeoc_0208_RankInv/experiment-design.rtf
deleted file mode 100644
index 322268a..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/experiment-design.rtf
+++ /dev/null
@@ -1,937 +0,0 @@
-This data set consists arrays processed in XX groups over a XX month period (from Month Year to Month Year). Most groups consisted of XX samples. All arrays in this data set were processed using a single protocol by a single operator, NAME HERE. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
-
-Error checking
-
-
- - Checked for genotypes of BXD strains on all chromosomes using a battery of test Mendelian transcripts (transcripts with a Mendelian segregation pattern in the BXDs). Peak LRS of 260.2 for Prdx2 using Illumina probe ILM5340577. There are no errors in the strain assignment but there are possible genotyping errors, such as:
- Thumpd1 (ILM7510148) in BXD34 using marker rs6271956
- H2-D2 (ILM2190725) in BXD69 using marker gnf17.035.152
- Fcer1g (ILM5550020) in BXD100 using marker rs3722740 (incorrectly scored as a heterozygote).
-
- These genotype discrepancies are either due to recombination between the marker and the probe or a genotyping errors. (RWW, Feb 27, 2008)
- - Total count of transcripts/probes with LOD greater than 10 is 1564 with 52 BXD strains (BXD1 through BXD43 from (n = 27) from JAX, and BXD43 through 100 (n = 25) from UTHSC).
- - Sex assignment checked using Xist probe ILM104280446.
- All female samples: Strains BXD43, BXD42, BXD68, BXD77, NZW/LacJ, and NZO/HlLtJ
- All male samples: Strains BXD1, PWK/PhJ, BXD66, BXD97, BXD10, BXD75, BXD44, BXD89, BXD86, BXD80, BXD69
-
-
-Data Table 1:
-
-This table lists all arrays by order of strain (index) and includes data on strain, sex, slide ID and slide position (A through F).
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Sex |
- Slide ID |
- Slide
- Position |
-
-
- | 1 |
- B6D2F1 |
- F |
- 1848071018 |
- D |
-
-
- | 2 |
- B6D2F1 |
- M |
- 1957998076 |
- B |
-
-
- | 3 |
- C57BL/6J |
- F |
- 1957998083 |
- A |
-
-
- | 4 |
- C57BL/6J |
- M |
- 1833451021 |
- A |
-
-
- | 5 |
- DBA/2J |
- F |
- 1957998083 |
- C |
-
-
- | 6 |
- DBA/2J |
- M |
- 1833451021 |
- C |
-
-
- | 7 |
- BXD1 |
- M |
- 4051964030 |
- B |
-
-
- | 8 |
- BXD5 |
- F |
- 1736925307 |
- A |
-
-
- | 9 |
- BXD5 |
- M |
- 4051964028 |
- C |
-
-
- | 10 |
- BXD6 |
- F |
- 4051964028 |
- F |
-
-
- | 11 |
- BXD6 |
- M |
- 1736925307 |
- D |
-
-
- | 12 |
- BXD8 |
- F |
- 4060001025 |
- A |
-
-
- | 13 |
- BXD8 |
- M |
- 1957998111 |
- E |
-
-
- | 14 |
- BXD9 |
- F |
- 4060001025 |
- D |
-
-
- | 15 |
- BXD9 |
- M |
- 1736925359 |
- B |
-
-
- | 16 |
- BXD11 |
- F |
- 4051964030 |
- D |
-
-
- | 17 |
- BXD11 |
- M |
- 1848071017 |
- B |
-
-
- | 18 |
- BXD12 |
- F |
- 4051964030 |
- E |
-
-
- | 19 |
- BXD12 |
- M |
- 1848071017 |
- C |
-
-
- | 20 |
- BXD13 |
- F |
- 4051964030 |
- F |
-
-
- | 21 |
- BXD13 |
- M |
- 1848071017 |
- D |
-
-
- | 22 |
- BXD14 |
- F |
- 4051964065 |
- A |
-
-
- | 23 |
- BXD14 |
- M |
- 1848071017 |
- E |
-
-
- | 24 |
- BXD15 |
- F |
- 4051964065 |
- B |
-
-
- | 25 |
- BXD15 |
- M |
- 1848071017 |
- F |
-
-
- | 26 |
- BXD16 |
- F |
- 1848071024 |
- A |
-
-
- | 27 |
- BXD16 |
- M |
- 4051964065 |
- C |
-
-
- | 28 |
- BXD18 |
- F |
- 4051964065 |
- D |
-
-
- | 29 |
- BXD18 |
- M |
- 1848071024 |
- B |
-
-
- | 30 |
- BXD19 |
- F |
- 4051964065 |
- E |
-
-
- | 31 |
- BXD19 |
- M |
- 1848071024 |
- C |
-
-
- | 32 |
- BXD21 |
- F |
- 1848071024 |
- D |
-
-
- | 33 |
- BXD21 |
- M |
- 4051964065 |
- F |
-
-
- | 34 |
- BXD23 |
- F |
- 1848071024 |
- E |
-
-
- | 35 |
- BXD23 |
- M |
- 4051964022 |
- A |
-
-
- | 36 |
- BXD27 |
- F |
- 1848071024 |
- F |
-
-
- | 37 |
- BXD27 |
- M |
- 4051964022 |
- B |
-
-
- | 38 |
- BXD28 |
- F |
- 1848071025 |
- A |
-
-
- | 39 |
- BXD28 |
- M |
- 4051964022 |
- C |
-
-
- | 40 |
- BXD31 |
- F |
- 4051964022 |
- D |
-
-
- | 41 |
- BXD31 |
- M |
- 1848071025 |
- B |
-
-
- | 42 |
- BXD32 |
- F |
- 4051964022 |
- E |
-
-
- | 43 |
- BXD32 |
- M |
- 1848071025 |
- C |
-
-
- | 44 |
- BXD33 |
- F |
- 4051964022 |
- F |
-
-
- | 45 |
- BXD33 |
- M |
- 1848071025 |
- D |
-
-
- | 46 |
- BXD34 |
- F |
- 4051964023 |
- A |
-
-
- | 47 |
- BXD34 |
- M |
- 1848071025 |
- E |
-
-
- | 48 |
- BXD36 |
- F |
- 1848071025 |
- F |
-
-
- | 49 |
- BXD36 |
- M |
- 4051964023 |
- B |
-
-
- | 50 |
- BXD38 |
- F |
- 4051964023 |
- C |
-
-
- | 51 |
- BXD38 |
- M |
- 1957998101 |
- A |
-
-
- | 52 |
- BXD39 |
- F |
- 4051964023 |
- D |
-
-
- | 53 |
- BXD39 |
- M |
- 1957998101 |
- B |
-
-
- | 54 |
- BXD40 |
- F |
- 4051964023 |
- E |
-
-
- | 55 |
- BXD40 |
- M |
- 1957998101 |
- C |
-
-
- | 56 |
- BXD42 |
- F |
- 4060001026 |
- B |
-
-
- | 57 |
- BXD43 |
- F |
- 1957998101 |
- D |
-
-
- | 58 |
- BXD43 |
- F |
- 4051964023 |
- F |
-
-
- | 59 |
- BXD44 |
- F |
- 1957998101 |
- E |
-
-
- | 60 |
- BXD44 |
- M |
- 4051964028 |
- A |
-
-
- | 61 |
- BXD45 |
- F |
- 4051964028 |
- B |
-
-
- | 62 |
- BXD45 |
- M |
- 1957998101 |
- F |
-
-
- | 63 |
- BXD51 |
- F |
- 4051964028 |
- D |
-
-
- | 64 |
- BXD51 |
- M |
- 1736925307 |
- B |
-
-
- | 65 |
- BXD55 |
- F |
- 1736925307 |
- C |
-
-
- | 66 |
- BXD55 |
- M |
- 4051964028 |
- E |
-
-
- | 67 |
- BXD60 |
- F |
- 4060001014 |
- A |
-
-
- | 68 |
- BXD60 |
- M |
- 1736925307 |
- E |
-
-
- | 69 |
- BXD61 |
- F |
- 4060001014 |
- B |
-
-
- | 70 |
- BXD61 |
- M |
- 1736925307 |
- F |
-
-
- | 71 |
- BXD62 |
- F |
- 4060001014 |
- C |
-
-
- | 72 |
- BXD62 |
- M |
- 1957998111 |
- A |
-
-
- | 73 |
- BXD65 |
- F |
- 1957998111 |
- B |
-
-
- | 74 |
- BXD65 |
- M |
- 4060001014 |
- D |
-
-
- | 75 |
- BXD66 |
- M |
- 4060001026 |
- C |
-
-
- | 76 |
- BXD68 |
- F |
- 4060001026 |
- D |
-
-
- | 77 |
- BXD69 |
- M |
- 1957998111 |
- C |
-
-
- | 78 |
- BXD69 |
- M |
- 4060001014 |
- E |
-
-
- | 79 |
- BXD70 |
- M |
- 4060001026 |
- E |
-
-
- | 80 |
- BXD73 |
- F |
- 1957998111 |
- D |
-
-
- | 81 |
- BXD73 |
- M |
- 4060001014 |
- F |
-
-
- | 82 |
- BXD75 |
- M |
- 4060001026 |
- F |
-
-
- | 83 |
- BXD77 |
- F |
- 4060001027 |
- A |
-
-
- | 84 |
- BXD80 |
- M |
- 4060001027 |
- B |
-
-
- | 85 |
- BXD84 |
- F |
- 1957998111 |
- F |
-
-
- | 86 |
- BXD84 |
- M |
- 4060001025 |
- B |
-
-
- | 87 |
- BXD86 |
- M |
- 4060001027 |
- C |
-
-
- | 88 |
- BXD87 |
- F |
- 4060001027 |
- F |
-
-
- | 89 |
- BXD87 |
- M |
- 4060001025 |
- C |
-
-
- | 90 |
- BXD89 |
- M |
- 4060001027 |
- D |
-
-
- | 91 |
- BXD90 |
- F |
- 1736925359 |
- C |
-
-
- | 92 |
- BXD90 |
- M |
- 4060001025 |
- E |
-
-
- | 93 |
- BXD96 |
- F |
- 4060001025 |
- F |
-
-
- | 94 |
- BXD96 |
- M |
- 1736925359 |
- D |
-
-
- | 95 |
- BXD97 |
- M |
- 4060001027 |
- E |
-
-
- | 96 |
- BXD100 |
- F |
- 1848071017 |
- A |
-
-
- | 97 |
- BXD100 |
- M |
- 4051964030 |
- C |
-
-
- | 98 |
- 129S1/SvImJ |
- F |
- 1736925359 |
- E |
-
-
- | 99 |
- 129S1/SvImJ |
- M |
- 1848071018 |
- A |
-
-
- | 100 |
- A/J |
- F |
- 1848071018 |
- B |
-
-
- | 101 |
- A/J |
- M |
- 1736925359 |
- F |
-
-
- | 102 |
- AKR/J |
- F |
- 1848071018 |
- C |
-
-
- | 103 |
- AKR/J |
- M |
- 1957998076 |
- A |
-
-
- | 104 |
- BALB/cByJ |
- F |
- 1957998076 |
- C |
-
-
- | 105 |
- BALB/cByJ |
- M |
- 1953348019 |
- A |
-
-
- | 106 |
- C3H/HeJ |
- F |
- 1953348019 |
- D |
-
-
- | 107 |
- C3H/HeJ |
- M |
- 1957998076 |
- F |
-
-
- | 108 |
- CAST/EiJ |
- F |
- 1833451021 |
- B |
-
-
- | 109 |
- CAST/EiJ |
- M |
- 1957998083 |
- B |
-
-
- | 110 |
- KK/HlJ |
- F |
- 1957998083 |
- E |
-
-
- | 111 |
- KK/HlJ |
- M |
- 1848071023 |
- F |
-
-
- | 112 |
- BXSB/MpJ |
- F |
- 1957998076 |
- E |
-
-
- | 113 |
- BXSB/MpJ |
- M |
- 1953348019 |
- C |
-
-
- | 114 |
- FVB/NJ |
- F |
- 1833451021 |
- D |
-
-
- | 115 |
- FVB/NJ |
- M |
- 1957998083 |
- D |
-
-
- | 116 |
- MOLF/EiJ |
- F |
- 1957998083 |
- F |
-
-
- | 117 |
- MOLF/EiJ |
- M |
- 1848071001 |
- B |
-
-
- | 118 |
- NOD/LtJ |
- F |
- 1848071001 |
- C |
-
-
- | 119 |
- NOD/LtJ |
- M |
- 4060001004 |
- A |
-
-
- | 120 |
- NZB/BlNJ |
- F |
- 4060001004 |
- B |
-
-
- | 121 |
- NZB/BlNJ |
- M |
- 1848071001 |
- D |
-
-
- | 122 |
- NZO/HlLtJ |
- F |
- 4060001004 |
- C |
-
-
- | 123 |
- NZW/LacJ |
- F |
- 4060001004 |
- D |
-
-
- | 124 |
- PWD/PhJ |
- F |
- 4060001004 |
- E |
-
-
- | 125 |
- PWK/PhJ |
- M |
- 4060001004 |
- F |
-
-
- | 126 |
- WSB/EiJ |
- F |
- 4051964030 |
- A |
-
-
- | 127 |
- BTBRT<+>tf/J |
- F |
- 1957998076 |
- D |
-
-
- | 128 |
- BTBRT<+>tf/J |
- M |
- 1953348019 |
- B |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HQFNeoc_0208_RankInv/platform.rtf b/general/datasets/HQFNeoc_0208_RankInv/platform.rtf
deleted file mode 100644
index f0c5210..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/platform.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Illumina Sentrix Mouse-6.1 BeadArray Platform (ILM6v1.1): The Mouse6.1 array consists of 46,643 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
-
-ANNOTATION: In summer of 2008, Xusheng Wang and Robert W. Williams reannotated the Illumina Mouse-6.1 array content. This new annotation is now incorporated into GeneNetwork. For 46643 probes on the Mouse 6.1 array platform (including control probes) we have identified XXXXX NCBI Entrez Gene IDs; XXXXX matched human Gene IDs; XXXXX matched rat Gene IDs; XXXXX NCBI HomoloGene IDs; and XXXXX OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/HQFNeoc_0208_RankInv/processing.rtf b/general/datasets/HQFNeoc_0208_RankInv/processing.rtf
deleted file mode 100644
index 895fa91..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
-Sex of the samples was validated using sex-specific probe set: Xist probe ILM104280446.
diff --git a/general/datasets/HQFNeoc_0208_RankInv/summary.rtf b/general/datasets/HQFNeoc_0208_RankInv/summary.rtf
deleted file mode 100644
index ca42527..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-The February 2008 High Q Foundation Neocortex data set provides estimates of mRNA expression in the cerebral cortex of 73 lines of mice, including 52 BXD strains, 20 standard inbred strains, and B6D2F1 isogenic hybrids. All samples are from normal adult control animals raised in a standard laboratory environment. All data were generated with funds provided by the High Q Foundation using the Illumina Mouse 6.1 bead array (the second version of the Illumina Mouse-6 platform).
-
-While this February data release is still a provisional, we are not aware of any specific errors.
-
-
-
-A total of 129 pooled neocortex samples were processed using approximately XX Illumina Sentrix Mouse-6.1 oligomer microarray BeadArray slides. XX Mouse-6.1 slides and a total of 128 samples passed stringent quality control and error checking. This data set is a companion to the High Q Foundation Striatum data set and was processed using very closely matched methods and most of the same samples. This is our third large data set generated using the Illumina platform. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Illumina (Feb 08) RankInv data set, 1564 probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-
- - Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
- - A movie of the dissection of the brain by Dr. Glenn Rosen.
-
diff --git a/general/datasets/HQFNeoc_0208_RankInv/tissue.rtf b/general/datasets/HQFNeoc_0208_RankInv/tissue.rtf
deleted file mode 100644
index 48d0a2c..0000000
--- a/general/datasets/HQFNeoc_0208_RankInv/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-All animals were raised at the Jackson Laboratory or at UTHSC in SPF facilities. All mice were killed by cervical dislocation. Whole brain dissections were performed at either Beth Israel Deaconess Medical Center by Glenn Rosen or at UTHSC by Lu Lu and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-A pool of dissected neocortical tissue from two to three naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia (CHECK LAST STATEMENT WITH LU).
-
-All animals used in this study were between XX and XX days of age (average of XX days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between December 2007 and January 2008. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from as many strains as possible. However, a number of strains are represented by samples from a single sex (see figure at bottom of page).
diff --git a/general/datasets/HQFNeoc_1210_RankInv/acknowledgment.rtf b/general/datasets/HQFNeoc_1210_RankInv/acknowledgment.rtf
deleted file mode 100644
index 3135d79..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/acknowledgment.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Data were generated with funds to RW Williams, Glenn D. Rosen, Weikuan Gu, and Lu Lu from the High Q Foundation. Informatics support also provided by NIH NIAAA INIA grants to RWW and LL.
-
-
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
-
diff --git a/general/datasets/HQFNeoc_1210_RankInv/cases.rtf b/general/datasets/HQFNeoc_1210_RankInv/cases.rtf
deleted file mode 100644
index a98a7ff..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/cases.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 25 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 20 inbred strains and an F1 hybrid (B6D2F1). These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1
- This F1 hybrid was generated by crossing C57BL/6J with DBA/2J.
-
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf b/general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf
deleted file mode 100644
index 322268a..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/experiment-design.rtf
+++ /dev/null
@@ -1,937 +0,0 @@
-This data set consists arrays processed in XX groups over a XX month period (from Month Year to Month Year). Most groups consisted of XX samples. All arrays in this data set were processed using a single protocol by a single operator, NAME HERE. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
-
-Error checking
-
-
- - Checked for genotypes of BXD strains on all chromosomes using a battery of test Mendelian transcripts (transcripts with a Mendelian segregation pattern in the BXDs). Peak LRS of 260.2 for Prdx2 using Illumina probe ILM5340577. There are no errors in the strain assignment but there are possible genotyping errors, such as:
- Thumpd1 (ILM7510148) in BXD34 using marker rs6271956
- H2-D2 (ILM2190725) in BXD69 using marker gnf17.035.152
- Fcer1g (ILM5550020) in BXD100 using marker rs3722740 (incorrectly scored as a heterozygote).
-
- These genotype discrepancies are either due to recombination between the marker and the probe or a genotyping errors. (RWW, Feb 27, 2008)
- - Total count of transcripts/probes with LOD greater than 10 is 1564 with 52 BXD strains (BXD1 through BXD43 from (n = 27) from JAX, and BXD43 through 100 (n = 25) from UTHSC).
- - Sex assignment checked using Xist probe ILM104280446.
- All female samples: Strains BXD43, BXD42, BXD68, BXD77, NZW/LacJ, and NZO/HlLtJ
- All male samples: Strains BXD1, PWK/PhJ, BXD66, BXD97, BXD10, BXD75, BXD44, BXD89, BXD86, BXD80, BXD69
-
-
-Data Table 1:
-
-This table lists all arrays by order of strain (index) and includes data on strain, sex, slide ID and slide position (A through F).
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Sex |
- Slide ID |
- Slide
- Position |
-
-
- | 1 |
- B6D2F1 |
- F |
- 1848071018 |
- D |
-
-
- | 2 |
- B6D2F1 |
- M |
- 1957998076 |
- B |
-
-
- | 3 |
- C57BL/6J |
- F |
- 1957998083 |
- A |
-
-
- | 4 |
- C57BL/6J |
- M |
- 1833451021 |
- A |
-
-
- | 5 |
- DBA/2J |
- F |
- 1957998083 |
- C |
-
-
- | 6 |
- DBA/2J |
- M |
- 1833451021 |
- C |
-
-
- | 7 |
- BXD1 |
- M |
- 4051964030 |
- B |
-
-
- | 8 |
- BXD5 |
- F |
- 1736925307 |
- A |
-
-
- | 9 |
- BXD5 |
- M |
- 4051964028 |
- C |
-
-
- | 10 |
- BXD6 |
- F |
- 4051964028 |
- F |
-
-
- | 11 |
- BXD6 |
- M |
- 1736925307 |
- D |
-
-
- | 12 |
- BXD8 |
- F |
- 4060001025 |
- A |
-
-
- | 13 |
- BXD8 |
- M |
- 1957998111 |
- E |
-
-
- | 14 |
- BXD9 |
- F |
- 4060001025 |
- D |
-
-
- | 15 |
- BXD9 |
- M |
- 1736925359 |
- B |
-
-
- | 16 |
- BXD11 |
- F |
- 4051964030 |
- D |
-
-
- | 17 |
- BXD11 |
- M |
- 1848071017 |
- B |
-
-
- | 18 |
- BXD12 |
- F |
- 4051964030 |
- E |
-
-
- | 19 |
- BXD12 |
- M |
- 1848071017 |
- C |
-
-
- | 20 |
- BXD13 |
- F |
- 4051964030 |
- F |
-
-
- | 21 |
- BXD13 |
- M |
- 1848071017 |
- D |
-
-
- | 22 |
- BXD14 |
- F |
- 4051964065 |
- A |
-
-
- | 23 |
- BXD14 |
- M |
- 1848071017 |
- E |
-
-
- | 24 |
- BXD15 |
- F |
- 4051964065 |
- B |
-
-
- | 25 |
- BXD15 |
- M |
- 1848071017 |
- F |
-
-
- | 26 |
- BXD16 |
- F |
- 1848071024 |
- A |
-
-
- | 27 |
- BXD16 |
- M |
- 4051964065 |
- C |
-
-
- | 28 |
- BXD18 |
- F |
- 4051964065 |
- D |
-
-
- | 29 |
- BXD18 |
- M |
- 1848071024 |
- B |
-
-
- | 30 |
- BXD19 |
- F |
- 4051964065 |
- E |
-
-
- | 31 |
- BXD19 |
- M |
- 1848071024 |
- C |
-
-
- | 32 |
- BXD21 |
- F |
- 1848071024 |
- D |
-
-
- | 33 |
- BXD21 |
- M |
- 4051964065 |
- F |
-
-
- | 34 |
- BXD23 |
- F |
- 1848071024 |
- E |
-
-
- | 35 |
- BXD23 |
- M |
- 4051964022 |
- A |
-
-
- | 36 |
- BXD27 |
- F |
- 1848071024 |
- F |
-
-
- | 37 |
- BXD27 |
- M |
- 4051964022 |
- B |
-
-
- | 38 |
- BXD28 |
- F |
- 1848071025 |
- A |
-
-
- | 39 |
- BXD28 |
- M |
- 4051964022 |
- C |
-
-
- | 40 |
- BXD31 |
- F |
- 4051964022 |
- D |
-
-
- | 41 |
- BXD31 |
- M |
- 1848071025 |
- B |
-
-
- | 42 |
- BXD32 |
- F |
- 4051964022 |
- E |
-
-
- | 43 |
- BXD32 |
- M |
- 1848071025 |
- C |
-
-
- | 44 |
- BXD33 |
- F |
- 4051964022 |
- F |
-
-
- | 45 |
- BXD33 |
- M |
- 1848071025 |
- D |
-
-
- | 46 |
- BXD34 |
- F |
- 4051964023 |
- A |
-
-
- | 47 |
- BXD34 |
- M |
- 1848071025 |
- E |
-
-
- | 48 |
- BXD36 |
- F |
- 1848071025 |
- F |
-
-
- | 49 |
- BXD36 |
- M |
- 4051964023 |
- B |
-
-
- | 50 |
- BXD38 |
- F |
- 4051964023 |
- C |
-
-
- | 51 |
- BXD38 |
- M |
- 1957998101 |
- A |
-
-
- | 52 |
- BXD39 |
- F |
- 4051964023 |
- D |
-
-
- | 53 |
- BXD39 |
- M |
- 1957998101 |
- B |
-
-
- | 54 |
- BXD40 |
- F |
- 4051964023 |
- E |
-
-
- | 55 |
- BXD40 |
- M |
- 1957998101 |
- C |
-
-
- | 56 |
- BXD42 |
- F |
- 4060001026 |
- B |
-
-
- | 57 |
- BXD43 |
- F |
- 1957998101 |
- D |
-
-
- | 58 |
- BXD43 |
- F |
- 4051964023 |
- F |
-
-
- | 59 |
- BXD44 |
- F |
- 1957998101 |
- E |
-
-
- | 60 |
- BXD44 |
- M |
- 4051964028 |
- A |
-
-
- | 61 |
- BXD45 |
- F |
- 4051964028 |
- B |
-
-
- | 62 |
- BXD45 |
- M |
- 1957998101 |
- F |
-
-
- | 63 |
- BXD51 |
- F |
- 4051964028 |
- D |
-
-
- | 64 |
- BXD51 |
- M |
- 1736925307 |
- B |
-
-
- | 65 |
- BXD55 |
- F |
- 1736925307 |
- C |
-
-
- | 66 |
- BXD55 |
- M |
- 4051964028 |
- E |
-
-
- | 67 |
- BXD60 |
- F |
- 4060001014 |
- A |
-
-
- | 68 |
- BXD60 |
- M |
- 1736925307 |
- E |
-
-
- | 69 |
- BXD61 |
- F |
- 4060001014 |
- B |
-
-
- | 70 |
- BXD61 |
- M |
- 1736925307 |
- F |
-
-
- | 71 |
- BXD62 |
- F |
- 4060001014 |
- C |
-
-
- | 72 |
- BXD62 |
- M |
- 1957998111 |
- A |
-
-
- | 73 |
- BXD65 |
- F |
- 1957998111 |
- B |
-
-
- | 74 |
- BXD65 |
- M |
- 4060001014 |
- D |
-
-
- | 75 |
- BXD66 |
- M |
- 4060001026 |
- C |
-
-
- | 76 |
- BXD68 |
- F |
- 4060001026 |
- D |
-
-
- | 77 |
- BXD69 |
- M |
- 1957998111 |
- C |
-
-
- | 78 |
- BXD69 |
- M |
- 4060001014 |
- E |
-
-
- | 79 |
- BXD70 |
- M |
- 4060001026 |
- E |
-
-
- | 80 |
- BXD73 |
- F |
- 1957998111 |
- D |
-
-
- | 81 |
- BXD73 |
- M |
- 4060001014 |
- F |
-
-
- | 82 |
- BXD75 |
- M |
- 4060001026 |
- F |
-
-
- | 83 |
- BXD77 |
- F |
- 4060001027 |
- A |
-
-
- | 84 |
- BXD80 |
- M |
- 4060001027 |
- B |
-
-
- | 85 |
- BXD84 |
- F |
- 1957998111 |
- F |
-
-
- | 86 |
- BXD84 |
- M |
- 4060001025 |
- B |
-
-
- | 87 |
- BXD86 |
- M |
- 4060001027 |
- C |
-
-
- | 88 |
- BXD87 |
- F |
- 4060001027 |
- F |
-
-
- | 89 |
- BXD87 |
- M |
- 4060001025 |
- C |
-
-
- | 90 |
- BXD89 |
- M |
- 4060001027 |
- D |
-
-
- | 91 |
- BXD90 |
- F |
- 1736925359 |
- C |
-
-
- | 92 |
- BXD90 |
- M |
- 4060001025 |
- E |
-
-
- | 93 |
- BXD96 |
- F |
- 4060001025 |
- F |
-
-
- | 94 |
- BXD96 |
- M |
- 1736925359 |
- D |
-
-
- | 95 |
- BXD97 |
- M |
- 4060001027 |
- E |
-
-
- | 96 |
- BXD100 |
- F |
- 1848071017 |
- A |
-
-
- | 97 |
- BXD100 |
- M |
- 4051964030 |
- C |
-
-
- | 98 |
- 129S1/SvImJ |
- F |
- 1736925359 |
- E |
-
-
- | 99 |
- 129S1/SvImJ |
- M |
- 1848071018 |
- A |
-
-
- | 100 |
- A/J |
- F |
- 1848071018 |
- B |
-
-
- | 101 |
- A/J |
- M |
- 1736925359 |
- F |
-
-
- | 102 |
- AKR/J |
- F |
- 1848071018 |
- C |
-
-
- | 103 |
- AKR/J |
- M |
- 1957998076 |
- A |
-
-
- | 104 |
- BALB/cByJ |
- F |
- 1957998076 |
- C |
-
-
- | 105 |
- BALB/cByJ |
- M |
- 1953348019 |
- A |
-
-
- | 106 |
- C3H/HeJ |
- F |
- 1953348019 |
- D |
-
-
- | 107 |
- C3H/HeJ |
- M |
- 1957998076 |
- F |
-
-
- | 108 |
- CAST/EiJ |
- F |
- 1833451021 |
- B |
-
-
- | 109 |
- CAST/EiJ |
- M |
- 1957998083 |
- B |
-
-
- | 110 |
- KK/HlJ |
- F |
- 1957998083 |
- E |
-
-
- | 111 |
- KK/HlJ |
- M |
- 1848071023 |
- F |
-
-
- | 112 |
- BXSB/MpJ |
- F |
- 1957998076 |
- E |
-
-
- | 113 |
- BXSB/MpJ |
- M |
- 1953348019 |
- C |
-
-
- | 114 |
- FVB/NJ |
- F |
- 1833451021 |
- D |
-
-
- | 115 |
- FVB/NJ |
- M |
- 1957998083 |
- D |
-
-
- | 116 |
- MOLF/EiJ |
- F |
- 1957998083 |
- F |
-
-
- | 117 |
- MOLF/EiJ |
- M |
- 1848071001 |
- B |
-
-
- | 118 |
- NOD/LtJ |
- F |
- 1848071001 |
- C |
-
-
- | 119 |
- NOD/LtJ |
- M |
- 4060001004 |
- A |
-
-
- | 120 |
- NZB/BlNJ |
- F |
- 4060001004 |
- B |
-
-
- | 121 |
- NZB/BlNJ |
- M |
- 1848071001 |
- D |
-
-
- | 122 |
- NZO/HlLtJ |
- F |
- 4060001004 |
- C |
-
-
- | 123 |
- NZW/LacJ |
- F |
- 4060001004 |
- D |
-
-
- | 124 |
- PWD/PhJ |
- F |
- 4060001004 |
- E |
-
-
- | 125 |
- PWK/PhJ |
- M |
- 4060001004 |
- F |
-
-
- | 126 |
- WSB/EiJ |
- F |
- 4051964030 |
- A |
-
-
- | 127 |
- BTBRT<+>tf/J |
- F |
- 1957998076 |
- D |
-
-
- | 128 |
- BTBRT<+>tf/J |
- M |
- 1953348019 |
- B |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HQFNeoc_1210_RankInv/platform.rtf b/general/datasets/HQFNeoc_1210_RankInv/platform.rtf
deleted file mode 100644
index f0c5210..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/platform.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Illumina Sentrix Mouse-6.1 BeadArray Platform (ILM6v1.1): The Mouse6.1 array consists of 46,643 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
-
-ANNOTATION: In summer of 2008, Xusheng Wang and Robert W. Williams reannotated the Illumina Mouse-6.1 array content. This new annotation is now incorporated into GeneNetwork. For 46643 probes on the Mouse 6.1 array platform (including control probes) we have identified XXXXX NCBI Entrez Gene IDs; XXXXX matched human Gene IDs; XXXXX matched rat Gene IDs; XXXXX NCBI HomoloGene IDs; and XXXXX OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/HQFNeoc_1210_RankInv/processing.rtf b/general/datasets/HQFNeoc_1210_RankInv/processing.rtf
deleted file mode 100644
index 895fa91..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
-Sex of the samples was validated using sex-specific probe set: Xist probe ILM104280446.
diff --git a/general/datasets/HQFNeoc_1210_RankInv/summary.rtf b/general/datasets/HQFNeoc_1210_RankInv/summary.rtf
deleted file mode 100644
index ca42527..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-The February 2008 High Q Foundation Neocortex data set provides estimates of mRNA expression in the cerebral cortex of 73 lines of mice, including 52 BXD strains, 20 standard inbred strains, and B6D2F1 isogenic hybrids. All samples are from normal adult control animals raised in a standard laboratory environment. All data were generated with funds provided by the High Q Foundation using the Illumina Mouse 6.1 bead array (the second version of the Illumina Mouse-6 platform).
-
-While this February data release is still a provisional, we are not aware of any specific errors.
-
-
-
-A total of 129 pooled neocortex samples were processed using approximately XX Illumina Sentrix Mouse-6.1 oligomer microarray BeadArray slides. XX Mouse-6.1 slides and a total of 128 samples passed stringent quality control and error checking. This data set is a companion to the High Q Foundation Striatum data set and was processed using very closely matched methods and most of the same samples. This is our third large data set generated using the Illumina platform. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Illumina (Feb 08) RankInv data set, 1564 probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-
- - Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
- - A movie of the dissection of the brain by Dr. Glenn Rosen.
-
diff --git a/general/datasets/HQFNeoc_1210_RankInv/tissue.rtf b/general/datasets/HQFNeoc_1210_RankInv/tissue.rtf
deleted file mode 100644
index 48d0a2c..0000000
--- a/general/datasets/HQFNeoc_1210_RankInv/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-All animals were raised at the Jackson Laboratory or at UTHSC in SPF facilities. All mice were killed by cervical dislocation. Whole brain dissections were performed at either Beth Israel Deaconess Medical Center by Glenn Rosen or at UTHSC by Lu Lu and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-A pool of dissected neocortical tissue from two to three naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia (CHECK LAST STATEMENT WITH LU).
-
-All animals used in this study were between XX and XX days of age (average of XX days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between December 2007 and January 2008. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from as many strains as possible. However, a number of strains are represented by samples from a single sex (see figure at bottom of page).
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/acknowledgment.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/acknowledgment.rtf
deleted file mode 100644
index 3135d79..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/acknowledgment.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Data were generated with funds to RW Williams, Glenn D. Rosen, Weikuan Gu, and Lu Lu from the High Q Foundation. Informatics support also provided by NIH NIAAA INIA grants to RWW and LL.
-
-
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
-
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/cases.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/cases.rtf
deleted file mode 100644
index a98a7ff..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/cases.rtf
+++ /dev/null
@@ -1,54 +0,0 @@
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 25 new inbred strains BXD (F21+) generated by Lu and Peirce. All of these strains were been genotyped at 13,377 SNPs in 2005 (Shifman et al., 2006).
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 20 inbred strains and an F1 hybrid (B6D2F1). These strains were selected for several reasons:
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.
-
-
- - 129S1/SvImJ
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list
- - A/J
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel
- - AKR/J
- Sequenced by NIEHS; Phenome Project B list
- - BALB/cByJ
- Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list
- - BALB/cJ
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - LG/J
- Paternal parent of the LGXSM panel
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - NZO/HlLtJ
- Collaborative Cross strain
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - B6D2F1
- This F1 hybrid was generated by crossing C57BL/6J with DBA/2J.
-
-
-These strains are available from The Jackson Laboratory. BXD43 through BXD100 strains are available from Lu Lu and colleagues at UTHSC.
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/experiment-design.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/experiment-design.rtf
deleted file mode 100644
index 322268a..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/experiment-design.rtf
+++ /dev/null
@@ -1,937 +0,0 @@
-This data set consists arrays processed in XX groups over a XX month period (from Month Year to Month Year). Most groups consisted of XX samples. All arrays in this data set were processed using a single protocol by a single operator, NAME HERE. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between Month Day and Month Day, Year. Details on sample assignment to slides and batches is provide in the table below.
-
-Error checking
-
-
- - Checked for genotypes of BXD strains on all chromosomes using a battery of test Mendelian transcripts (transcripts with a Mendelian segregation pattern in the BXDs). Peak LRS of 260.2 for Prdx2 using Illumina probe ILM5340577. There are no errors in the strain assignment but there are possible genotyping errors, such as:
- Thumpd1 (ILM7510148) in BXD34 using marker rs6271956
- H2-D2 (ILM2190725) in BXD69 using marker gnf17.035.152
- Fcer1g (ILM5550020) in BXD100 using marker rs3722740 (incorrectly scored as a heterozygote).
-
- These genotype discrepancies are either due to recombination between the marker and the probe or a genotyping errors. (RWW, Feb 27, 2008)
- - Total count of transcripts/probes with LOD greater than 10 is 1564 with 52 BXD strains (BXD1 through BXD43 from (n = 27) from JAX, and BXD43 through 100 (n = 25) from UTHSC).
- - Sex assignment checked using Xist probe ILM104280446.
- All female samples: Strains BXD43, BXD42, BXD68, BXD77, NZW/LacJ, and NZO/HlLtJ
- All male samples: Strains BXD1, PWK/PhJ, BXD66, BXD97, BXD10, BXD75, BXD44, BXD89, BXD86, BXD80, BXD69
-
-
-Data Table 1:
-
-This table lists all arrays by order of strain (index) and includes data on strain, sex, slide ID and slide position (A through F).
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Sex |
- Slide ID |
- Slide
- Position |
-
-
- | 1 |
- B6D2F1 |
- F |
- 1848071018 |
- D |
-
-
- | 2 |
- B6D2F1 |
- M |
- 1957998076 |
- B |
-
-
- | 3 |
- C57BL/6J |
- F |
- 1957998083 |
- A |
-
-
- | 4 |
- C57BL/6J |
- M |
- 1833451021 |
- A |
-
-
- | 5 |
- DBA/2J |
- F |
- 1957998083 |
- C |
-
-
- | 6 |
- DBA/2J |
- M |
- 1833451021 |
- C |
-
-
- | 7 |
- BXD1 |
- M |
- 4051964030 |
- B |
-
-
- | 8 |
- BXD5 |
- F |
- 1736925307 |
- A |
-
-
- | 9 |
- BXD5 |
- M |
- 4051964028 |
- C |
-
-
- | 10 |
- BXD6 |
- F |
- 4051964028 |
- F |
-
-
- | 11 |
- BXD6 |
- M |
- 1736925307 |
- D |
-
-
- | 12 |
- BXD8 |
- F |
- 4060001025 |
- A |
-
-
- | 13 |
- BXD8 |
- M |
- 1957998111 |
- E |
-
-
- | 14 |
- BXD9 |
- F |
- 4060001025 |
- D |
-
-
- | 15 |
- BXD9 |
- M |
- 1736925359 |
- B |
-
-
- | 16 |
- BXD11 |
- F |
- 4051964030 |
- D |
-
-
- | 17 |
- BXD11 |
- M |
- 1848071017 |
- B |
-
-
- | 18 |
- BXD12 |
- F |
- 4051964030 |
- E |
-
-
- | 19 |
- BXD12 |
- M |
- 1848071017 |
- C |
-
-
- | 20 |
- BXD13 |
- F |
- 4051964030 |
- F |
-
-
- | 21 |
- BXD13 |
- M |
- 1848071017 |
- D |
-
-
- | 22 |
- BXD14 |
- F |
- 4051964065 |
- A |
-
-
- | 23 |
- BXD14 |
- M |
- 1848071017 |
- E |
-
-
- | 24 |
- BXD15 |
- F |
- 4051964065 |
- B |
-
-
- | 25 |
- BXD15 |
- M |
- 1848071017 |
- F |
-
-
- | 26 |
- BXD16 |
- F |
- 1848071024 |
- A |
-
-
- | 27 |
- BXD16 |
- M |
- 4051964065 |
- C |
-
-
- | 28 |
- BXD18 |
- F |
- 4051964065 |
- D |
-
-
- | 29 |
- BXD18 |
- M |
- 1848071024 |
- B |
-
-
- | 30 |
- BXD19 |
- F |
- 4051964065 |
- E |
-
-
- | 31 |
- BXD19 |
- M |
- 1848071024 |
- C |
-
-
- | 32 |
- BXD21 |
- F |
- 1848071024 |
- D |
-
-
- | 33 |
- BXD21 |
- M |
- 4051964065 |
- F |
-
-
- | 34 |
- BXD23 |
- F |
- 1848071024 |
- E |
-
-
- | 35 |
- BXD23 |
- M |
- 4051964022 |
- A |
-
-
- | 36 |
- BXD27 |
- F |
- 1848071024 |
- F |
-
-
- | 37 |
- BXD27 |
- M |
- 4051964022 |
- B |
-
-
- | 38 |
- BXD28 |
- F |
- 1848071025 |
- A |
-
-
- | 39 |
- BXD28 |
- M |
- 4051964022 |
- C |
-
-
- | 40 |
- BXD31 |
- F |
- 4051964022 |
- D |
-
-
- | 41 |
- BXD31 |
- M |
- 1848071025 |
- B |
-
-
- | 42 |
- BXD32 |
- F |
- 4051964022 |
- E |
-
-
- | 43 |
- BXD32 |
- M |
- 1848071025 |
- C |
-
-
- | 44 |
- BXD33 |
- F |
- 4051964022 |
- F |
-
-
- | 45 |
- BXD33 |
- M |
- 1848071025 |
- D |
-
-
- | 46 |
- BXD34 |
- F |
- 4051964023 |
- A |
-
-
- | 47 |
- BXD34 |
- M |
- 1848071025 |
- E |
-
-
- | 48 |
- BXD36 |
- F |
- 1848071025 |
- F |
-
-
- | 49 |
- BXD36 |
- M |
- 4051964023 |
- B |
-
-
- | 50 |
- BXD38 |
- F |
- 4051964023 |
- C |
-
-
- | 51 |
- BXD38 |
- M |
- 1957998101 |
- A |
-
-
- | 52 |
- BXD39 |
- F |
- 4051964023 |
- D |
-
-
- | 53 |
- BXD39 |
- M |
- 1957998101 |
- B |
-
-
- | 54 |
- BXD40 |
- F |
- 4051964023 |
- E |
-
-
- | 55 |
- BXD40 |
- M |
- 1957998101 |
- C |
-
-
- | 56 |
- BXD42 |
- F |
- 4060001026 |
- B |
-
-
- | 57 |
- BXD43 |
- F |
- 1957998101 |
- D |
-
-
- | 58 |
- BXD43 |
- F |
- 4051964023 |
- F |
-
-
- | 59 |
- BXD44 |
- F |
- 1957998101 |
- E |
-
-
- | 60 |
- BXD44 |
- M |
- 4051964028 |
- A |
-
-
- | 61 |
- BXD45 |
- F |
- 4051964028 |
- B |
-
-
- | 62 |
- BXD45 |
- M |
- 1957998101 |
- F |
-
-
- | 63 |
- BXD51 |
- F |
- 4051964028 |
- D |
-
-
- | 64 |
- BXD51 |
- M |
- 1736925307 |
- B |
-
-
- | 65 |
- BXD55 |
- F |
- 1736925307 |
- C |
-
-
- | 66 |
- BXD55 |
- M |
- 4051964028 |
- E |
-
-
- | 67 |
- BXD60 |
- F |
- 4060001014 |
- A |
-
-
- | 68 |
- BXD60 |
- M |
- 1736925307 |
- E |
-
-
- | 69 |
- BXD61 |
- F |
- 4060001014 |
- B |
-
-
- | 70 |
- BXD61 |
- M |
- 1736925307 |
- F |
-
-
- | 71 |
- BXD62 |
- F |
- 4060001014 |
- C |
-
-
- | 72 |
- BXD62 |
- M |
- 1957998111 |
- A |
-
-
- | 73 |
- BXD65 |
- F |
- 1957998111 |
- B |
-
-
- | 74 |
- BXD65 |
- M |
- 4060001014 |
- D |
-
-
- | 75 |
- BXD66 |
- M |
- 4060001026 |
- C |
-
-
- | 76 |
- BXD68 |
- F |
- 4060001026 |
- D |
-
-
- | 77 |
- BXD69 |
- M |
- 1957998111 |
- C |
-
-
- | 78 |
- BXD69 |
- M |
- 4060001014 |
- E |
-
-
- | 79 |
- BXD70 |
- M |
- 4060001026 |
- E |
-
-
- | 80 |
- BXD73 |
- F |
- 1957998111 |
- D |
-
-
- | 81 |
- BXD73 |
- M |
- 4060001014 |
- F |
-
-
- | 82 |
- BXD75 |
- M |
- 4060001026 |
- F |
-
-
- | 83 |
- BXD77 |
- F |
- 4060001027 |
- A |
-
-
- | 84 |
- BXD80 |
- M |
- 4060001027 |
- B |
-
-
- | 85 |
- BXD84 |
- F |
- 1957998111 |
- F |
-
-
- | 86 |
- BXD84 |
- M |
- 4060001025 |
- B |
-
-
- | 87 |
- BXD86 |
- M |
- 4060001027 |
- C |
-
-
- | 88 |
- BXD87 |
- F |
- 4060001027 |
- F |
-
-
- | 89 |
- BXD87 |
- M |
- 4060001025 |
- C |
-
-
- | 90 |
- BXD89 |
- M |
- 4060001027 |
- D |
-
-
- | 91 |
- BXD90 |
- F |
- 1736925359 |
- C |
-
-
- | 92 |
- BXD90 |
- M |
- 4060001025 |
- E |
-
-
- | 93 |
- BXD96 |
- F |
- 4060001025 |
- F |
-
-
- | 94 |
- BXD96 |
- M |
- 1736925359 |
- D |
-
-
- | 95 |
- BXD97 |
- M |
- 4060001027 |
- E |
-
-
- | 96 |
- BXD100 |
- F |
- 1848071017 |
- A |
-
-
- | 97 |
- BXD100 |
- M |
- 4051964030 |
- C |
-
-
- | 98 |
- 129S1/SvImJ |
- F |
- 1736925359 |
- E |
-
-
- | 99 |
- 129S1/SvImJ |
- M |
- 1848071018 |
- A |
-
-
- | 100 |
- A/J |
- F |
- 1848071018 |
- B |
-
-
- | 101 |
- A/J |
- M |
- 1736925359 |
- F |
-
-
- | 102 |
- AKR/J |
- F |
- 1848071018 |
- C |
-
-
- | 103 |
- AKR/J |
- M |
- 1957998076 |
- A |
-
-
- | 104 |
- BALB/cByJ |
- F |
- 1957998076 |
- C |
-
-
- | 105 |
- BALB/cByJ |
- M |
- 1953348019 |
- A |
-
-
- | 106 |
- C3H/HeJ |
- F |
- 1953348019 |
- D |
-
-
- | 107 |
- C3H/HeJ |
- M |
- 1957998076 |
- F |
-
-
- | 108 |
- CAST/EiJ |
- F |
- 1833451021 |
- B |
-
-
- | 109 |
- CAST/EiJ |
- M |
- 1957998083 |
- B |
-
-
- | 110 |
- KK/HlJ |
- F |
- 1957998083 |
- E |
-
-
- | 111 |
- KK/HlJ |
- M |
- 1848071023 |
- F |
-
-
- | 112 |
- BXSB/MpJ |
- F |
- 1957998076 |
- E |
-
-
- | 113 |
- BXSB/MpJ |
- M |
- 1953348019 |
- C |
-
-
- | 114 |
- FVB/NJ |
- F |
- 1833451021 |
- D |
-
-
- | 115 |
- FVB/NJ |
- M |
- 1957998083 |
- D |
-
-
- | 116 |
- MOLF/EiJ |
- F |
- 1957998083 |
- F |
-
-
- | 117 |
- MOLF/EiJ |
- M |
- 1848071001 |
- B |
-
-
- | 118 |
- NOD/LtJ |
- F |
- 1848071001 |
- C |
-
-
- | 119 |
- NOD/LtJ |
- M |
- 4060001004 |
- A |
-
-
- | 120 |
- NZB/BlNJ |
- F |
- 4060001004 |
- B |
-
-
- | 121 |
- NZB/BlNJ |
- M |
- 1848071001 |
- D |
-
-
- | 122 |
- NZO/HlLtJ |
- F |
- 4060001004 |
- C |
-
-
- | 123 |
- NZW/LacJ |
- F |
- 4060001004 |
- D |
-
-
- | 124 |
- PWD/PhJ |
- F |
- 4060001004 |
- E |
-
-
- | 125 |
- PWK/PhJ |
- M |
- 4060001004 |
- F |
-
-
- | 126 |
- WSB/EiJ |
- F |
- 4051964030 |
- A |
-
-
- | 127 |
- BTBRT<+>tf/J |
- F |
- 1957998076 |
- D |
-
-
- | 128 |
- BTBRT<+>tf/J |
- M |
- 1953348019 |
- B |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/platform.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/platform.rtf
deleted file mode 100644
index f0c5210..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/platform.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Illumina Sentrix Mouse-6.1 BeadArray Platform (ILM6v1.1): The Mouse6.1 array consists of 46,643 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
-
-ANNOTATION: In summer of 2008, Xusheng Wang and Robert W. Williams reannotated the Illumina Mouse-6.1 array content. This new annotation is now incorporated into GeneNetwork. For 46643 probes on the Mouse 6.1 array platform (including control probes) we have identified XXXXX NCBI Entrez Gene IDs; XXXXX matched human Gene IDs; XXXXX matched rat Gene IDs; XXXXX NCBI HomoloGene IDs; and XXXXX OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/processing.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/processing.rtf
deleted file mode 100644
index 895fa91..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
-Sex of the samples was validated using sex-specific probe set: Xist probe ILM104280446.
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/summary.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/summary.rtf
deleted file mode 100644
index ca42527..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-The February 2008 High Q Foundation Neocortex data set provides estimates of mRNA expression in the cerebral cortex of 73 lines of mice, including 52 BXD strains, 20 standard inbred strains, and B6D2F1 isogenic hybrids. All samples are from normal adult control animals raised in a standard laboratory environment. All data were generated with funds provided by the High Q Foundation using the Illumina Mouse 6.1 bead array (the second version of the Illumina Mouse-6 platform).
-
-While this February data release is still a provisional, we are not aware of any specific errors.
-
-
-
-A total of 129 pooled neocortex samples were processed using approximately XX Illumina Sentrix Mouse-6.1 oligomer microarray BeadArray slides. XX Mouse-6.1 slides and a total of 128 samples passed stringent quality control and error checking. This data set is a companion to the High Q Foundation Striatum data set and was processed using very closely matched methods and most of the same samples. This is our third large data set generated using the Illumina platform. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from XXX (very low or no expression) to XXXX (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Neocortex Illumina (Feb 08) RankInv data set, 1564 probes have LRS values >46 (LOD >10).
-
-Users of these mouse neocortex data may also find the following complementary resources and papers useful:
-
-
- - Rossner and colleagues, 2006: a paper on the transcriptome of identified subtypes of neurons in the mouse neocortex.
- - A movie of the dissection of the brain by Dr. Glenn Rosen.
-
diff --git a/general/datasets/HQFNeoc_1210v2_RankInv/tissue.rtf b/general/datasets/HQFNeoc_1210v2_RankInv/tissue.rtf
deleted file mode 100644
index 48d0a2c..0000000
--- a/general/datasets/HQFNeoc_1210v2_RankInv/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-All animals were raised at the Jackson Laboratory or at UTHSC in SPF facilities. All mice were killed by cervical dislocation. Whole brain dissections were performed at either Beth Israel Deaconess Medical Center by Glenn Rosen or at UTHSC by Lu Lu and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.
-
-A pool of dissected neocortical tissue from two to three naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia (CHECK LAST STATEMENT WITH LU).
-
-All animals used in this study were between XX and XX days of age (average of XX days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between December 2007 and January 2008. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from as many strains as possible. However, a number of strains are represented by samples from a single sex (see figure at bottom of page).
diff --git a/general/datasets/HXBBXHGeno/summary.rtf b/general/datasets/HXBBXHGeno/summary.rtf
deleted file mode 100644
index 098796a..0000000
--- a/general/datasets/HXBBXHGeno/summary.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-UCSC Genome Browser assembly ID: rn6
-Sequencing/Assembly provider ID: RGSC Rnor_6.0
-Assembly date: Jul. 2014
-Accession ID: GCA_000001895.4
-NCBI Genome ID: 73 (Rattus norvegicus)
-NCBI Assembly ID: 191871 (Rnor_6.0)
-NCBI BioProject ID: 10629
diff --git a/general/datasets/HXB_Adrenal_1208/acknowledgment.rtf b/general/datasets/HXB_Adrenal_1208/acknowledgment.rtf
deleted file mode 100644
index d0e4106..0000000
--- a/general/datasets/HXB_Adrenal_1208/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Initiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
diff --git a/general/datasets/HXB_Adrenal_1208/cases.rtf b/general/datasets/HXB_Adrenal_1208/cases.rtf
deleted file mode 100644
index f105019..0000000
--- a/general/datasets/HXB_Adrenal_1208/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv, abbreviated SHR or HSR = H) and Brown Norway (BN-Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-
-The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth generation of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of multiple tissues (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hübner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
diff --git a/general/datasets/HXB_Adrenal_1208/experiment-design.rtf b/general/datasets/HXB_Adrenal_1208/experiment-design.rtf
deleted file mode 100644
index e7386b3..0000000
--- a/general/datasets/HXB_Adrenal_1208/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.
diff --git a/general/datasets/HXB_Adrenal_1208/notes.rtf b/general/datasets/HXB_Adrenal_1208/notes.rtf
deleted file mode 100644
index e4b510d..0000000
--- a/general/datasets/HXB_Adrenal_1208/notes.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Entered by Arthur Centeno, Dec 18, 2008. Data from Herbert Schulz. CEL files processed by AC. Data normalized by AC and RWW (2z+8).
-
-Access to this data set is currently limited to the three teams of researchers who generated the data: Norbert Hübner (MDC, Berlin), Timothy Aitman (UC London), and Michal Pravenec (CAS, Prague). For access to data please contact N. Hübner by email.
-
-The text below was copied from the INFO file for the older (2005) kidney gene expression data set by RWW (Dec 20, 2008). It contains errors and will need to be corrected with the guidance of the data generators and owners.
-
-
-This text file originally copied from the old kidney INFO file that was generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman. This version entered into the adrenal INFO file, December 19, 2008, by RWW, Kathrin Saar Dec 23.
-
diff --git a/general/datasets/HXB_Adrenal_1208/platform.rtf b/general/datasets/HXB_Adrenal_1208/platform.rtf
deleted file mode 100644
index 372ab1c..0000000
--- a/general/datasets/HXB_Adrenal_1208/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 230A GeneChip: Expression data were generated using the Affymetrix 230A array. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
diff --git a/general/datasets/HXB_Adrenal_1208/processing.rtf b/general/datasets/HXB_Adrenal_1208/processing.rtf
deleted file mode 100644
index 584e49b..0000000
--- a/general/datasets/HXB_Adrenal_1208/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of pixel measured in each cell.
-Probe set data: The original CEL values were processed using RMA and log2 transformed using our standard 2z +8 transform. This recenters each array to a mean of 8 units and a SD of 2 units. Probe set values are typically the averages of four biological replicates within strain.
-
diff --git a/general/datasets/HXB_Adrenal_1208/summary.rtf b/general/datasets/HXB_Adrenal_1208/summary.rtf
deleted file mode 100644
index 6c7a859..0000000
--- a/general/datasets/HXB_Adrenal_1208/summary.rtf
+++ /dev/null
@@ -1,19 +0,0 @@
-This December 2008 data set provides estimates of mRNA expression in normal adrenal glands of 31 strains of rats including the hypertensive SHR strain (aka HSR), the normotensive BN strain, and 29 HXB/BXH recombinant inbred strains. Most strains were sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by Norbert Hübner and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of approximately 124 Affymetrix RAE230A array processed using the RMA protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a standard deviation of 2 (mean and variance stabilized). This data set complements the kidney and fat data set exploited by Hübner and colleagues 2005.
-
-These data may also be viewed using the eQTL Explorer Java application by John Mangion, Tim Aitman, and colleagues (Mueller et al. 2006).
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/HXB_Adrenal_1208/tissue.rtf b/general/datasets/HXB_Adrenal_1208/tissue.rtf
deleted file mode 100644
index d0d0236..0000000
--- a/general/datasets/HXB_Adrenal_1208/tissue.rtf
+++ /dev/null
@@ -1,530 +0,0 @@
-All tissues were collected at the age of 6 weeks. Adrenal glands and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction. THIS IS AN OLD TABLE FOR THE KIDNEY DATA IN THIS INFO FILE ONLY AS A PLACEHOLDER. The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR3 |
-
-
- | HSR |
- HSR4 |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN4 |
-
-
- | BN |
- BN5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-3 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- RI 02-4 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- *RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HXB10 |
- RI 10-1 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-3 |
-
-
- | HXB15 |
- RI 15-4 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- RI 24-4 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-2 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- *RI 25-4 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-3 |
-
-
- | HXB29 |
- RI 29-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-3 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- RI 05c-3 |
-
-
- | BXH5 |
- RI 05c-4 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-2 |
-
-
- | BXH6 |
- RI 06c-3 |
-
-
- | BXH6 |
- RI 06c-4 |
-
-
- | BXH8 |
- RI 08c-1 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-3 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HXB_Heart_1208/acknowledgment.rtf b/general/datasets/HXB_Heart_1208/acknowledgment.rtf
deleted file mode 100644
index ea86842..0000000
--- a/general/datasets/HXB_Heart_1208/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Initiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
diff --git a/general/datasets/HXB_Heart_1208/cases.rtf b/general/datasets/HXB_Heart_1208/cases.rtf
deleted file mode 100644
index 34c7d7a..0000000
--- a/general/datasets/HXB_Heart_1208/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv, abbreviated SHR or HSR = H) and Brown Norway (BN-Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth generation of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of multiple tissues (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hübner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
-
diff --git a/general/datasets/HXB_Heart_1208/experiment-design.rtf b/general/datasets/HXB_Heart_1208/experiment-design.rtf
deleted file mode 100644
index 984be42..0000000
--- a/general/datasets/HXB_Heart_1208/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.
-
diff --git a/general/datasets/HXB_Heart_1208/notes.rtf b/general/datasets/HXB_Heart_1208/notes.rtf
deleted file mode 100644
index 91c8b67..0000000
--- a/general/datasets/HXB_Heart_1208/notes.rtf
+++ /dev/null
@@ -1,21 +0,0 @@
-
-Heart Left Ventricle
-
-http://www.expressionanalysis.com/pdf/Affymetrix/GXRat230v2.pdf
-
-GEO platform id http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1355
-
-Data entered by Evan Williams and Rob Williams, Jan 2, 2009.
-
-Mapping of probes http://compbio.dcs.gla.ac.uk/sf/index.html#230map
-
-Entered by Arthur Centeno, Dec 18, 2008. Data from Herbert Schulz. CEL files processed by AC. Data normalized by AC and RWW (2z+8).
-
-Access to this data set is currently limited to the three teams of researchers who generated the data: Norbert Hübner (MDC, Berlin), Timothy Aitman (UC London), and Michal Pravenec (CAS, Prague). For access to data please contact N. Hübner by email.
-
-The text below was copied from the INFO file for the older (2005) kidney gene expression data set by RWW (Dec 20, 2008). It contains errors and will need to be corrected with the guidance of the data generators and owners.
-
-
-
-This text file originally copied from the old kidney INFO file that was generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman. This version entered into the adrenal INFO file, December 19, 2008, by RWW, Kathrin Saar Dec 23.
-
diff --git a/general/datasets/HXB_Heart_1208/platform.rtf b/general/datasets/HXB_Heart_1208/platform.rtf
deleted file mode 100644
index b6eb818..0000000
--- a/general/datasets/HXB_Heart_1208/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 230Av2 GeneChip: Expression data were generated using the Affymetrix 230Av2 array (GEO_GPL341). The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
-
diff --git a/general/datasets/HXB_Heart_1208/processing.rtf b/general/datasets/HXB_Heart_1208/processing.rtf
deleted file mode 100644
index 9bb9584..0000000
--- a/general/datasets/HXB_Heart_1208/processing.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of pixel measured in each cell.
-
-Probe set data: The original CEL values were processed using RMA and log2 transformed using our standard 2z +8 transform. This recenters each array to a mean of 8 units and a SD of 2 units. Probe set values are typically the averages of four biological replicates within strain.
-
diff --git a/general/datasets/HXB_Heart_1208/summary.rtf b/general/datasets/HXB_Heart_1208/summary.rtf
deleted file mode 100644
index 88bf1b8..0000000
--- a/general/datasets/HXB_Heart_1208/summary.rtf
+++ /dev/null
@@ -1,19 +0,0 @@
-This December 2008 data set provides estimates of mRNA expression in normal hearts of 31 strains of rats including the hypertensive SHR strain (aka HSR), the normotensive BN strain, and 29 HXB/BXH recombinant inbred strains. Most strains were sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by Norbert Hübner and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of approximately XXX Affymetrix RAE230A array processed using the RMA protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a standard deviation of 2 (mean and variance stabilized). This data set complements the kidney and fat data set exploited by Hübner and colleagues 2005.
-
-These data may also be viewed using the eQTL Explorer Java application by John Mangion, Tim Aitman, and colleagues (Mueller et al. 2006).
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/HXB_Heart_1208/tissue.rtf b/general/datasets/HXB_Heart_1208/tissue.rtf
deleted file mode 100644
index 485694f..0000000
--- a/general/datasets/HXB_Heart_1208/tissue.rtf
+++ /dev/null
@@ -1,530 +0,0 @@
-All tissues were collected at the age of 6 weeks. Hearts and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction. THIS IS AN OLD TABLE FOR THE KIDNEY DATA IN THIS INFO FILE ONLY AS A PLACEHOLDER. The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR3 |
-
-
- | HSR |
- HSR4 |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN4 |
-
-
- | BN |
- BN5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-3 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- RI 02-4 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- *RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HXB10 |
- RI 10-1 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-3 |
-
-
- | HXB15 |
- RI 15-4 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- RI 24-4 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-2 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- *RI 25-4 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-3 |
-
-
- | HXB29 |
- RI 29-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-3 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- RI 05c-3 |
-
-
- | BXH5 |
- RI 05c-4 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-2 |
-
-
- | BXH6 |
- RI 06c-3 |
-
-
- | BXH6 |
- RI 06c-4 |
-
-
- | BXH8 |
- RI 08c-1 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-3 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/HXB_Liver_1208/acknowledgment.rtf b/general/datasets/HXB_Liver_1208/acknowledgment.rtf
deleted file mode 100644
index ea86842..0000000
--- a/general/datasets/HXB_Liver_1208/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Initiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
diff --git a/general/datasets/HXB_Liver_1208/platform.rtf b/general/datasets/HXB_Liver_1208/platform.rtf
deleted file mode 100644
index b6eb818..0000000
--- a/general/datasets/HXB_Liver_1208/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 230Av2 GeneChip: Expression data were generated using the Affymetrix 230Av2 array (GEO_GPL341). The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
-
diff --git a/general/datasets/HXB_Liver_1208/summary.rtf b/general/datasets/HXB_Liver_1208/summary.rtf
deleted file mode 100644
index d524ef3..0000000
--- a/general/datasets/HXB_Liver_1208/summary.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/HZI_0408_M/cases.rtf b/general/datasets/HZI_0408_M/cases.rtf
deleted file mode 100644
index 83b146d..0000000
--- a/general/datasets/HZI_0408_M/cases.rtf
+++ /dev/null
@@ -1,784 +0,0 @@
-
-
-
-
-
-
-
-
- | Index |
- Array |
- Sample |
- Strain |
- Sex |
- Age |
- Color |
- Pool Size |
- Source |
-
-
- | 1 |
- R4435LU.CEL |
- R4435LU |
- BXD100 |
- F |
- 64 |
- black |
- 2 |
- UTM RW |
-
-
- | 2 |
- R4436LU.CEL |
- R4436LU |
- BXD14 |
- F |
- 85 |
- black |
- 2 |
- UTM RW |
-
-
- | 3 |
- R4437LU.CEL |
- R4437LU |
- BXD34 |
- F |
- 58 |
- black |
- 5 |
- UTM RW |
-
-
- | 4 |
- R4438LU.CEL |
- R4438LU |
- BXD39 |
- F |
- 63 |
- gray |
- 3 |
- UTM RW |
-
-
- | 5 |
- R4439LU.CEL |
- R4439LU |
- BXD40 |
- F |
- 54 |
- gray |
- 3 |
- ORNL |
-
-
- | 6 |
- R4440LU.CEL |
- R4440LU |
- BXD45 |
- F |
- 60 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 7 |
- R4441LU.CEL |
- R4441LU |
- BXD50 |
- F |
- 64 |
- dilute brown DBA |
- 4 |
- ORNL |
-
-
- | 8 |
- R4442LU.CEL |
- R4442LU |
- BXD1 |
- F |
- 88 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 9 |
- R4443LU.CEL |
- R4443LU |
- BXD16 |
- F |
- 79 |
- gray |
- 3 |
- ORNL |
-
-
- | 10 |
- R4444LU.CEL |
- R4444LU |
- BXD12 |
- F |
- 61 |
- gray |
- 5 |
- UTM RW |
-
-
- | 11 |
- R4445LU.CEL |
- R4445LU |
- BXD21 |
- F |
- 50 |
- dilute brown DBA |
- 3 |
- ORNL |
-
-
- | 12 |
- R4446LU.CEL |
- R4446LU |
- BXD19 |
- F |
- 49 |
- gray |
- 3 |
- ORNL |
-
-
- | 13 |
- R4447LU.CEL |
- R4447LU |
- BXD27 |
- F |
- 85 |
- brown |
- 3 |
- UTM RW |
-
-
- | 14 |
- R4448LU.CEL |
- R4448LU |
- BXD31 |
- F |
- 81 |
- black |
- 3 |
- UTM RW |
-
-
- | 15 |
- R4449LU.CEL |
- R4449LU |
- BXD32 |
- F |
- 68 |
- black |
- 5 |
- ORNL |
-
-
- | 16 |
- R4450LU.CEL |
- R4450LU |
- BXD33 |
- F |
- 61 |
- gray |
- 2 |
- ORNL |
-
-
- | 17 |
- R4451LU.CEL |
- R4451LU |
- BXD42 |
- F |
- 65 |
- black |
- 2 |
- UTM RW |
-
-
- | 18 |
- R4452LU.CEL |
- R4452LU |
- BXD43 |
- F |
- 79 |
- black |
- 2 |
- UTM RW |
-
-
- | 19 |
- R4453LU.CEL |
- R4453LU |
- BXD45 |
- F |
- 60 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 20 |
- R4454LU.CEL |
- R4454LU |
- BXD55 |
- M |
- 80 |
- brown |
- 3 |
- UTM RW |
-
-
- | 21 |
- R4455LU.CEL |
- R4455LU |
- BXD56 |
- M |
- 91 |
- black |
- 3 |
- UTM RW |
-
-
- | 22 |
- R4456LU.CEL |
- R4456LU |
- BXD66 |
- F |
- 80 |
- brown |
- 3 |
- UTM RW |
-
-
- | 23 |
- R4457LU.CEL |
- R4457LU |
- BXD68 |
- F |
- 65 |
- brown |
- 4 |
- UTM RW |
-
-
- | 24 |
- R4459LU-re.CEL |
- R4459LU |
- BXD89 |
- F |
- 79 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 25 |
- R4460LU.CEL |
- R4460LU |
- BXD51 |
- M |
- 81 |
- black |
- 2 |
- UTM RW |
-
-
- | 26 |
- R4461LU.CEL |
- R4461LU |
- BXD97 |
- F |
- N/A |
- N/A |
- N/A |
- N/A |
-
-
- | 27 |
- R4462LU.CEL |
- R4462LU |
- BXD48 |
- F |
- 61 |
- black |
- 3 |
- ORNL |
-
-
- | 28 |
- R4463LU.CEL |
- R4463LU |
- BXD60 |
- M |
- 93 |
- brown |
- 2 |
- UTM RW |
-
-
- | 29 |
- R4464LU.CEL |
- R4464LU |
- BXD62 |
- M |
- 80 |
- brown |
- 2 |
- UTM RW |
-
-
- | 30 |
- R4465LU.CEL |
- R4465LU |
- BXD69 |
- M |
- 63 |
- dilute brown DBA |
- 5 |
- UTM RW |
-
-
- | 31 |
- R4466LU.CEL |
- R4466LU |
- BXD70 |
- M |
- 75 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 32 |
- R4467LU.CEL |
- R4467LU |
- BXD71 |
- M |
- 64 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 33 |
- R4468LU.CEL |
- R4468LU |
- BXD73 |
- M |
- 59 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 34 |
- R4469L.CEL |
- R4469LU |
- BXD75 |
- M |
- 51 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 35 |
- R4470L.CEL |
- R4470LU |
- BXD2 |
- M |
- 84 |
- black |
- 3 |
- UTM RW |
-
-
- | 36 |
- R4471H-re.CEL |
- R4471LU |
- BXD83 |
- M |
- 75 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 37 |
- R4472L.CEL |
- R4472LU |
- BXD84 |
- M |
- 78 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 38 |
- R4473LU.CEL |
- R4473LU |
- BXD86 |
- M |
- 77 |
- black |
- 3 |
- UTM RW |
-
-
- | 39 |
- R4474LU.CEL |
- R4474LU |
- BXD87 |
- M |
- 67 |
- black |
- 3 |
- UTM RW |
-
-
- | 40 |
- R4475LU.CEL |
- R4475LU |
- BXD9 |
- M |
- 78 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 41 |
- R4476LU.CEL |
- R4476LU |
- BXD90 |
- M |
- 63 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 42 |
- R4477LU.CEL |
- R4477LU |
- BXD65 |
- M |
- 59 |
- brown |
- 3 |
- ORNL |
-
-
- | 43 |
- R4478LU.CEL |
- R4478LU |
- BXD6 |
- M |
- 92 |
- gray |
- 3 |
- UTM RW |
-
-
- | 44 |
- R4479LU.CEL |
- R4479LU |
- BXD96 |
- M |
- 71 |
- black |
- 3 |
- UTM RW |
-
-
- | 45 |
- R4480LU.CEL |
- R4480LU |
- BXD97 |
- M |
- 80 |
- brown |
- 3 |
- UTM RW |
-
-
- | 46 |
- R4481LU.CEL |
- R4481LU |
- BXD98 |
- M |
- 80 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 47 |
- R4482LU.CEL |
- R4482LU |
- BXD99 |
- M |
- 72 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 48 |
- R4483LU.CEL |
- R4483LU |
- BXD22 |
- M |
- 66 |
- gray |
- 2 |
- UTM RW |
-
-
- | 49 |
- R4484LU.CEL |
- R4484LU |
- BXD25 |
- M |
- 54 |
- brown |
- 3 |
- UTM RW |
-
-
- | 50 |
- R4485LU.CEL |
- R4485LU |
- B6D2F1 |
- M |
- 62 |
- black |
- 5 |
- UTM RW |
-
-
- | 51 |
- R4486LU.CEL |
- R4486LU |
- B6D2F1 |
- F |
- 70 |
- black |
- 2 |
- UTM RW |
-
-
- | 52 |
- R4487LU.CEL |
- R4487LU |
- BALB/cByJ |
- F |
- 91 |
- white |
- 3 |
- UTM RW |
-
-
- | 53 |
- R4488LU.CEL |
- R4488LU |
- BALB/cByJ |
- M |
- 91 |
- white |
- 2 |
- UTM RW |
-
-
- | 54 |
- R4489LU.CEL |
- R4489LU |
- D2B6F1 |
- F |
- 61 |
- black |
- 2 |
- UTM RW |
-
-
- | 55 |
- R4490LU.CEL |
- R4490LU |
- D2B6F1 |
- M |
- 61 |
- black |
- 3 |
- UTM RW |
-
-
- | 56 |
- R4491LU.CEL |
- R4491LU |
- FVB/NJ |
- F |
- 62 |
- white |
- 5 |
- UTM RW |
-
-
- | 57 |
- R4492LU.CEL |
- R4492LU |
- FVB/NJ |
- M |
- 73 |
- white |
- 3 |
- UTM RW |
-
-
- | 58 |
- R4493LU.CEL |
- R4493LU |
- WSB/EiJ |
- F |
- 76 |
- agouti |
- 3 |
- UTM RW |
-
-
- | 59 |
- R4494LU.CEL |
- R4494LU |
- WSB/EiJ |
- M |
- 76 |
- agouti |
- 3 |
- UTM RW |
-
-
- | 60 |
- R4495LU.CEL |
- R4495LU |
- C57BL/6J |
- F |
- 65 |
- black |
- 3 |
- UTM RW |
-
-
- | 61 |
- R4496LU.CEL |
- R4496LU |
- C57BL/6J |
- M |
- 65 |
- black |
- 2 |
- UTM RW |
-
-
- | 62 |
- R4497LU.CEL |
- R4497LU |
- 129X1/SvJ |
- F |
- 65 |
- white |
- 4 |
- JAX |
-
-
- | 63 |
- R4498LU.CEL |
- R4498LU |
- 129X1/SvJ |
- M |
- 66 |
- white |
- 4 |
- JAX |
-
-
- | 64 |
- R4499LU.CEL |
- R4499LU |
- DBA/2J |
- F |
- 65 |
- dilute brown DBA |
- 3 |
- ORNL |
-
-
- | 65 |
- R4500LU.CEL |
- R4500LU |
- DBA/2J |
- M |
- 59 |
- dilute brown DBA |
- 2 |
- JAX |
-
-
- | 66 |
- R4501LU.CEL |
- R4501LU |
- LP/J |
- F |
- 65 |
- agouti |
- 4 |
- JAX |
-
-
- | 67 |
- R4502LU.CEL |
- R4502LU |
- LP/J |
- M |
- 65 |
- agouti |
- 4 |
- JAX |
-
-
- | 68 |
- R4503LU.CEL |
- R4503LU |
- SJL/J |
- F |
- 63 |
- white |
- 4 |
- JAX |
-
-
- | 69 |
- R4504LU.CEL |
- R4504LU |
- SJL/J |
- M |
- 65 |
- white |
- 4 |
- JAX |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/HZI_0408_M/summary.rtf b/general/datasets/HZI_0408_M/summary.rtf
deleted file mode 100644
index 5d3c1a7..0000000
--- a/general/datasets/HZI_0408_M/summary.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Phase I of BXD lung transcriptome mapping project. Project organized by Drs. Robert Williams, Klaus Schughart, Lu Lu. Started November 29, 2008. There are total 70 samples in phase I including 50 BXD strains and 10 paired inbred strains.
-
-Respir Res. 2011 May 2;12:61. doi: 10.1186/1465-9921-12-61.
-
-Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures.
-
-Alberts R1, Lu L, Williams RW, Schughart K.
-
-
-
-Erratum in
-
-
- - Respir Res. 2012;13(1):5.
-
-
-Abstract
-
-BACKGROUND:
-
-The lung is critical in surveillance and initial defense against pathogens. In humans, as in mice, individual genetic differences strongly modulate pulmonary responses to infectious agents, severity of lung disease, and potential allergic reactions. In a first step towards understanding genetic predisposition and pulmonary molecular networks that underlie individual differences in disease vulnerability, we performed a global analysis of normative lung gene expression levels in inbred mouse strains and a large family of BXD strains that are widely used for systems genetics. Our goal is to provide a key community resource on the genetics of the normative lungtranscriptome that can serve as a foundation for experimental analysis and allow predicting genetic predisposition and response to pathogens, allergens, and xenobiotics.
-
-METHODS:
-
-Steady-state polyA+ mRNA levels were assayed across a diverse and fully genotyped panel of 57 isogenic strains using the Affymetrix M430 2.0 array. Correlations of expression levels between genes were determined. Global expression QTL (eQTL) analysis and network covariance analysis was performed using tools and resources in GeneNetwork http://www.genenetwork.org.
-
-RESULTS:
-
-Expression values were highly variable across strains and in many cases exhibited a high heritability factor. Several genes which showed a restricted expression to lung tissue were identified. Using correlations between gene expression values across all strains, we defined and extended memberships of several important molecular networks in the lung. Furthermore, we were able to extract signatures of immune cell subpopulations and characterize co-variation and shared genetic modulation. Known QTL regions for respiratory infection susceptibility were investigated and several cis-eQTL genes were identified. Numerous cis- and trans-regulated transcripts and chromosomal intervals with strong regulatory activity were mapped. The Cyp1a1 P450 transcript had a strong trans-acting eQTL (LOD 11.8) on Chr 12 at 36 ± 1 Mb. This interval contains the transcription factor Ahr that has a critical mis-sense allele in the DBA/2J haplotype and evidently modulates transcriptional activation by AhR.
-
-CONCLUSIONS:
-
-Large-scale gene expression analyses in genetic reference populations revealed lung-specific and immune-cell gene expression profiles and suggested specific gene regulatory interactions.
-
-
- - PMID:21535883 PMCID:PMC3105947 DOI:10.1186/1465-9921-12-61
-
diff --git a/general/datasets/HZI_0408_R/cases.rtf b/general/datasets/HZI_0408_R/cases.rtf
deleted file mode 100644
index 83b146d..0000000
--- a/general/datasets/HZI_0408_R/cases.rtf
+++ /dev/null
@@ -1,784 +0,0 @@
-
-
-
-
-
-
-
-
- | Index |
- Array |
- Sample |
- Strain |
- Sex |
- Age |
- Color |
- Pool Size |
- Source |
-
-
- | 1 |
- R4435LU.CEL |
- R4435LU |
- BXD100 |
- F |
- 64 |
- black |
- 2 |
- UTM RW |
-
-
- | 2 |
- R4436LU.CEL |
- R4436LU |
- BXD14 |
- F |
- 85 |
- black |
- 2 |
- UTM RW |
-
-
- | 3 |
- R4437LU.CEL |
- R4437LU |
- BXD34 |
- F |
- 58 |
- black |
- 5 |
- UTM RW |
-
-
- | 4 |
- R4438LU.CEL |
- R4438LU |
- BXD39 |
- F |
- 63 |
- gray |
- 3 |
- UTM RW |
-
-
- | 5 |
- R4439LU.CEL |
- R4439LU |
- BXD40 |
- F |
- 54 |
- gray |
- 3 |
- ORNL |
-
-
- | 6 |
- R4440LU.CEL |
- R4440LU |
- BXD45 |
- F |
- 60 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 7 |
- R4441LU.CEL |
- R4441LU |
- BXD50 |
- F |
- 64 |
- dilute brown DBA |
- 4 |
- ORNL |
-
-
- | 8 |
- R4442LU.CEL |
- R4442LU |
- BXD1 |
- F |
- 88 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 9 |
- R4443LU.CEL |
- R4443LU |
- BXD16 |
- F |
- 79 |
- gray |
- 3 |
- ORNL |
-
-
- | 10 |
- R4444LU.CEL |
- R4444LU |
- BXD12 |
- F |
- 61 |
- gray |
- 5 |
- UTM RW |
-
-
- | 11 |
- R4445LU.CEL |
- R4445LU |
- BXD21 |
- F |
- 50 |
- dilute brown DBA |
- 3 |
- ORNL |
-
-
- | 12 |
- R4446LU.CEL |
- R4446LU |
- BXD19 |
- F |
- 49 |
- gray |
- 3 |
- ORNL |
-
-
- | 13 |
- R4447LU.CEL |
- R4447LU |
- BXD27 |
- F |
- 85 |
- brown |
- 3 |
- UTM RW |
-
-
- | 14 |
- R4448LU.CEL |
- R4448LU |
- BXD31 |
- F |
- 81 |
- black |
- 3 |
- UTM RW |
-
-
- | 15 |
- R4449LU.CEL |
- R4449LU |
- BXD32 |
- F |
- 68 |
- black |
- 5 |
- ORNL |
-
-
- | 16 |
- R4450LU.CEL |
- R4450LU |
- BXD33 |
- F |
- 61 |
- gray |
- 2 |
- ORNL |
-
-
- | 17 |
- R4451LU.CEL |
- R4451LU |
- BXD42 |
- F |
- 65 |
- black |
- 2 |
- UTM RW |
-
-
- | 18 |
- R4452LU.CEL |
- R4452LU |
- BXD43 |
- F |
- 79 |
- black |
- 2 |
- UTM RW |
-
-
- | 19 |
- R4453LU.CEL |
- R4453LU |
- BXD45 |
- F |
- 60 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 20 |
- R4454LU.CEL |
- R4454LU |
- BXD55 |
- M |
- 80 |
- brown |
- 3 |
- UTM RW |
-
-
- | 21 |
- R4455LU.CEL |
- R4455LU |
- BXD56 |
- M |
- 91 |
- black |
- 3 |
- UTM RW |
-
-
- | 22 |
- R4456LU.CEL |
- R4456LU |
- BXD66 |
- F |
- 80 |
- brown |
- 3 |
- UTM RW |
-
-
- | 23 |
- R4457LU.CEL |
- R4457LU |
- BXD68 |
- F |
- 65 |
- brown |
- 4 |
- UTM RW |
-
-
- | 24 |
- R4459LU-re.CEL |
- R4459LU |
- BXD89 |
- F |
- 79 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 25 |
- R4460LU.CEL |
- R4460LU |
- BXD51 |
- M |
- 81 |
- black |
- 2 |
- UTM RW |
-
-
- | 26 |
- R4461LU.CEL |
- R4461LU |
- BXD97 |
- F |
- N/A |
- N/A |
- N/A |
- N/A |
-
-
- | 27 |
- R4462LU.CEL |
- R4462LU |
- BXD48 |
- F |
- 61 |
- black |
- 3 |
- ORNL |
-
-
- | 28 |
- R4463LU.CEL |
- R4463LU |
- BXD60 |
- M |
- 93 |
- brown |
- 2 |
- UTM RW |
-
-
- | 29 |
- R4464LU.CEL |
- R4464LU |
- BXD62 |
- M |
- 80 |
- brown |
- 2 |
- UTM RW |
-
-
- | 30 |
- R4465LU.CEL |
- R4465LU |
- BXD69 |
- M |
- 63 |
- dilute brown DBA |
- 5 |
- UTM RW |
-
-
- | 31 |
- R4466LU.CEL |
- R4466LU |
- BXD70 |
- M |
- 75 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 32 |
- R4467LU.CEL |
- R4467LU |
- BXD71 |
- M |
- 64 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 33 |
- R4468LU.CEL |
- R4468LU |
- BXD73 |
- M |
- 59 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 34 |
- R4469L.CEL |
- R4469LU |
- BXD75 |
- M |
- 51 |
- dilute brown DBA |
- 4 |
- UTM RW |
-
-
- | 35 |
- R4470L.CEL |
- R4470LU |
- BXD2 |
- M |
- 84 |
- black |
- 3 |
- UTM RW |
-
-
- | 36 |
- R4471H-re.CEL |
- R4471LU |
- BXD83 |
- M |
- 75 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 37 |
- R4472L.CEL |
- R4472LU |
- BXD84 |
- M |
- 78 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 38 |
- R4473LU.CEL |
- R4473LU |
- BXD86 |
- M |
- 77 |
- black |
- 3 |
- UTM RW |
-
-
- | 39 |
- R4474LU.CEL |
- R4474LU |
- BXD87 |
- M |
- 67 |
- black |
- 3 |
- UTM RW |
-
-
- | 40 |
- R4475LU.CEL |
- R4475LU |
- BXD9 |
- M |
- 78 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 41 |
- R4476LU.CEL |
- R4476LU |
- BXD90 |
- M |
- 63 |
- dilute brown DBA |
- 3 |
- UTM RW |
-
-
- | 42 |
- R4477LU.CEL |
- R4477LU |
- BXD65 |
- M |
- 59 |
- brown |
- 3 |
- ORNL |
-
-
- | 43 |
- R4478LU.CEL |
- R4478LU |
- BXD6 |
- M |
- 92 |
- gray |
- 3 |
- UTM RW |
-
-
- | 44 |
- R4479LU.CEL |
- R4479LU |
- BXD96 |
- M |
- 71 |
- black |
- 3 |
- UTM RW |
-
-
- | 45 |
- R4480LU.CEL |
- R4480LU |
- BXD97 |
- M |
- 80 |
- brown |
- 3 |
- UTM RW |
-
-
- | 46 |
- R4481LU.CEL |
- R4481LU |
- BXD98 |
- M |
- 80 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 47 |
- R4482LU.CEL |
- R4482LU |
- BXD99 |
- M |
- 72 |
- dilute brown DBA |
- 2 |
- UTM RW |
-
-
- | 48 |
- R4483LU.CEL |
- R4483LU |
- BXD22 |
- M |
- 66 |
- gray |
- 2 |
- UTM RW |
-
-
- | 49 |
- R4484LU.CEL |
- R4484LU |
- BXD25 |
- M |
- 54 |
- brown |
- 3 |
- UTM RW |
-
-
- | 50 |
- R4485LU.CEL |
- R4485LU |
- B6D2F1 |
- M |
- 62 |
- black |
- 5 |
- UTM RW |
-
-
- | 51 |
- R4486LU.CEL |
- R4486LU |
- B6D2F1 |
- F |
- 70 |
- black |
- 2 |
- UTM RW |
-
-
- | 52 |
- R4487LU.CEL |
- R4487LU |
- BALB/cByJ |
- F |
- 91 |
- white |
- 3 |
- UTM RW |
-
-
- | 53 |
- R4488LU.CEL |
- R4488LU |
- BALB/cByJ |
- M |
- 91 |
- white |
- 2 |
- UTM RW |
-
-
- | 54 |
- R4489LU.CEL |
- R4489LU |
- D2B6F1 |
- F |
- 61 |
- black |
- 2 |
- UTM RW |
-
-
- | 55 |
- R4490LU.CEL |
- R4490LU |
- D2B6F1 |
- M |
- 61 |
- black |
- 3 |
- UTM RW |
-
-
- | 56 |
- R4491LU.CEL |
- R4491LU |
- FVB/NJ |
- F |
- 62 |
- white |
- 5 |
- UTM RW |
-
-
- | 57 |
- R4492LU.CEL |
- R4492LU |
- FVB/NJ |
- M |
- 73 |
- white |
- 3 |
- UTM RW |
-
-
- | 58 |
- R4493LU.CEL |
- R4493LU |
- WSB/EiJ |
- F |
- 76 |
- agouti |
- 3 |
- UTM RW |
-
-
- | 59 |
- R4494LU.CEL |
- R4494LU |
- WSB/EiJ |
- M |
- 76 |
- agouti |
- 3 |
- UTM RW |
-
-
- | 60 |
- R4495LU.CEL |
- R4495LU |
- C57BL/6J |
- F |
- 65 |
- black |
- 3 |
- UTM RW |
-
-
- | 61 |
- R4496LU.CEL |
- R4496LU |
- C57BL/6J |
- M |
- 65 |
- black |
- 2 |
- UTM RW |
-
-
- | 62 |
- R4497LU.CEL |
- R4497LU |
- 129X1/SvJ |
- F |
- 65 |
- white |
- 4 |
- JAX |
-
-
- | 63 |
- R4498LU.CEL |
- R4498LU |
- 129X1/SvJ |
- M |
- 66 |
- white |
- 4 |
- JAX |
-
-
- | 64 |
- R4499LU.CEL |
- R4499LU |
- DBA/2J |
- F |
- 65 |
- dilute brown DBA |
- 3 |
- ORNL |
-
-
- | 65 |
- R4500LU.CEL |
- R4500LU |
- DBA/2J |
- M |
- 59 |
- dilute brown DBA |
- 2 |
- JAX |
-
-
- | 66 |
- R4501LU.CEL |
- R4501LU |
- LP/J |
- F |
- 65 |
- agouti |
- 4 |
- JAX |
-
-
- | 67 |
- R4502LU.CEL |
- R4502LU |
- LP/J |
- M |
- 65 |
- agouti |
- 4 |
- JAX |
-
-
- | 68 |
- R4503LU.CEL |
- R4503LU |
- SJL/J |
- F |
- 63 |
- white |
- 4 |
- JAX |
-
-
- | 69 |
- R4504LU.CEL |
- R4504LU |
- SJL/J |
- M |
- 65 |
- white |
- 4 |
- JAX |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/HZI_0408_R/summary.rtf b/general/datasets/HZI_0408_R/summary.rtf
deleted file mode 100644
index 5d3c1a7..0000000
--- a/general/datasets/HZI_0408_R/summary.rtf
+++ /dev/null
@@ -1,37 +0,0 @@
-Phase I of BXD lung transcriptome mapping project. Project organized by Drs. Robert Williams, Klaus Schughart, Lu Lu. Started November 29, 2008. There are total 70 samples in phase I including 50 BXD strains and 10 paired inbred strains.
-
-Respir Res. 2011 May 2;12:61. doi: 10.1186/1465-9921-12-61.
-
-Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures.
-
-Alberts R1, Lu L, Williams RW, Schughart K.
-
-
-
-Erratum in
-
-
- - Respir Res. 2012;13(1):5.
-
-
-Abstract
-
-BACKGROUND:
-
-The lung is critical in surveillance and initial defense against pathogens. In humans, as in mice, individual genetic differences strongly modulate pulmonary responses to infectious agents, severity of lung disease, and potential allergic reactions. In a first step towards understanding genetic predisposition and pulmonary molecular networks that underlie individual differences in disease vulnerability, we performed a global analysis of normative lung gene expression levels in inbred mouse strains and a large family of BXD strains that are widely used for systems genetics. Our goal is to provide a key community resource on the genetics of the normative lungtranscriptome that can serve as a foundation for experimental analysis and allow predicting genetic predisposition and response to pathogens, allergens, and xenobiotics.
-
-METHODS:
-
-Steady-state polyA+ mRNA levels were assayed across a diverse and fully genotyped panel of 57 isogenic strains using the Affymetrix M430 2.0 array. Correlations of expression levels between genes were determined. Global expression QTL (eQTL) analysis and network covariance analysis was performed using tools and resources in GeneNetwork http://www.genenetwork.org.
-
-RESULTS:
-
-Expression values were highly variable across strains and in many cases exhibited a high heritability factor. Several genes which showed a restricted expression to lung tissue were identified. Using correlations between gene expression values across all strains, we defined and extended memberships of several important molecular networks in the lung. Furthermore, we were able to extract signatures of immune cell subpopulations and characterize co-variation and shared genetic modulation. Known QTL regions for respiratory infection susceptibility were investigated and several cis-eQTL genes were identified. Numerous cis- and trans-regulated transcripts and chromosomal intervals with strong regulatory activity were mapped. The Cyp1a1 P450 transcript had a strong trans-acting eQTL (LOD 11.8) on Chr 12 at 36 ± 1 Mb. This interval contains the transcription factor Ahr that has a critical mis-sense allele in the DBA/2J haplotype and evidently modulates transcriptional activation by AhR.
-
-CONCLUSIONS:
-
-Large-scale gene expression analyses in genetic reference populations revealed lung-specific and immune-cell gene expression profiles and suggested specific gene regulatory interactions.
-
-
- - PMID:21535883 PMCID:PMC3105947 DOI:10.1186/1465-9921-12-61
-
diff --git a/general/datasets/Heioncvscretilm6_0911/experiment-type.rtf b/general/datasets/Heioncvscretilm6_0911/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Heioncvscretilm6_0911/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/acknowledgment.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/acknowledgment.rtf
deleted file mode 100644
index 959532f..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/acknowledgment.rtf
+++ /dev/null
@@ -1,8 +0,0 @@
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA.
-
-
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
-
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/cases.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/cases.rtf
deleted file mode 100644
index f3302c7..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-The LXS genetic reference panel of recombinant inbred strains consists of just over 77 strains. All of these strains have been inbred for more than 23 generations (F23). All strains have been genotyped at 13,377 SNPs. Thanks to the efforts of Dr. Timothy Wiltshire at the Genome Institute of the Novartis Research Foundation, the two parental strains have been genotyped at 156,551 SNPs. These genotypes are incorporated in the GeneNetwork SNP Browser.
-
-Strains are currently available from Drs. Beth Bennett and Tom Johnson at the Institute of Behavioral Genetics (IBG) in Boulder Colorado.
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/experiment-design.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/experiment-design.rtf
deleted file mode 100644
index da9d781..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/experiment-design.rtf
+++ /dev/null
@@ -1,2123 +0,0 @@
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between July 25 and Dec 20, 2006. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on the original Mouse-6 v 1.0 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each strain. While all strains were orginally represented by matched male and female samples, one strain LXS34 consists of two female samples. Given the expression of Xist, we suspect that strain LXS114 is represented by two male pools (see figure at bottom of page).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
-
-
-This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/notes.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/notes.rtf
deleted file mode 100644
index 4ae3a03..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data uploaded by Hongqiang Li, Oct 30, 2006. This text file originally generated by LL and RWW on November 29, 2006. Updated by LL, Dec 1, 2006. Updated March 25, April 25 by RWW.
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/platform.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/platform.rtf
deleted file mode 100644
index cb0e31f..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/platform.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
-
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/processing.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/processing.rtf
deleted file mode 100644
index 678856e..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/processing.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-
-All data links (right-most column above) will be made active as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
-
-
-
-This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
-Sex of the samples was validated using sex-specific probe set: Xist (probe ILM106520068, also known as scl00213742.1_141-S).
-
-
-
-Legend: Checking that the sex of samples was labeled correctly in mouse array data sets using Xist expression measured by probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample. In contrast LXS34 has very high expression and no error bar because the sample is from a single female pool.
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/summary.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/summary.rtf
deleted file mode 100644
index 357e642..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/summary.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-ILLUMINA Mouse-6 DATA SET: The LXS Hippocampus Illumina Rank Invariant data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains and ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics).All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray (GEO GPL6099) BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were are not included. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from 6.141 average (very low or no expression) to 19.987 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this initial data set, 1170 probes have LRS values >46. The maximum LRS achieved in this data set is 358.8 for probe ILM103520706 (Disabled 1; Dab1).
-
-
-
-Legend: Bar chart of the expression of Dab1 probe ILM103520706 in the LXS data set. This probe has a Mendelian segregation pattern and is associated with a LOD score of 77.7 (LRS 358.8). The two parental strains are shown to the far left, followed by all of the LXS strains for which we have acquired mRNA expression estimates in the hippocampus.
-
-
-
-ABOUT THE HIPPOCAMPUS. The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval. This region of the brain is particularly vulnerable to the effects of environmental stressors and is a key upstream modulator of the hypothalamic-pituitary-adrenal axis (the HPA). The hippocampus is also often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators supported by numerous agencies described in the Acknowledgments section.
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_0507/tissue.rtf b/general/datasets/Hipp_Illumina_RankInv_0507/tissue.rtf
deleted file mode 100644
index 04565fc..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_0507/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/acknowledgment.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/acknowledgment.rtf
deleted file mode 100644
index 959532f..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/acknowledgment.rtf
+++ /dev/null
@@ -1,8 +0,0 @@
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA.
-
-
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
-
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/cases.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/cases.rtf
deleted file mode 100644
index f3302c7..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-The LXS genetic reference panel of recombinant inbred strains consists of just over 77 strains. All of these strains have been inbred for more than 23 generations (F23). All strains have been genotyped at 13,377 SNPs. Thanks to the efforts of Dr. Timothy Wiltshire at the Genome Institute of the Novartis Research Foundation, the two parental strains have been genotyped at 156,551 SNPs. These genotypes are incorporated in the GeneNetwork SNP Browser.
-
-Strains are currently available from Drs. Beth Bennett and Tom Johnson at the Institute of Behavioral Genetics (IBG) in Boulder Colorado.
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/experiment-design.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/experiment-design.rtf
deleted file mode 100644
index da9d781..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/experiment-design.rtf
+++ /dev/null
@@ -1,2123 +0,0 @@
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between July 25 and Dec 20, 2006. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on the original Mouse-6 v 1.0 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each strain. While all strains were orginally represented by matched male and female samples, one strain LXS34 consists of two female samples. Given the expression of Xist, we suspect that strain LXS114 is represented by two male pools (see figure at bottom of page).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
-
-
-This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/notes.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/notes.rtf
deleted file mode 100644
index 4ae3a03..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data uploaded by Hongqiang Li, Oct 30, 2006. This text file originally generated by LL and RWW on November 29, 2006. Updated by LL, Dec 1, 2006. Updated March 25, April 25 by RWW.
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/platform.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/platform.rtf
deleted file mode 100644
index cb0e31f..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/platform.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
-
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/processing.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/processing.rtf
deleted file mode 100644
index 678856e..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/processing.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-
-All data links (right-most column above) will be made active as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
-
-
-
-This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
-Sex of the samples was validated using sex-specific probe set: Xist (probe ILM106520068, also known as scl00213742.1_141-S).
-
-
-
-Legend: Checking that the sex of samples was labeled correctly in mouse array data sets using Xist expression measured by probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample. In contrast LXS34 has very high expression and no error bar because the sample is from a single female pool.
-
diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/summary.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/summary.rtf
deleted file mode 100644
index 357e642..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/summary.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-ILLUMINA Mouse-6 DATA SET: The LXS Hippocampus Illumina Rank Invariant data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains and ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics).All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray (GEO GPL6099) BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were are not included. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from 6.141 average (very low or no expression) to 19.987 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this initial data set, 1170 probes have LRS values >46. The maximum LRS achieved in this data set is 358.8 for probe ILM103520706 (Disabled 1; Dab1).
-
-
-
-Legend: Bar chart of the expression of Dab1 probe ILM103520706 in the LXS data set. This probe has a Mendelian segregation pattern and is associated with a LOD score of 77.7 (LRS 358.8). The two parental strains are shown to the far left, followed by all of the LXS strains for which we have acquired mRNA expression estimates in the hippocampus.
-
-
-
-ABOUT THE HIPPOCAMPUS. The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval. This region of the brain is particularly vulnerable to the effects of environmental stressors and is a key upstream modulator of the hypothalamic-pituitary-adrenal axis (the HPA). The hippocampus is also often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators supported by numerous agencies described in the Acknowledgments section.
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diff --git a/general/datasets/Hipp_Illumina_RankInv_1006/tissue.rtf b/general/datasets/Hipp_Illumina_RankInv_1006/tissue.rtf
deleted file mode 100644
index 04565fc..0000000
--- a/general/datasets/Hipp_Illumina_RankInv_1006/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf b/general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf
deleted file mode 100644
index 959532f..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/acknowledgment.rtf
+++ /dev/null
@@ -1,8 +0,0 @@
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA.
-
-
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
-
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/cases.rtf b/general/datasets/Hipp_Illumina_Rank_1006/cases.rtf
deleted file mode 100644
index f3302c7..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-The LXS genetic reference panel of recombinant inbred strains consists of just over 77 strains. All of these strains have been inbred for more than 23 generations (F23). All strains have been genotyped at 13,377 SNPs. Thanks to the efforts of Dr. Timothy Wiltshire at the Genome Institute of the Novartis Research Foundation, the two parental strains have been genotyped at 156,551 SNPs. These genotypes are incorporated in the GeneNetwork SNP Browser.
-
-Strains are currently available from Drs. Beth Bennett and Tom Johnson at the Institute of Behavioral Genetics (IBG) in Boulder Colorado.
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf b/general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf
deleted file mode 100644
index da9d781..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/experiment-design.rtf
+++ /dev/null
@@ -1,2123 +0,0 @@
-
-Sample Processing: Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between July 25 and Dec 20, 2006. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on the original Mouse-6 v 1.0 slide. The slides were hybridized and washed following standard Illumina protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each strain. While all strains were orginally represented by matched male and female samples, one strain LXS34 consists of two female samples. Given the expression of Xist, we suspect that strain LXS114 is represented by two male pools (see figure at bottom of page).
-
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
-
-
-This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/notes.rtf b/general/datasets/Hipp_Illumina_Rank_1006/notes.rtf
deleted file mode 100644
index 4ae3a03..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data uploaded by Hongqiang Li, Oct 30, 2006. This text file originally generated by LL and RWW on November 29, 2006. Updated by LL, Dec 1, 2006. Updated March 25, April 25 by RWW.
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/platform.rtf b/general/datasets/Hipp_Illumina_Rank_1006/platform.rtf
deleted file mode 100644
index cb0e31f..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/platform.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
-
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/processing.rtf b/general/datasets/Hipp_Illumina_Rank_1006/processing.rtf
deleted file mode 100644
index 678856e..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/processing.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-
-All data links (right-most column above) will be made active as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
-
-
-
-This data set uses the standard Rank Invariant method developed by Illumina and described in their BeadStation Studio documentation.
-
-Sex of the samples was validated using sex-specific probe set: Xist (probe ILM106520068, also known as scl00213742.1_141-S).
-
-
-
-Legend: Checking that the sex of samples was labeled correctly in mouse array data sets using Xist expression measured by probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample. In contrast LXS34 has very high expression and no error bar because the sample is from a single female pool.
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/summary.rtf b/general/datasets/Hipp_Illumina_Rank_1006/summary.rtf
deleted file mode 100644
index 357e642..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/summary.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-ILLUMINA Mouse-6 DATA SET: The LXS Hippocampus Illumina Rank Invariant data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains and ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics).All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray (GEO GPL6099) BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were are not included. This particular data set was processed using the Illumina "Rank Invariant" protocol. Values were log2 transformed and the current data range from 6.141 average (very low or no expression) to 19.987 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this initial data set, 1170 probes have LRS values >46. The maximum LRS achieved in this data set is 358.8 for probe ILM103520706 (Disabled 1; Dab1).
-
-
-
-Legend: Bar chart of the expression of Dab1 probe ILM103520706 in the LXS data set. This probe has a Mendelian segregation pattern and is associated with a LOD score of 77.7 (LRS 358.8). The two parental strains are shown to the far left, followed by all of the LXS strains for which we have acquired mRNA expression estimates in the hippocampus.
-
-
-
-ABOUT THE HIPPOCAMPUS. The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval. This region of the brain is particularly vulnerable to the effects of environmental stressors and is a key upstream modulator of the hypothalamic-pituitary-adrenal axis (the HPA). The hippocampus is also often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators supported by numerous agencies described in the Acknowledgments section.
-
diff --git a/general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf b/general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf
deleted file mode 100644
index 04565fc..0000000
--- a/general/datasets/Hipp_Illumina_Rank_1006/tissue.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
diff --git a/general/datasets/Hqfneoc_0208_rankinv/experiment-type.rtf b/general/datasets/Hqfneoc_0208_rankinv/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Hqfneoc_0208_rankinv/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf b/general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Hqfneoc_1210_rankinv/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Hqfneoc_1210v2_rankinv/experiment-type.rtf b/general/datasets/Hqfneoc_1210v2_rankinv/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Hqfneoc_1210v2_rankinv/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Hzi_pr8m_q_0612/experiment-type.rtf b/general/datasets/Hzi_pr8m_q_0612/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Hzi_pr8m_q_0612/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/IBR_M_0106_P/acknowledgment.rtf b/general/datasets/IBR_M_0106_P/acknowledgment.rtf
deleted file mode 100644
index a1563a6..0000000
--- a/general/datasets/IBR_M_0106_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0106_P/cases.rtf b/general/datasets/IBR_M_0106_P/cases.rtf
deleted file mode 100644
index 8794b88..0000000
--- a/general/datasets/IBR_M_0106_P/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues
-
-
-All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).
-
diff --git a/general/datasets/IBR_M_0106_P/notes.rtf b/general/datasets/IBR_M_0106_P/notes.rtf
deleted file mode 100644
index 72bad83..0000000
--- a/general/datasets/IBR_M_0106_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.
-
diff --git a/general/datasets/IBR_M_0106_P/platform.rtf b/general/datasets/IBR_M_0106_P/platform.rtf
deleted file mode 100644
index 028fe23..0000000
--- a/general/datasets/IBR_M_0106_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/IBR_M_0106_P/processing.rtf b/general/datasets/IBR_M_0106_P/processing.rtf
deleted file mode 100644
index 243e5c0..0000000
--- a/general/datasets/IBR_M_0106_P/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/IBR_M_0106_P/summary.rtf b/general/datasets/IBR_M_0106_P/summary.rtf
deleted file mode 100644
index 6fe94b1..0000000
--- a/general/datasets/IBR_M_0106_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/IBR_M_0106_P/tissue.rtf b/general/datasets/IBR_M_0106_P/tissue.rtf
deleted file mode 100644
index 841d879..0000000
--- a/general/datasets/IBR_M_0106_P/tissue.rtf
+++ /dev/null
@@ -1,977 +0,0 @@
-The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).
-
-Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.
-
-The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.
-
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
- Sample_name |
- Result date |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Nov03 |
- UTM RW |
-
-
- | 2 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Jan04 |
- UTM RW |
-
-
- | 3 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Nov03 |
- UTM RW |
-
-
- | 4 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Jan04 |
- UTM RW |
-
-
- | 5 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Feb05 |
- UTM RW |
-
-
- | 6 |
- C57BL/6J |
- M |
- 76 |
- R0997F1 |
- Feb05 |
- UTM RW |
-
-
- | 7 |
- D2B6F1 |
- F |
- 57 |
- R1066F1 |
- Feb05 |
- UTM RW |
-
-
- | 8 |
- D2B6F1 |
- M |
- 59 |
- R1381F1 |
- Feb05 |
- UTM RW |
-
-
- | 9 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Nov03 |
- UTM RW |
-
-
- | 10 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Feb05 |
- UTM RW |
-
-
- | 11 |
- DBA/2J |
- F |
- 60 |
- R0917F2 |
- Jan04 |
- UTM RW |
-
-
- | 12 |
- DBA/2J |
- F |
- 64 |
- R1123F1 |
- Feb05 |
- UTM RW |
-
-
- | 13 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Nov03 |
- UTM RW |
-
-
- | 14 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Jan04 |
- UTM RW |
-
-
- | 15 |
- DBA/2J |
- M |
- 73 |
- R1009F1 |
- Feb05 |
- UTM RW |
-
-
- | 16 |
- B6D2F1 |
- F |
- 127 |
- R0919F1 |
- Jan04 |
- UTM JB |
-
-
- | 17 |
- B6D2F1 |
- F |
- 127 |
- R0919F2 |
- Jan04 |
- UTM JB |
-
-
- | 18 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 19 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 20 |
- B6D2F1 |
- M |
- 127 |
- R0920F1 |
- Jan04 |
- UTM JB |
-
-
- | 21 |
- B6D2F1 |
- M |
- 127 |
- R0920F2 |
- Jan04 |
- UTM JB |
-
-
- | 22 |
- B6D2F1 |
- M |
- 66 |
- R1057F1 |
- Feb05 |
- UTM RW |
-
-
- | 23 |
- BXD1 |
- M |
- 181 |
- R0956F1 |
- Feb05 |
- UTM JB |
-
-
- | 24 |
- BXD1 |
- F |
- 95 |
- R0895F1 |
- Jan04 |
- UMemphis |
-
-
- | 25 |
- BXD2 |
- F |
- 142 |
- R0907F1 |
- Feb05 |
- UAB |
-
-
- | 26 |
- BXD5 |
- F |
- 56 |
- R0744F1 |
- Feb05 |
- UMemphis |
-
-
- | 27 |
- BXD5 |
- M |
- 71 |
- R0728F1 |
- Jan04 |
- UMemphis |
-
-
- | 28 |
- BXD6 |
- F |
- 57 |
- R1711F1 |
- Feb05 |
- JAX |
-
-
- | 29 |
- BXD6 |
- F |
- 92 |
- R0901F1 |
- Feb05 |
- UMemphis |
-
-
- | 30 |
- BXD6 |
- M |
- 92 |
- R0902F1 |
- Jan04 |
- UMemphis |
-
-
- | 31 |
- BXD8 |
- F |
- 72 |
- R0167F1 |
- Jan04 |
- UAB |
-
-
- | 32 |
- BXD9 |
- F |
- 86 |
- R0908F1 |
- Feb05 |
- UMemphis |
-
-
- | 33 |
- BXD9 |
- M |
- 86 |
- R0909F1 |
- Jan04 |
- UMemphis |
-
-
- | 34 |
- BXD11 |
- F |
- 97 |
- R0745F1 |
- Feb05 |
- UAB |
-
-
- | 35 |
- BXD11 |
- M |
- 92 |
- R0666F1 |
- Feb05 |
- UMemphis |
-
-
- | 36 |
- BXD12 |
- F |
- 64 |
- R0896F1 |
- Feb05 |
- UMemphis |
-
-
- | 37 |
- BXD12 |
- M |
- 64 |
- R0897F1 |
- Jan04 |
- UMemphis |
-
-
- | 38 |
- BXD13 |
- F |
- 86 |
- R0730F1 |
- Feb05 |
- UMemphis |
-
-
- | 39 |
- BXD13 |
- F |
- 86 |
- R0748F1 |
- Jan04 |
- UMemphis |
-
-
- | 40 |
- BXD13 |
- M |
- 76 |
- R0929F1 |
- Feb05 |
- UMemphis |
-
-
- | 41 |
- BXD14 |
- M |
- 91 |
- R0912F1 |
- Jan04 |
- UMemphis |
-
-
- | 42 |
- BXD14 |
- M |
- 68 |
- R1051F1 |
- Feb05 |
- UTM RW |
-
-
- | 43 |
- BXD15 |
- F |
- 80 |
- R0928F1 |
- Feb05 |
- UMemphis |
-
-
- | 44 |
- BXD18 |
- F |
- 108 |
- R0771F1 |
- Jan04 |
- UAB |
-
-
- | 45 |
- BXD19 |
- M |
- 157 |
- R1229F1 |
- Feb05 |
- UTM JB |
-
-
- | 46 |
- BXD19 |
- F |
- 56 |
- R0236F1 |
- Jan04 |
- UAB |
-
-
- | 47 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Jan04 |
- UAB |
-
-
- | 48 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Feb05 |
- UAB |
-
-
- | 49 |
- BXD23 |
- F |
- 66 |
- R1035F1 |
- Feb05 |
- UTM RW |
-
-
- | 50 |
- BXD23 |
- M |
- 66 |
- R1037F1 |
- Feb05 |
- UTM RW |
-
-
- | 51 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Jan04 |
- UAB |
-
-
- | 52 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Feb05 |
- UAB |
-
-
- | 53 |
- BXD24 |
- F |
- 71 |
- R0914F1 |
- Feb05 |
- UMemphis |
-
-
- | 54 |
- BXD24 |
- M |
- 71 |
- R0913F1 |
- Jan04 |
- UMemphis |
-
-
- | 55 |
- BXD25 |
- F |
- 74 |
- R0373F1 |
- Jan04 |
- UTM RW |
-
-
- | 56 |
- BXD28 |
- F |
- 79 |
- R0910F1 |
- Jan04 |
- UMemphis |
-
-
- | 57 |
- BXD28 |
- M |
- 79 |
- R0911F1 |
- Feb05 |
- UMemphis |
-
-
- | 58 |
- BXD28 |
- F |
- 113 |
- R0892F1 |
- Feb05 |
- UTM RW |
-
-
- | 59 |
- BXD29 |
- F |
- 76 |
- R0693F1 |
- Jan04 |
- UMemphis |
-
-
- | 60 |
- BXD31 |
- F |
- 61 |
- R1199F1 |
- Feb05 |
- UTM RW |
-
-
- | 61 |
- BXD31 |
- M |
- 61 |
- R1141F1 |
- Feb05 |
- UTM RW |
-
-
- | 62 |
- BXD32 |
- F |
- 93 |
- R0898F1 |
- Jan04 |
- UAB |
-
-
- | 63 |
- BXD32 |
- F |
- 76 |
- R1214F1 |
- Feb05 |
- UMemphis |
-
-
- | 64 |
- BXD32 |
- M |
- 65 |
- R1478F1 |
- Feb05 |
- UMemphis |
-
-
- | 65 |
- BXD33 |
- M |
- 77 |
- R0915F1 |
- Jan04 |
- UMemphis |
-
-
- | 66 |
- BXD34 |
- F |
- 92 |
- R0900F1 |
- Feb05 |
- UMemphis |
-
-
- | 67 |
- BXD34 |
- M |
- 56 |
- R0617F1 |
- Feb05 |
- UMemphis |
-
-
- | 68 |
- BXD34 |
- M |
- 72 |
- R0916F1 |
- Jan04 |
- UMemphis |
-
-
- | 69 |
- BXD36 |
- F |
- 61 |
- R1145F1 |
- Feb05 |
- UTM RW |
-
-
- | 70 |
- BXD36 |
- M |
- 77 |
- R0926F1 |
- Jan04 |
- UMemphis |
-
-
- | 71 |
- BXD36 |
- M |
- 61 |
- R1211F1 |
- Feb05 |
- UMemphis |
-
-
- | 72 |
- BXD38 |
- M |
- 83 |
- R1208F1 |
- Feb05 |
- UMemphis |
-
-
- | 73 |
- BXD38 |
- F |
- 69 |
- R0729F1 |
- Feb05 |
- UMemphis |
-
-
- | 74 |
- BXD38 |
- M |
- 69 |
- R0731F1 |
- Jan04 |
- UMemphis |
-
-
- | 75 |
- BXD39 |
- F |
- 76 |
- R1712F1 |
- Feb05 |
- JAX |
-
-
- | 76 |
- BXD39 |
- M |
- 71 |
- R0602F1 |
- Feb05 |
- UAB |
-
-
- | 77 |
- BXD40 |
- F |
- 184 |
- R0741F1 |
- Feb05 |
- UAB |
-
-
- | 78 |
- BXD40 |
- M |
- 56 |
- R0894F1 |
- Feb05 |
- UMemphis |
-
-
- | 79 |
- BXD42 |
- F |
- 100 |
- R0742F1 |
- Feb05 |
- UAB |
-
-
- | 80 |
- BXD42 |
- M |
- 97 |
- R0936F1 |
- Jan04 |
- UMemphis |
-
-
- | 81 |
- BXD42 |
- M |
- 105 |
- R0937F1 |
- Feb05 |
- UMemphis |
-
-
- | 82 |
- BXD43 |
- M |
- 63 |
- R1047F1 |
- Feb05 |
- UTM RW |
-
-
- | 83 |
- BXD44 |
- F |
- 57 |
- R1069F1 |
- Feb05 |
- UTM RW |
-
-
- | 84 |
- BXD44 |
- M |
- 58 |
- R1072F1 |
- Feb05 |
- UTM RW |
-
-
- | 85 |
- BXD45 |
- F |
- 58 |
- R1398F1 |
- Feb05 |
- UTM RW |
-
-
- | 86 |
- BXD48 |
- F |
- 59 |
- R0946F1 |
- Feb05 |
- UTM RW |
-
-
- | 87 |
- BXD48 |
- M |
- 64 |
- R0970F1 |
- Feb05 |
- UTM RW |
-
-
- | 88 |
- BXD51 |
- F |
- 63 |
- R1430F1 |
- Feb05 |
- UTM RW |
-
-
- | 89 |
- BXD51 |
- M |
- 65 |
- R1001F1 |
- Feb05 |
- UTM RW |
-
-
- | 90 |
- BXD60 |
- F |
- 64 |
- R0976F1 |
- Feb05 |
- UTM RW |
-
-
- | 91 |
- BXD60 |
- M |
- 59 |
- R1075F1 |
- Feb05 |
- UTM RW |
-
-
- | 92 |
- BXD62 |
- F |
- 59 |
- R1033F1 |
- Feb05 |
- UTM RW |
-
-
- | 93 |
- BXD62 |
- M |
- 58 |
- R1027F1 |
- Feb05 |
- UTM RW |
-
-
- | 94 |
- BXD69 |
- F |
- 60 |
- R1438F1 |
- Feb05 |
- UTM RW |
-
-
- | 95 |
- BXD69 |
- M |
- 64 |
- R1193F1 |
- Feb05 |
- UTM RW |
-
-
- | 96 |
- BXD73 |
- F |
- 60 |
- R1275F1 |
- Feb05 |
- UTM RW |
-
-
- | 97 |
- BXD73 |
- M |
- 76 |
- R1442F1 |
- Feb05 |
- UTM RW |
-
-
- | 98 |
- BXD77 |
- M |
- 61 |
- R1426F1 |
- Feb05 |
- UTM RW |
-
-
- | 99 |
- BXD86 |
- F |
- 77 |
- R1414F1 |
- Feb05 |
- UTM RW |
-
-
- | 100 |
- BXD86 |
- M |
- 77 |
- R1418F1 |
- Feb05 |
- UTM RW |
-
-
- | 101 |
- BXD87 |
- F |
- 89 |
- R1713F1 |
- Feb05 |
- UTM RW |
-
-
- | 102 |
- BXD87 |
- M |
- 84 |
- R1709F1 |
- Feb05 |
- UTM RW |
-
-
- | 103 |
- BXD90 |
- M |
- 61 |
- R1452F |
- Feb05 |
- UTM RW |
-
-
- | 104 |
- BXD92 |
- F |
- 58 |
- R1299F1 |
- Feb05 |
- UTM RW |
-
-
- | 105 |
- BXD92 |
- M |
- 59 |
- R1307F1 |
- Feb05 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/IBR_M_0106_R/acknowledgment.rtf b/general/datasets/IBR_M_0106_R/acknowledgment.rtf
deleted file mode 100644
index a1563a6..0000000
--- a/general/datasets/IBR_M_0106_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0106_R/cases.rtf b/general/datasets/IBR_M_0106_R/cases.rtf
deleted file mode 100644
index 8794b88..0000000
--- a/general/datasets/IBR_M_0106_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues
-
-
-All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).
-
diff --git a/general/datasets/IBR_M_0106_R/notes.rtf b/general/datasets/IBR_M_0106_R/notes.rtf
deleted file mode 100644
index 72bad83..0000000
--- a/general/datasets/IBR_M_0106_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.
-
diff --git a/general/datasets/IBR_M_0106_R/platform.rtf b/general/datasets/IBR_M_0106_R/platform.rtf
deleted file mode 100644
index 028fe23..0000000
--- a/general/datasets/IBR_M_0106_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/IBR_M_0106_R/processing.rtf b/general/datasets/IBR_M_0106_R/processing.rtf
deleted file mode 100644
index 243e5c0..0000000
--- a/general/datasets/IBR_M_0106_R/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/IBR_M_0106_R/summary.rtf b/general/datasets/IBR_M_0106_R/summary.rtf
deleted file mode 100644
index 6fe94b1..0000000
--- a/general/datasets/IBR_M_0106_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/IBR_M_0106_R/tissue.rtf b/general/datasets/IBR_M_0106_R/tissue.rtf
deleted file mode 100644
index 841d879..0000000
--- a/general/datasets/IBR_M_0106_R/tissue.rtf
+++ /dev/null
@@ -1,977 +0,0 @@
-The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).
-
-Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.
-
-The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.
-
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
- Sample_name |
- Result date |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Nov03 |
- UTM RW |
-
-
- | 2 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Jan04 |
- UTM RW |
-
-
- | 3 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Nov03 |
- UTM RW |
-
-
- | 4 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Jan04 |
- UTM RW |
-
-
- | 5 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Feb05 |
- UTM RW |
-
-
- | 6 |
- C57BL/6J |
- M |
- 76 |
- R0997F1 |
- Feb05 |
- UTM RW |
-
-
- | 7 |
- D2B6F1 |
- F |
- 57 |
- R1066F1 |
- Feb05 |
- UTM RW |
-
-
- | 8 |
- D2B6F1 |
- M |
- 59 |
- R1381F1 |
- Feb05 |
- UTM RW |
-
-
- | 9 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Nov03 |
- UTM RW |
-
-
- | 10 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Feb05 |
- UTM RW |
-
-
- | 11 |
- DBA/2J |
- F |
- 60 |
- R0917F2 |
- Jan04 |
- UTM RW |
-
-
- | 12 |
- DBA/2J |
- F |
- 64 |
- R1123F1 |
- Feb05 |
- UTM RW |
-
-
- | 13 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Nov03 |
- UTM RW |
-
-
- | 14 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Jan04 |
- UTM RW |
-
-
- | 15 |
- DBA/2J |
- M |
- 73 |
- R1009F1 |
- Feb05 |
- UTM RW |
-
-
- | 16 |
- B6D2F1 |
- F |
- 127 |
- R0919F1 |
- Jan04 |
- UTM JB |
-
-
- | 17 |
- B6D2F1 |
- F |
- 127 |
- R0919F2 |
- Jan04 |
- UTM JB |
-
-
- | 18 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 19 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 20 |
- B6D2F1 |
- M |
- 127 |
- R0920F1 |
- Jan04 |
- UTM JB |
-
-
- | 21 |
- B6D2F1 |
- M |
- 127 |
- R0920F2 |
- Jan04 |
- UTM JB |
-
-
- | 22 |
- B6D2F1 |
- M |
- 66 |
- R1057F1 |
- Feb05 |
- UTM RW |
-
-
- | 23 |
- BXD1 |
- M |
- 181 |
- R0956F1 |
- Feb05 |
- UTM JB |
-
-
- | 24 |
- BXD1 |
- F |
- 95 |
- R0895F1 |
- Jan04 |
- UMemphis |
-
-
- | 25 |
- BXD2 |
- F |
- 142 |
- R0907F1 |
- Feb05 |
- UAB |
-
-
- | 26 |
- BXD5 |
- F |
- 56 |
- R0744F1 |
- Feb05 |
- UMemphis |
-
-
- | 27 |
- BXD5 |
- M |
- 71 |
- R0728F1 |
- Jan04 |
- UMemphis |
-
-
- | 28 |
- BXD6 |
- F |
- 57 |
- R1711F1 |
- Feb05 |
- JAX |
-
-
- | 29 |
- BXD6 |
- F |
- 92 |
- R0901F1 |
- Feb05 |
- UMemphis |
-
-
- | 30 |
- BXD6 |
- M |
- 92 |
- R0902F1 |
- Jan04 |
- UMemphis |
-
-
- | 31 |
- BXD8 |
- F |
- 72 |
- R0167F1 |
- Jan04 |
- UAB |
-
-
- | 32 |
- BXD9 |
- F |
- 86 |
- R0908F1 |
- Feb05 |
- UMemphis |
-
-
- | 33 |
- BXD9 |
- M |
- 86 |
- R0909F1 |
- Jan04 |
- UMemphis |
-
-
- | 34 |
- BXD11 |
- F |
- 97 |
- R0745F1 |
- Feb05 |
- UAB |
-
-
- | 35 |
- BXD11 |
- M |
- 92 |
- R0666F1 |
- Feb05 |
- UMemphis |
-
-
- | 36 |
- BXD12 |
- F |
- 64 |
- R0896F1 |
- Feb05 |
- UMemphis |
-
-
- | 37 |
- BXD12 |
- M |
- 64 |
- R0897F1 |
- Jan04 |
- UMemphis |
-
-
- | 38 |
- BXD13 |
- F |
- 86 |
- R0730F1 |
- Feb05 |
- UMemphis |
-
-
- | 39 |
- BXD13 |
- F |
- 86 |
- R0748F1 |
- Jan04 |
- UMemphis |
-
-
- | 40 |
- BXD13 |
- M |
- 76 |
- R0929F1 |
- Feb05 |
- UMemphis |
-
-
- | 41 |
- BXD14 |
- M |
- 91 |
- R0912F1 |
- Jan04 |
- UMemphis |
-
-
- | 42 |
- BXD14 |
- M |
- 68 |
- R1051F1 |
- Feb05 |
- UTM RW |
-
-
- | 43 |
- BXD15 |
- F |
- 80 |
- R0928F1 |
- Feb05 |
- UMemphis |
-
-
- | 44 |
- BXD18 |
- F |
- 108 |
- R0771F1 |
- Jan04 |
- UAB |
-
-
- | 45 |
- BXD19 |
- M |
- 157 |
- R1229F1 |
- Feb05 |
- UTM JB |
-
-
- | 46 |
- BXD19 |
- F |
- 56 |
- R0236F1 |
- Jan04 |
- UAB |
-
-
- | 47 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Jan04 |
- UAB |
-
-
- | 48 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Feb05 |
- UAB |
-
-
- | 49 |
- BXD23 |
- F |
- 66 |
- R1035F1 |
- Feb05 |
- UTM RW |
-
-
- | 50 |
- BXD23 |
- M |
- 66 |
- R1037F1 |
- Feb05 |
- UTM RW |
-
-
- | 51 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Jan04 |
- UAB |
-
-
- | 52 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Feb05 |
- UAB |
-
-
- | 53 |
- BXD24 |
- F |
- 71 |
- R0914F1 |
- Feb05 |
- UMemphis |
-
-
- | 54 |
- BXD24 |
- M |
- 71 |
- R0913F1 |
- Jan04 |
- UMemphis |
-
-
- | 55 |
- BXD25 |
- F |
- 74 |
- R0373F1 |
- Jan04 |
- UTM RW |
-
-
- | 56 |
- BXD28 |
- F |
- 79 |
- R0910F1 |
- Jan04 |
- UMemphis |
-
-
- | 57 |
- BXD28 |
- M |
- 79 |
- R0911F1 |
- Feb05 |
- UMemphis |
-
-
- | 58 |
- BXD28 |
- F |
- 113 |
- R0892F1 |
- Feb05 |
- UTM RW |
-
-
- | 59 |
- BXD29 |
- F |
- 76 |
- R0693F1 |
- Jan04 |
- UMemphis |
-
-
- | 60 |
- BXD31 |
- F |
- 61 |
- R1199F1 |
- Feb05 |
- UTM RW |
-
-
- | 61 |
- BXD31 |
- M |
- 61 |
- R1141F1 |
- Feb05 |
- UTM RW |
-
-
- | 62 |
- BXD32 |
- F |
- 93 |
- R0898F1 |
- Jan04 |
- UAB |
-
-
- | 63 |
- BXD32 |
- F |
- 76 |
- R1214F1 |
- Feb05 |
- UMemphis |
-
-
- | 64 |
- BXD32 |
- M |
- 65 |
- R1478F1 |
- Feb05 |
- UMemphis |
-
-
- | 65 |
- BXD33 |
- M |
- 77 |
- R0915F1 |
- Jan04 |
- UMemphis |
-
-
- | 66 |
- BXD34 |
- F |
- 92 |
- R0900F1 |
- Feb05 |
- UMemphis |
-
-
- | 67 |
- BXD34 |
- M |
- 56 |
- R0617F1 |
- Feb05 |
- UMemphis |
-
-
- | 68 |
- BXD34 |
- M |
- 72 |
- R0916F1 |
- Jan04 |
- UMemphis |
-
-
- | 69 |
- BXD36 |
- F |
- 61 |
- R1145F1 |
- Feb05 |
- UTM RW |
-
-
- | 70 |
- BXD36 |
- M |
- 77 |
- R0926F1 |
- Jan04 |
- UMemphis |
-
-
- | 71 |
- BXD36 |
- M |
- 61 |
- R1211F1 |
- Feb05 |
- UMemphis |
-
-
- | 72 |
- BXD38 |
- M |
- 83 |
- R1208F1 |
- Feb05 |
- UMemphis |
-
-
- | 73 |
- BXD38 |
- F |
- 69 |
- R0729F1 |
- Feb05 |
- UMemphis |
-
-
- | 74 |
- BXD38 |
- M |
- 69 |
- R0731F1 |
- Jan04 |
- UMemphis |
-
-
- | 75 |
- BXD39 |
- F |
- 76 |
- R1712F1 |
- Feb05 |
- JAX |
-
-
- | 76 |
- BXD39 |
- M |
- 71 |
- R0602F1 |
- Feb05 |
- UAB |
-
-
- | 77 |
- BXD40 |
- F |
- 184 |
- R0741F1 |
- Feb05 |
- UAB |
-
-
- | 78 |
- BXD40 |
- M |
- 56 |
- R0894F1 |
- Feb05 |
- UMemphis |
-
-
- | 79 |
- BXD42 |
- F |
- 100 |
- R0742F1 |
- Feb05 |
- UAB |
-
-
- | 80 |
- BXD42 |
- M |
- 97 |
- R0936F1 |
- Jan04 |
- UMemphis |
-
-
- | 81 |
- BXD42 |
- M |
- 105 |
- R0937F1 |
- Feb05 |
- UMemphis |
-
-
- | 82 |
- BXD43 |
- M |
- 63 |
- R1047F1 |
- Feb05 |
- UTM RW |
-
-
- | 83 |
- BXD44 |
- F |
- 57 |
- R1069F1 |
- Feb05 |
- UTM RW |
-
-
- | 84 |
- BXD44 |
- M |
- 58 |
- R1072F1 |
- Feb05 |
- UTM RW |
-
-
- | 85 |
- BXD45 |
- F |
- 58 |
- R1398F1 |
- Feb05 |
- UTM RW |
-
-
- | 86 |
- BXD48 |
- F |
- 59 |
- R0946F1 |
- Feb05 |
- UTM RW |
-
-
- | 87 |
- BXD48 |
- M |
- 64 |
- R0970F1 |
- Feb05 |
- UTM RW |
-
-
- | 88 |
- BXD51 |
- F |
- 63 |
- R1430F1 |
- Feb05 |
- UTM RW |
-
-
- | 89 |
- BXD51 |
- M |
- 65 |
- R1001F1 |
- Feb05 |
- UTM RW |
-
-
- | 90 |
- BXD60 |
- F |
- 64 |
- R0976F1 |
- Feb05 |
- UTM RW |
-
-
- | 91 |
- BXD60 |
- M |
- 59 |
- R1075F1 |
- Feb05 |
- UTM RW |
-
-
- | 92 |
- BXD62 |
- F |
- 59 |
- R1033F1 |
- Feb05 |
- UTM RW |
-
-
- | 93 |
- BXD62 |
- M |
- 58 |
- R1027F1 |
- Feb05 |
- UTM RW |
-
-
- | 94 |
- BXD69 |
- F |
- 60 |
- R1438F1 |
- Feb05 |
- UTM RW |
-
-
- | 95 |
- BXD69 |
- M |
- 64 |
- R1193F1 |
- Feb05 |
- UTM RW |
-
-
- | 96 |
- BXD73 |
- F |
- 60 |
- R1275F1 |
- Feb05 |
- UTM RW |
-
-
- | 97 |
- BXD73 |
- M |
- 76 |
- R1442F1 |
- Feb05 |
- UTM RW |
-
-
- | 98 |
- BXD77 |
- M |
- 61 |
- R1426F1 |
- Feb05 |
- UTM RW |
-
-
- | 99 |
- BXD86 |
- F |
- 77 |
- R1414F1 |
- Feb05 |
- UTM RW |
-
-
- | 100 |
- BXD86 |
- M |
- 77 |
- R1418F1 |
- Feb05 |
- UTM RW |
-
-
- | 101 |
- BXD87 |
- F |
- 89 |
- R1713F1 |
- Feb05 |
- UTM RW |
-
-
- | 102 |
- BXD87 |
- M |
- 84 |
- R1709F1 |
- Feb05 |
- UTM RW |
-
-
- | 103 |
- BXD90 |
- M |
- 61 |
- R1452F |
- Feb05 |
- UTM RW |
-
-
- | 104 |
- BXD92 |
- F |
- 58 |
- R1299F1 |
- Feb05 |
- UTM RW |
-
-
- | 105 |
- BXD92 |
- M |
- 59 |
- R1307F1 |
- Feb05 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/IBR_M_0204_M/acknowledgment.rtf b/general/datasets/IBR_M_0204_M/acknowledgment.rtf
deleted file mode 100644
index 7b62a11..0000000
--- a/general/datasets/IBR_M_0204_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data for the microarrays were generously provided by support from NIAAA INIA grants to RWW and Thomas Sutter. Support for sample acquistion and WebQTL have been provided by NIMH Human Brain Project, and the Dunavant Chair of Excellence, University of Tennessee Health Science Center. All arrays were processed at the University of Memphis by Dr. Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0204_M/cases.rtf b/general/datasets/IBR_M_0204_M/cases.rtf
deleted file mode 100644
index 9dc5cbe..0000000
--- a/general/datasets/IBR_M_0204_M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B) and DBA/2J (D). Both B and D strains have been almost fully sequence (8x coverage for B by a public consortium and approximately 1.5x coverage for D by Celera).
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
diff --git a/general/datasets/IBR_M_0204_M/notes.rtf b/general/datasets/IBR_M_0204_M/notes.rtf
deleted file mode 100644
index f3ea488..0000000
--- a/general/datasets/IBR_M_0204_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004.
diff --git a/general/datasets/IBR_M_0204_M/platform.rtf b/general/datasets/IBR_M_0204_M/platform.rtf
deleted file mode 100644
index 51cbff2..0000000
--- a/general/datasets/IBR_M_0204_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 430A and 430B GeneChip Set: Expression data were generated using 430AB array pairs. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on either the Verify UCSC and Verify Ensembl links in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/IBR_M_0204_M/processing.rtf b/general/datasets/IBR_M_0204_M/processing.rtf
deleted file mode 100644
index 4663b88..0000000
--- a/general/datasets/IBR_M_0204_M/processing.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: We corrected for technical variance introduced by two batches. Means separated by the first batch for each gene are corrected same as means of the second batch.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-
-
-
-Probe set data: The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
-
-PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
-
-When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
-
-
-About the array probe sets names:
-
-
-Most probe sets on the mouse 430A and 430B arrays consist of a total of 22 probes, divided into 11 perfect match(PM) probes and 11 mismatch (MM) controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, several suffix characters that highlight design features, a a final A or B character to specify the array pair member. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene.
-
diff --git a/general/datasets/IBR_M_0204_M/summary.rtf b/general/datasets/IBR_M_0204_M/summary.rtf
deleted file mode 100644
index c32676a..0000000
--- a/general/datasets/IBR_M_0204_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This October 2004 data freeze provides initial estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix M430AB microarrays. In contast to the U74Av2 array, this new data set provides broader coverage (~45,000 transcripts) but does not include replicates or as many strains (25 vs 35). Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Data were processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
diff --git a/general/datasets/IBR_M_0204_M/tissue.rtf b/general/datasets/IBR_M_0204_M/tissue.rtf
deleted file mode 100644
index cac878a..0000000
--- a/general/datasets/IBR_M_0204_M/tissue.rtf
+++ /dev/null
@@ -1,261 +0,0 @@
-The data set consists of a single batch of Affymetrix mouse expression 430A and 430B GeneChip array pairs. Each AB pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter and colleagues at the University of Memphis. Before running the main batch of 30 pairs of array, we ran four "test" samples (one male and one female pool from each of the two parental strains, C57BL/6J and DBA/2J). The main set of 30 array pairs includes the same four samples (in other words we have four technical replicates), two F1 hybrid sample (each run two times for a within-batch technical replication), and 22 BXD strains. The data set therefore consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. We should note that the four technical replicates between batches were eventually combined with a correction for a highly significant batch effect. This was done at both the probe and probe set levels to "align" the test batch values with the two main batches. (The ratio of the probe average in the four test arrays to the average of the same probe in the four corresponding main batch arrays was used as a correction factor.) The F1 within-batch technical replicates were simply averaged. In the next batch we will reverse the sex of the BXD samples to achieve a balance with at least 22 BXD strains with one male and one female sample each.
-
-The table below lists the arrays by strain, sex, age, sample identifier, and data results were obtained from the Bioanalytical Core at the University of Memphis. Each array was hybridized to a pool of mRNA from three mice.
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Date |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F2 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F2 |
- Jan04 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F2 |
- Jan03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F2 |
- Jan04 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F1 |
- Nov03 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F2 |
- Jan04 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F1 |
- Nov03 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F2 |
- Jan04 |
-
-
- | BXD1 |
- F |
- 95 |
- 895-F1 |
- Jan04 |
-
-
- | BXD5 |
- M |
- 71 |
- 728-F1 |
- Jan04 |
-
-
- | BXD6 |
- M |
- 92 |
- 902-F1 |
- Jan04 |
-
-
- | BXD8 |
- F |
- 72 |
- S167-F1 |
- Jan04 |
-
-
- | BXD9 |
- M |
- 86 |
- 909-F1 |
- Jan04 |
-
-
- | BXD12 |
- M |
- 64 |
- 897-F1 |
- Jan04 |
-
-
- | BXD13 |
- F |
- 86 |
- 748-F1 |
- Jan04 |
-
-
- | BXD14 |
- M |
- 91 |
- 912-F1 |
- Jan04 |
-
-
- | BXD18 |
- F |
- 108 |
- 771-F1 |
- Jan04 |
-
-
- | BXD19 |
- F |
- 56 |
- S236-F1 |
- Jan04 |
-
-
- | BXD21 |
- F |
- 67 |
- 740-F1 |
- Jan04 |
-
-
- | BXD23 |
- F |
- 88 |
- 815-F1 |
- Jan04 |
-
-
- | BXD24 |
- M |
- 71 |
- 913-F1 |
- Jan04 |
-
-
- | BXD25 |
- F |
- 74 |
- S373-F1 |
- Jan04 |
-
-
- | BXD28 |
- F |
- 79 |
- 910-F1 |
- Jan04 |
-
-
- | BXD29 |
- F |
- 76 |
- 693-F1 |
- Jan04 |
-
-
- | BXD32 |
- F |
- 93 |
- 898-F1 |
- Jan04 |
-
-
- | BXD33 |
- M |
- 77 |
- 915-F1 |
- Jan04 |
-
-
- | BXD34 |
- M |
- 72 |
- 916-F1 |
- Jan04 |
-
-
- | BXD36 |
- M |
- 77 |
- 926-F1 |
- Jan04 |
-
-
- | BXD38 |
- M |
- 69 |
- 731-F1 |
- Jan04 |
-
-
- | BXD42 |
- M |
- 97 |
- 936-F1 |
- Jan04 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/IBR_M_0405_M/acknowledgment.rtf b/general/datasets/IBR_M_0405_M/acknowledgment.rtf
deleted file mode 100644
index a1563a6..0000000
--- a/general/datasets/IBR_M_0405_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0405_M/cases.rtf b/general/datasets/IBR_M_0405_M/cases.rtf
deleted file mode 100644
index 8794b88..0000000
--- a/general/datasets/IBR_M_0405_M/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues
-
-
-All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).
-
diff --git a/general/datasets/IBR_M_0405_M/notes.rtf b/general/datasets/IBR_M_0405_M/notes.rtf
deleted file mode 100644
index 72bad83..0000000
--- a/general/datasets/IBR_M_0405_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.
-
diff --git a/general/datasets/IBR_M_0405_M/platform.rtf b/general/datasets/IBR_M_0405_M/platform.rtf
deleted file mode 100644
index 028fe23..0000000
--- a/general/datasets/IBR_M_0405_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/IBR_M_0405_M/processing.rtf b/general/datasets/IBR_M_0405_M/processing.rtf
deleted file mode 100644
index 243e5c0..0000000
--- a/general/datasets/IBR_M_0405_M/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/IBR_M_0405_M/summary.rtf b/general/datasets/IBR_M_0405_M/summary.rtf
deleted file mode 100644
index 6fe94b1..0000000
--- a/general/datasets/IBR_M_0405_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/IBR_M_0405_M/tissue.rtf b/general/datasets/IBR_M_0405_M/tissue.rtf
deleted file mode 100644
index 841d879..0000000
--- a/general/datasets/IBR_M_0405_M/tissue.rtf
+++ /dev/null
@@ -1,977 +0,0 @@
-The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).
-
-Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.
-
-The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.
-
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
- Sample_name |
- Result date |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Nov03 |
- UTM RW |
-
-
- | 2 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Jan04 |
- UTM RW |
-
-
- | 3 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Nov03 |
- UTM RW |
-
-
- | 4 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Jan04 |
- UTM RW |
-
-
- | 5 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Feb05 |
- UTM RW |
-
-
- | 6 |
- C57BL/6J |
- M |
- 76 |
- R0997F1 |
- Feb05 |
- UTM RW |
-
-
- | 7 |
- D2B6F1 |
- F |
- 57 |
- R1066F1 |
- Feb05 |
- UTM RW |
-
-
- | 8 |
- D2B6F1 |
- M |
- 59 |
- R1381F1 |
- Feb05 |
- UTM RW |
-
-
- | 9 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Nov03 |
- UTM RW |
-
-
- | 10 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Feb05 |
- UTM RW |
-
-
- | 11 |
- DBA/2J |
- F |
- 60 |
- R0917F2 |
- Jan04 |
- UTM RW |
-
-
- | 12 |
- DBA/2J |
- F |
- 64 |
- R1123F1 |
- Feb05 |
- UTM RW |
-
-
- | 13 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Nov03 |
- UTM RW |
-
-
- | 14 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Jan04 |
- UTM RW |
-
-
- | 15 |
- DBA/2J |
- M |
- 73 |
- R1009F1 |
- Feb05 |
- UTM RW |
-
-
- | 16 |
- B6D2F1 |
- F |
- 127 |
- R0919F1 |
- Jan04 |
- UTM JB |
-
-
- | 17 |
- B6D2F1 |
- F |
- 127 |
- R0919F2 |
- Jan04 |
- UTM JB |
-
-
- | 18 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 19 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 20 |
- B6D2F1 |
- M |
- 127 |
- R0920F1 |
- Jan04 |
- UTM JB |
-
-
- | 21 |
- B6D2F1 |
- M |
- 127 |
- R0920F2 |
- Jan04 |
- UTM JB |
-
-
- | 22 |
- B6D2F1 |
- M |
- 66 |
- R1057F1 |
- Feb05 |
- UTM RW |
-
-
- | 23 |
- BXD1 |
- M |
- 181 |
- R0956F1 |
- Feb05 |
- UTM JB |
-
-
- | 24 |
- BXD1 |
- F |
- 95 |
- R0895F1 |
- Jan04 |
- UMemphis |
-
-
- | 25 |
- BXD2 |
- F |
- 142 |
- R0907F1 |
- Feb05 |
- UAB |
-
-
- | 26 |
- BXD5 |
- F |
- 56 |
- R0744F1 |
- Feb05 |
- UMemphis |
-
-
- | 27 |
- BXD5 |
- M |
- 71 |
- R0728F1 |
- Jan04 |
- UMemphis |
-
-
- | 28 |
- BXD6 |
- F |
- 57 |
- R1711F1 |
- Feb05 |
- JAX |
-
-
- | 29 |
- BXD6 |
- F |
- 92 |
- R0901F1 |
- Feb05 |
- UMemphis |
-
-
- | 30 |
- BXD6 |
- M |
- 92 |
- R0902F1 |
- Jan04 |
- UMemphis |
-
-
- | 31 |
- BXD8 |
- F |
- 72 |
- R0167F1 |
- Jan04 |
- UAB |
-
-
- | 32 |
- BXD9 |
- F |
- 86 |
- R0908F1 |
- Feb05 |
- UMemphis |
-
-
- | 33 |
- BXD9 |
- M |
- 86 |
- R0909F1 |
- Jan04 |
- UMemphis |
-
-
- | 34 |
- BXD11 |
- F |
- 97 |
- R0745F1 |
- Feb05 |
- UAB |
-
-
- | 35 |
- BXD11 |
- M |
- 92 |
- R0666F1 |
- Feb05 |
- UMemphis |
-
-
- | 36 |
- BXD12 |
- F |
- 64 |
- R0896F1 |
- Feb05 |
- UMemphis |
-
-
- | 37 |
- BXD12 |
- M |
- 64 |
- R0897F1 |
- Jan04 |
- UMemphis |
-
-
- | 38 |
- BXD13 |
- F |
- 86 |
- R0730F1 |
- Feb05 |
- UMemphis |
-
-
- | 39 |
- BXD13 |
- F |
- 86 |
- R0748F1 |
- Jan04 |
- UMemphis |
-
-
- | 40 |
- BXD13 |
- M |
- 76 |
- R0929F1 |
- Feb05 |
- UMemphis |
-
-
- | 41 |
- BXD14 |
- M |
- 91 |
- R0912F1 |
- Jan04 |
- UMemphis |
-
-
- | 42 |
- BXD14 |
- M |
- 68 |
- R1051F1 |
- Feb05 |
- UTM RW |
-
-
- | 43 |
- BXD15 |
- F |
- 80 |
- R0928F1 |
- Feb05 |
- UMemphis |
-
-
- | 44 |
- BXD18 |
- F |
- 108 |
- R0771F1 |
- Jan04 |
- UAB |
-
-
- | 45 |
- BXD19 |
- M |
- 157 |
- R1229F1 |
- Feb05 |
- UTM JB |
-
-
- | 46 |
- BXD19 |
- F |
- 56 |
- R0236F1 |
- Jan04 |
- UAB |
-
-
- | 47 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Jan04 |
- UAB |
-
-
- | 48 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Feb05 |
- UAB |
-
-
- | 49 |
- BXD23 |
- F |
- 66 |
- R1035F1 |
- Feb05 |
- UTM RW |
-
-
- | 50 |
- BXD23 |
- M |
- 66 |
- R1037F1 |
- Feb05 |
- UTM RW |
-
-
- | 51 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Jan04 |
- UAB |
-
-
- | 52 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Feb05 |
- UAB |
-
-
- | 53 |
- BXD24 |
- F |
- 71 |
- R0914F1 |
- Feb05 |
- UMemphis |
-
-
- | 54 |
- BXD24 |
- M |
- 71 |
- R0913F1 |
- Jan04 |
- UMemphis |
-
-
- | 55 |
- BXD25 |
- F |
- 74 |
- R0373F1 |
- Jan04 |
- UTM RW |
-
-
- | 56 |
- BXD28 |
- F |
- 79 |
- R0910F1 |
- Jan04 |
- UMemphis |
-
-
- | 57 |
- BXD28 |
- M |
- 79 |
- R0911F1 |
- Feb05 |
- UMemphis |
-
-
- | 58 |
- BXD28 |
- F |
- 113 |
- R0892F1 |
- Feb05 |
- UTM RW |
-
-
- | 59 |
- BXD29 |
- F |
- 76 |
- R0693F1 |
- Jan04 |
- UMemphis |
-
-
- | 60 |
- BXD31 |
- F |
- 61 |
- R1199F1 |
- Feb05 |
- UTM RW |
-
-
- | 61 |
- BXD31 |
- M |
- 61 |
- R1141F1 |
- Feb05 |
- UTM RW |
-
-
- | 62 |
- BXD32 |
- F |
- 93 |
- R0898F1 |
- Jan04 |
- UAB |
-
-
- | 63 |
- BXD32 |
- F |
- 76 |
- R1214F1 |
- Feb05 |
- UMemphis |
-
-
- | 64 |
- BXD32 |
- M |
- 65 |
- R1478F1 |
- Feb05 |
- UMemphis |
-
-
- | 65 |
- BXD33 |
- M |
- 77 |
- R0915F1 |
- Jan04 |
- UMemphis |
-
-
- | 66 |
- BXD34 |
- F |
- 92 |
- R0900F1 |
- Feb05 |
- UMemphis |
-
-
- | 67 |
- BXD34 |
- M |
- 56 |
- R0617F1 |
- Feb05 |
- UMemphis |
-
-
- | 68 |
- BXD34 |
- M |
- 72 |
- R0916F1 |
- Jan04 |
- UMemphis |
-
-
- | 69 |
- BXD36 |
- F |
- 61 |
- R1145F1 |
- Feb05 |
- UTM RW |
-
-
- | 70 |
- BXD36 |
- M |
- 77 |
- R0926F1 |
- Jan04 |
- UMemphis |
-
-
- | 71 |
- BXD36 |
- M |
- 61 |
- R1211F1 |
- Feb05 |
- UMemphis |
-
-
- | 72 |
- BXD38 |
- M |
- 83 |
- R1208F1 |
- Feb05 |
- UMemphis |
-
-
- | 73 |
- BXD38 |
- F |
- 69 |
- R0729F1 |
- Feb05 |
- UMemphis |
-
-
- | 74 |
- BXD38 |
- M |
- 69 |
- R0731F1 |
- Jan04 |
- UMemphis |
-
-
- | 75 |
- BXD39 |
- F |
- 76 |
- R1712F1 |
- Feb05 |
- JAX |
-
-
- | 76 |
- BXD39 |
- M |
- 71 |
- R0602F1 |
- Feb05 |
- UAB |
-
-
- | 77 |
- BXD40 |
- F |
- 184 |
- R0741F1 |
- Feb05 |
- UAB |
-
-
- | 78 |
- BXD40 |
- M |
- 56 |
- R0894F1 |
- Feb05 |
- UMemphis |
-
-
- | 79 |
- BXD42 |
- F |
- 100 |
- R0742F1 |
- Feb05 |
- UAB |
-
-
- | 80 |
- BXD42 |
- M |
- 97 |
- R0936F1 |
- Jan04 |
- UMemphis |
-
-
- | 81 |
- BXD42 |
- M |
- 105 |
- R0937F1 |
- Feb05 |
- UMemphis |
-
-
- | 82 |
- BXD43 |
- M |
- 63 |
- R1047F1 |
- Feb05 |
- UTM RW |
-
-
- | 83 |
- BXD44 |
- F |
- 57 |
- R1069F1 |
- Feb05 |
- UTM RW |
-
-
- | 84 |
- BXD44 |
- M |
- 58 |
- R1072F1 |
- Feb05 |
- UTM RW |
-
-
- | 85 |
- BXD45 |
- F |
- 58 |
- R1398F1 |
- Feb05 |
- UTM RW |
-
-
- | 86 |
- BXD48 |
- F |
- 59 |
- R0946F1 |
- Feb05 |
- UTM RW |
-
-
- | 87 |
- BXD48 |
- M |
- 64 |
- R0970F1 |
- Feb05 |
- UTM RW |
-
-
- | 88 |
- BXD51 |
- F |
- 63 |
- R1430F1 |
- Feb05 |
- UTM RW |
-
-
- | 89 |
- BXD51 |
- M |
- 65 |
- R1001F1 |
- Feb05 |
- UTM RW |
-
-
- | 90 |
- BXD60 |
- F |
- 64 |
- R0976F1 |
- Feb05 |
- UTM RW |
-
-
- | 91 |
- BXD60 |
- M |
- 59 |
- R1075F1 |
- Feb05 |
- UTM RW |
-
-
- | 92 |
- BXD62 |
- F |
- 59 |
- R1033F1 |
- Feb05 |
- UTM RW |
-
-
- | 93 |
- BXD62 |
- M |
- 58 |
- R1027F1 |
- Feb05 |
- UTM RW |
-
-
- | 94 |
- BXD69 |
- F |
- 60 |
- R1438F1 |
- Feb05 |
- UTM RW |
-
-
- | 95 |
- BXD69 |
- M |
- 64 |
- R1193F1 |
- Feb05 |
- UTM RW |
-
-
- | 96 |
- BXD73 |
- F |
- 60 |
- R1275F1 |
- Feb05 |
- UTM RW |
-
-
- | 97 |
- BXD73 |
- M |
- 76 |
- R1442F1 |
- Feb05 |
- UTM RW |
-
-
- | 98 |
- BXD77 |
- M |
- 61 |
- R1426F1 |
- Feb05 |
- UTM RW |
-
-
- | 99 |
- BXD86 |
- F |
- 77 |
- R1414F1 |
- Feb05 |
- UTM RW |
-
-
- | 100 |
- BXD86 |
- M |
- 77 |
- R1418F1 |
- Feb05 |
- UTM RW |
-
-
- | 101 |
- BXD87 |
- F |
- 89 |
- R1713F1 |
- Feb05 |
- UTM RW |
-
-
- | 102 |
- BXD87 |
- M |
- 84 |
- R1709F1 |
- Feb05 |
- UTM RW |
-
-
- | 103 |
- BXD90 |
- M |
- 61 |
- R1452F |
- Feb05 |
- UTM RW |
-
-
- | 104 |
- BXD92 |
- F |
- 58 |
- R1299F1 |
- Feb05 |
- UTM RW |
-
-
- | 105 |
- BXD92 |
- M |
- 59 |
- R1307F1 |
- Feb05 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/IBR_M_0405_P/acknowledgment.rtf b/general/datasets/IBR_M_0405_P/acknowledgment.rtf
deleted file mode 100644
index a1563a6..0000000
--- a/general/datasets/IBR_M_0405_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0405_P/cases.rtf b/general/datasets/IBR_M_0405_P/cases.rtf
deleted file mode 100644
index 8794b88..0000000
--- a/general/datasets/IBR_M_0405_P/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues
-
-
-All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).
-
diff --git a/general/datasets/IBR_M_0405_P/notes.rtf b/general/datasets/IBR_M_0405_P/notes.rtf
deleted file mode 100644
index 72bad83..0000000
--- a/general/datasets/IBR_M_0405_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.
-
diff --git a/general/datasets/IBR_M_0405_P/platform.rtf b/general/datasets/IBR_M_0405_P/platform.rtf
deleted file mode 100644
index 028fe23..0000000
--- a/general/datasets/IBR_M_0405_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/IBR_M_0405_P/processing.rtf b/general/datasets/IBR_M_0405_P/processing.rtf
deleted file mode 100644
index 243e5c0..0000000
--- a/general/datasets/IBR_M_0405_P/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/IBR_M_0405_P/summary.rtf b/general/datasets/IBR_M_0405_P/summary.rtf
deleted file mode 100644
index 6fe94b1..0000000
--- a/general/datasets/IBR_M_0405_P/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/IBR_M_0405_P/tissue.rtf b/general/datasets/IBR_M_0405_P/tissue.rtf
deleted file mode 100644
index 841d879..0000000
--- a/general/datasets/IBR_M_0405_P/tissue.rtf
+++ /dev/null
@@ -1,977 +0,0 @@
-The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).
-
-Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.
-
-The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.
-
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
- Sample_name |
- Result date |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Nov03 |
- UTM RW |
-
-
- | 2 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Jan04 |
- UTM RW |
-
-
- | 3 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Nov03 |
- UTM RW |
-
-
- | 4 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Jan04 |
- UTM RW |
-
-
- | 5 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Feb05 |
- UTM RW |
-
-
- | 6 |
- C57BL/6J |
- M |
- 76 |
- R0997F1 |
- Feb05 |
- UTM RW |
-
-
- | 7 |
- D2B6F1 |
- F |
- 57 |
- R1066F1 |
- Feb05 |
- UTM RW |
-
-
- | 8 |
- D2B6F1 |
- M |
- 59 |
- R1381F1 |
- Feb05 |
- UTM RW |
-
-
- | 9 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Nov03 |
- UTM RW |
-
-
- | 10 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Feb05 |
- UTM RW |
-
-
- | 11 |
- DBA/2J |
- F |
- 60 |
- R0917F2 |
- Jan04 |
- UTM RW |
-
-
- | 12 |
- DBA/2J |
- F |
- 64 |
- R1123F1 |
- Feb05 |
- UTM RW |
-
-
- | 13 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Nov03 |
- UTM RW |
-
-
- | 14 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Jan04 |
- UTM RW |
-
-
- | 15 |
- DBA/2J |
- M |
- 73 |
- R1009F1 |
- Feb05 |
- UTM RW |
-
-
- | 16 |
- B6D2F1 |
- F |
- 127 |
- R0919F1 |
- Jan04 |
- UTM JB |
-
-
- | 17 |
- B6D2F1 |
- F |
- 127 |
- R0919F2 |
- Jan04 |
- UTM JB |
-
-
- | 18 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 19 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 20 |
- B6D2F1 |
- M |
- 127 |
- R0920F1 |
- Jan04 |
- UTM JB |
-
-
- | 21 |
- B6D2F1 |
- M |
- 127 |
- R0920F2 |
- Jan04 |
- UTM JB |
-
-
- | 22 |
- B6D2F1 |
- M |
- 66 |
- R1057F1 |
- Feb05 |
- UTM RW |
-
-
- | 23 |
- BXD1 |
- M |
- 181 |
- R0956F1 |
- Feb05 |
- UTM JB |
-
-
- | 24 |
- BXD1 |
- F |
- 95 |
- R0895F1 |
- Jan04 |
- UMemphis |
-
-
- | 25 |
- BXD2 |
- F |
- 142 |
- R0907F1 |
- Feb05 |
- UAB |
-
-
- | 26 |
- BXD5 |
- F |
- 56 |
- R0744F1 |
- Feb05 |
- UMemphis |
-
-
- | 27 |
- BXD5 |
- M |
- 71 |
- R0728F1 |
- Jan04 |
- UMemphis |
-
-
- | 28 |
- BXD6 |
- F |
- 57 |
- R1711F1 |
- Feb05 |
- JAX |
-
-
- | 29 |
- BXD6 |
- F |
- 92 |
- R0901F1 |
- Feb05 |
- UMemphis |
-
-
- | 30 |
- BXD6 |
- M |
- 92 |
- R0902F1 |
- Jan04 |
- UMemphis |
-
-
- | 31 |
- BXD8 |
- F |
- 72 |
- R0167F1 |
- Jan04 |
- UAB |
-
-
- | 32 |
- BXD9 |
- F |
- 86 |
- R0908F1 |
- Feb05 |
- UMemphis |
-
-
- | 33 |
- BXD9 |
- M |
- 86 |
- R0909F1 |
- Jan04 |
- UMemphis |
-
-
- | 34 |
- BXD11 |
- F |
- 97 |
- R0745F1 |
- Feb05 |
- UAB |
-
-
- | 35 |
- BXD11 |
- M |
- 92 |
- R0666F1 |
- Feb05 |
- UMemphis |
-
-
- | 36 |
- BXD12 |
- F |
- 64 |
- R0896F1 |
- Feb05 |
- UMemphis |
-
-
- | 37 |
- BXD12 |
- M |
- 64 |
- R0897F1 |
- Jan04 |
- UMemphis |
-
-
- | 38 |
- BXD13 |
- F |
- 86 |
- R0730F1 |
- Feb05 |
- UMemphis |
-
-
- | 39 |
- BXD13 |
- F |
- 86 |
- R0748F1 |
- Jan04 |
- UMemphis |
-
-
- | 40 |
- BXD13 |
- M |
- 76 |
- R0929F1 |
- Feb05 |
- UMemphis |
-
-
- | 41 |
- BXD14 |
- M |
- 91 |
- R0912F1 |
- Jan04 |
- UMemphis |
-
-
- | 42 |
- BXD14 |
- M |
- 68 |
- R1051F1 |
- Feb05 |
- UTM RW |
-
-
- | 43 |
- BXD15 |
- F |
- 80 |
- R0928F1 |
- Feb05 |
- UMemphis |
-
-
- | 44 |
- BXD18 |
- F |
- 108 |
- R0771F1 |
- Jan04 |
- UAB |
-
-
- | 45 |
- BXD19 |
- M |
- 157 |
- R1229F1 |
- Feb05 |
- UTM JB |
-
-
- | 46 |
- BXD19 |
- F |
- 56 |
- R0236F1 |
- Jan04 |
- UAB |
-
-
- | 47 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Jan04 |
- UAB |
-
-
- | 48 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Feb05 |
- UAB |
-
-
- | 49 |
- BXD23 |
- F |
- 66 |
- R1035F1 |
- Feb05 |
- UTM RW |
-
-
- | 50 |
- BXD23 |
- M |
- 66 |
- R1037F1 |
- Feb05 |
- UTM RW |
-
-
- | 51 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Jan04 |
- UAB |
-
-
- | 52 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Feb05 |
- UAB |
-
-
- | 53 |
- BXD24 |
- F |
- 71 |
- R0914F1 |
- Feb05 |
- UMemphis |
-
-
- | 54 |
- BXD24 |
- M |
- 71 |
- R0913F1 |
- Jan04 |
- UMemphis |
-
-
- | 55 |
- BXD25 |
- F |
- 74 |
- R0373F1 |
- Jan04 |
- UTM RW |
-
-
- | 56 |
- BXD28 |
- F |
- 79 |
- R0910F1 |
- Jan04 |
- UMemphis |
-
-
- | 57 |
- BXD28 |
- M |
- 79 |
- R0911F1 |
- Feb05 |
- UMemphis |
-
-
- | 58 |
- BXD28 |
- F |
- 113 |
- R0892F1 |
- Feb05 |
- UTM RW |
-
-
- | 59 |
- BXD29 |
- F |
- 76 |
- R0693F1 |
- Jan04 |
- UMemphis |
-
-
- | 60 |
- BXD31 |
- F |
- 61 |
- R1199F1 |
- Feb05 |
- UTM RW |
-
-
- | 61 |
- BXD31 |
- M |
- 61 |
- R1141F1 |
- Feb05 |
- UTM RW |
-
-
- | 62 |
- BXD32 |
- F |
- 93 |
- R0898F1 |
- Jan04 |
- UAB |
-
-
- | 63 |
- BXD32 |
- F |
- 76 |
- R1214F1 |
- Feb05 |
- UMemphis |
-
-
- | 64 |
- BXD32 |
- M |
- 65 |
- R1478F1 |
- Feb05 |
- UMemphis |
-
-
- | 65 |
- BXD33 |
- M |
- 77 |
- R0915F1 |
- Jan04 |
- UMemphis |
-
-
- | 66 |
- BXD34 |
- F |
- 92 |
- R0900F1 |
- Feb05 |
- UMemphis |
-
-
- | 67 |
- BXD34 |
- M |
- 56 |
- R0617F1 |
- Feb05 |
- UMemphis |
-
-
- | 68 |
- BXD34 |
- M |
- 72 |
- R0916F1 |
- Jan04 |
- UMemphis |
-
-
- | 69 |
- BXD36 |
- F |
- 61 |
- R1145F1 |
- Feb05 |
- UTM RW |
-
-
- | 70 |
- BXD36 |
- M |
- 77 |
- R0926F1 |
- Jan04 |
- UMemphis |
-
-
- | 71 |
- BXD36 |
- M |
- 61 |
- R1211F1 |
- Feb05 |
- UMemphis |
-
-
- | 72 |
- BXD38 |
- M |
- 83 |
- R1208F1 |
- Feb05 |
- UMemphis |
-
-
- | 73 |
- BXD38 |
- F |
- 69 |
- R0729F1 |
- Feb05 |
- UMemphis |
-
-
- | 74 |
- BXD38 |
- M |
- 69 |
- R0731F1 |
- Jan04 |
- UMemphis |
-
-
- | 75 |
- BXD39 |
- F |
- 76 |
- R1712F1 |
- Feb05 |
- JAX |
-
-
- | 76 |
- BXD39 |
- M |
- 71 |
- R0602F1 |
- Feb05 |
- UAB |
-
-
- | 77 |
- BXD40 |
- F |
- 184 |
- R0741F1 |
- Feb05 |
- UAB |
-
-
- | 78 |
- BXD40 |
- M |
- 56 |
- R0894F1 |
- Feb05 |
- UMemphis |
-
-
- | 79 |
- BXD42 |
- F |
- 100 |
- R0742F1 |
- Feb05 |
- UAB |
-
-
- | 80 |
- BXD42 |
- M |
- 97 |
- R0936F1 |
- Jan04 |
- UMemphis |
-
-
- | 81 |
- BXD42 |
- M |
- 105 |
- R0937F1 |
- Feb05 |
- UMemphis |
-
-
- | 82 |
- BXD43 |
- M |
- 63 |
- R1047F1 |
- Feb05 |
- UTM RW |
-
-
- | 83 |
- BXD44 |
- F |
- 57 |
- R1069F1 |
- Feb05 |
- UTM RW |
-
-
- | 84 |
- BXD44 |
- M |
- 58 |
- R1072F1 |
- Feb05 |
- UTM RW |
-
-
- | 85 |
- BXD45 |
- F |
- 58 |
- R1398F1 |
- Feb05 |
- UTM RW |
-
-
- | 86 |
- BXD48 |
- F |
- 59 |
- R0946F1 |
- Feb05 |
- UTM RW |
-
-
- | 87 |
- BXD48 |
- M |
- 64 |
- R0970F1 |
- Feb05 |
- UTM RW |
-
-
- | 88 |
- BXD51 |
- F |
- 63 |
- R1430F1 |
- Feb05 |
- UTM RW |
-
-
- | 89 |
- BXD51 |
- M |
- 65 |
- R1001F1 |
- Feb05 |
- UTM RW |
-
-
- | 90 |
- BXD60 |
- F |
- 64 |
- R0976F1 |
- Feb05 |
- UTM RW |
-
-
- | 91 |
- BXD60 |
- M |
- 59 |
- R1075F1 |
- Feb05 |
- UTM RW |
-
-
- | 92 |
- BXD62 |
- F |
- 59 |
- R1033F1 |
- Feb05 |
- UTM RW |
-
-
- | 93 |
- BXD62 |
- M |
- 58 |
- R1027F1 |
- Feb05 |
- UTM RW |
-
-
- | 94 |
- BXD69 |
- F |
- 60 |
- R1438F1 |
- Feb05 |
- UTM RW |
-
-
- | 95 |
- BXD69 |
- M |
- 64 |
- R1193F1 |
- Feb05 |
- UTM RW |
-
-
- | 96 |
- BXD73 |
- F |
- 60 |
- R1275F1 |
- Feb05 |
- UTM RW |
-
-
- | 97 |
- BXD73 |
- M |
- 76 |
- R1442F1 |
- Feb05 |
- UTM RW |
-
-
- | 98 |
- BXD77 |
- M |
- 61 |
- R1426F1 |
- Feb05 |
- UTM RW |
-
-
- | 99 |
- BXD86 |
- F |
- 77 |
- R1414F1 |
- Feb05 |
- UTM RW |
-
-
- | 100 |
- BXD86 |
- M |
- 77 |
- R1418F1 |
- Feb05 |
- UTM RW |
-
-
- | 101 |
- BXD87 |
- F |
- 89 |
- R1713F1 |
- Feb05 |
- UTM RW |
-
-
- | 102 |
- BXD87 |
- M |
- 84 |
- R1709F1 |
- Feb05 |
- UTM RW |
-
-
- | 103 |
- BXD90 |
- M |
- 61 |
- R1452F |
- Feb05 |
- UTM RW |
-
-
- | 104 |
- BXD92 |
- F |
- 58 |
- R1299F1 |
- Feb05 |
- UTM RW |
-
-
- | 105 |
- BXD92 |
- M |
- 59 |
- R1307F1 |
- Feb05 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/IBR_M_0405_R/acknowledgment.rtf b/general/datasets/IBR_M_0405_R/acknowledgment.rtf
deleted file mode 100644
index a1563a6..0000000
--- a/general/datasets/IBR_M_0405_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0405_R/cases.rtf b/general/datasets/IBR_M_0405_R/cases.rtf
deleted file mode 100644
index 8794b88..0000000
--- a/general/datasets/IBR_M_0405_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues
-
-
-All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).
-
diff --git a/general/datasets/IBR_M_0405_R/notes.rtf b/general/datasets/IBR_M_0405_R/notes.rtf
deleted file mode 100644
index 72bad83..0000000
--- a/general/datasets/IBR_M_0405_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.
-
diff --git a/general/datasets/IBR_M_0405_R/platform.rtf b/general/datasets/IBR_M_0405_R/platform.rtf
deleted file mode 100644
index 028fe23..0000000
--- a/general/datasets/IBR_M_0405_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/IBR_M_0405_R/processing.rtf b/general/datasets/IBR_M_0405_R/processing.rtf
deleted file mode 100644
index 243e5c0..0000000
--- a/general/datasets/IBR_M_0405_R/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/IBR_M_0405_R/summary.rtf b/general/datasets/IBR_M_0405_R/summary.rtf
deleted file mode 100644
index 6fe94b1..0000000
--- a/general/datasets/IBR_M_0405_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/IBR_M_0405_R/tissue.rtf b/general/datasets/IBR_M_0405_R/tissue.rtf
deleted file mode 100644
index 841d879..0000000
--- a/general/datasets/IBR_M_0405_R/tissue.rtf
+++ /dev/null
@@ -1,977 +0,0 @@
-The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).
-
-Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.
-
-The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.
-
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
- Sample_name |
- Result date |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Nov03 |
- UTM RW |
-
-
- | 2 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Jan04 |
- UTM RW |
-
-
- | 3 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Nov03 |
- UTM RW |
-
-
- | 4 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Jan04 |
- UTM RW |
-
-
- | 5 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Feb05 |
- UTM RW |
-
-
- | 6 |
- C57BL/6J |
- M |
- 76 |
- R0997F1 |
- Feb05 |
- UTM RW |
-
-
- | 7 |
- D2B6F1 |
- F |
- 57 |
- R1066F1 |
- Feb05 |
- UTM RW |
-
-
- | 8 |
- D2B6F1 |
- M |
- 59 |
- R1381F1 |
- Feb05 |
- UTM RW |
-
-
- | 9 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Nov03 |
- UTM RW |
-
-
- | 10 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Feb05 |
- UTM RW |
-
-
- | 11 |
- DBA/2J |
- F |
- 60 |
- R0917F2 |
- Jan04 |
- UTM RW |
-
-
- | 12 |
- DBA/2J |
- F |
- 64 |
- R1123F1 |
- Feb05 |
- UTM RW |
-
-
- | 13 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Nov03 |
- UTM RW |
-
-
- | 14 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Jan04 |
- UTM RW |
-
-
- | 15 |
- DBA/2J |
- M |
- 73 |
- R1009F1 |
- Feb05 |
- UTM RW |
-
-
- | 16 |
- B6D2F1 |
- F |
- 127 |
- R0919F1 |
- Jan04 |
- UTM JB |
-
-
- | 17 |
- B6D2F1 |
- F |
- 127 |
- R0919F2 |
- Jan04 |
- UTM JB |
-
-
- | 18 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 19 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 20 |
- B6D2F1 |
- M |
- 127 |
- R0920F1 |
- Jan04 |
- UTM JB |
-
-
- | 21 |
- B6D2F1 |
- M |
- 127 |
- R0920F2 |
- Jan04 |
- UTM JB |
-
-
- | 22 |
- B6D2F1 |
- M |
- 66 |
- R1057F1 |
- Feb05 |
- UTM RW |
-
-
- | 23 |
- BXD1 |
- M |
- 181 |
- R0956F1 |
- Feb05 |
- UTM JB |
-
-
- | 24 |
- BXD1 |
- F |
- 95 |
- R0895F1 |
- Jan04 |
- UMemphis |
-
-
- | 25 |
- BXD2 |
- F |
- 142 |
- R0907F1 |
- Feb05 |
- UAB |
-
-
- | 26 |
- BXD5 |
- F |
- 56 |
- R0744F1 |
- Feb05 |
- UMemphis |
-
-
- | 27 |
- BXD5 |
- M |
- 71 |
- R0728F1 |
- Jan04 |
- UMemphis |
-
-
- | 28 |
- BXD6 |
- F |
- 57 |
- R1711F1 |
- Feb05 |
- JAX |
-
-
- | 29 |
- BXD6 |
- F |
- 92 |
- R0901F1 |
- Feb05 |
- UMemphis |
-
-
- | 30 |
- BXD6 |
- M |
- 92 |
- R0902F1 |
- Jan04 |
- UMemphis |
-
-
- | 31 |
- BXD8 |
- F |
- 72 |
- R0167F1 |
- Jan04 |
- UAB |
-
-
- | 32 |
- BXD9 |
- F |
- 86 |
- R0908F1 |
- Feb05 |
- UMemphis |
-
-
- | 33 |
- BXD9 |
- M |
- 86 |
- R0909F1 |
- Jan04 |
- UMemphis |
-
-
- | 34 |
- BXD11 |
- F |
- 97 |
- R0745F1 |
- Feb05 |
- UAB |
-
-
- | 35 |
- BXD11 |
- M |
- 92 |
- R0666F1 |
- Feb05 |
- UMemphis |
-
-
- | 36 |
- BXD12 |
- F |
- 64 |
- R0896F1 |
- Feb05 |
- UMemphis |
-
-
- | 37 |
- BXD12 |
- M |
- 64 |
- R0897F1 |
- Jan04 |
- UMemphis |
-
-
- | 38 |
- BXD13 |
- F |
- 86 |
- R0730F1 |
- Feb05 |
- UMemphis |
-
-
- | 39 |
- BXD13 |
- F |
- 86 |
- R0748F1 |
- Jan04 |
- UMemphis |
-
-
- | 40 |
- BXD13 |
- M |
- 76 |
- R0929F1 |
- Feb05 |
- UMemphis |
-
-
- | 41 |
- BXD14 |
- M |
- 91 |
- R0912F1 |
- Jan04 |
- UMemphis |
-
-
- | 42 |
- BXD14 |
- M |
- 68 |
- R1051F1 |
- Feb05 |
- UTM RW |
-
-
- | 43 |
- BXD15 |
- F |
- 80 |
- R0928F1 |
- Feb05 |
- UMemphis |
-
-
- | 44 |
- BXD18 |
- F |
- 108 |
- R0771F1 |
- Jan04 |
- UAB |
-
-
- | 45 |
- BXD19 |
- M |
- 157 |
- R1229F1 |
- Feb05 |
- UTM JB |
-
-
- | 46 |
- BXD19 |
- F |
- 56 |
- R0236F1 |
- Jan04 |
- UAB |
-
-
- | 47 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Jan04 |
- UAB |
-
-
- | 48 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Feb05 |
- UAB |
-
-
- | 49 |
- BXD23 |
- F |
- 66 |
- R1035F1 |
- Feb05 |
- UTM RW |
-
-
- | 50 |
- BXD23 |
- M |
- 66 |
- R1037F1 |
- Feb05 |
- UTM RW |
-
-
- | 51 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Jan04 |
- UAB |
-
-
- | 52 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Feb05 |
- UAB |
-
-
- | 53 |
- BXD24 |
- F |
- 71 |
- R0914F1 |
- Feb05 |
- UMemphis |
-
-
- | 54 |
- BXD24 |
- M |
- 71 |
- R0913F1 |
- Jan04 |
- UMemphis |
-
-
- | 55 |
- BXD25 |
- F |
- 74 |
- R0373F1 |
- Jan04 |
- UTM RW |
-
-
- | 56 |
- BXD28 |
- F |
- 79 |
- R0910F1 |
- Jan04 |
- UMemphis |
-
-
- | 57 |
- BXD28 |
- M |
- 79 |
- R0911F1 |
- Feb05 |
- UMemphis |
-
-
- | 58 |
- BXD28 |
- F |
- 113 |
- R0892F1 |
- Feb05 |
- UTM RW |
-
-
- | 59 |
- BXD29 |
- F |
- 76 |
- R0693F1 |
- Jan04 |
- UMemphis |
-
-
- | 60 |
- BXD31 |
- F |
- 61 |
- R1199F1 |
- Feb05 |
- UTM RW |
-
-
- | 61 |
- BXD31 |
- M |
- 61 |
- R1141F1 |
- Feb05 |
- UTM RW |
-
-
- | 62 |
- BXD32 |
- F |
- 93 |
- R0898F1 |
- Jan04 |
- UAB |
-
-
- | 63 |
- BXD32 |
- F |
- 76 |
- R1214F1 |
- Feb05 |
- UMemphis |
-
-
- | 64 |
- BXD32 |
- M |
- 65 |
- R1478F1 |
- Feb05 |
- UMemphis |
-
-
- | 65 |
- BXD33 |
- M |
- 77 |
- R0915F1 |
- Jan04 |
- UMemphis |
-
-
- | 66 |
- BXD34 |
- F |
- 92 |
- R0900F1 |
- Feb05 |
- UMemphis |
-
-
- | 67 |
- BXD34 |
- M |
- 56 |
- R0617F1 |
- Feb05 |
- UMemphis |
-
-
- | 68 |
- BXD34 |
- M |
- 72 |
- R0916F1 |
- Jan04 |
- UMemphis |
-
-
- | 69 |
- BXD36 |
- F |
- 61 |
- R1145F1 |
- Feb05 |
- UTM RW |
-
-
- | 70 |
- BXD36 |
- M |
- 77 |
- R0926F1 |
- Jan04 |
- UMemphis |
-
-
- | 71 |
- BXD36 |
- M |
- 61 |
- R1211F1 |
- Feb05 |
- UMemphis |
-
-
- | 72 |
- BXD38 |
- M |
- 83 |
- R1208F1 |
- Feb05 |
- UMemphis |
-
-
- | 73 |
- BXD38 |
- F |
- 69 |
- R0729F1 |
- Feb05 |
- UMemphis |
-
-
- | 74 |
- BXD38 |
- M |
- 69 |
- R0731F1 |
- Jan04 |
- UMemphis |
-
-
- | 75 |
- BXD39 |
- F |
- 76 |
- R1712F1 |
- Feb05 |
- JAX |
-
-
- | 76 |
- BXD39 |
- M |
- 71 |
- R0602F1 |
- Feb05 |
- UAB |
-
-
- | 77 |
- BXD40 |
- F |
- 184 |
- R0741F1 |
- Feb05 |
- UAB |
-
-
- | 78 |
- BXD40 |
- M |
- 56 |
- R0894F1 |
- Feb05 |
- UMemphis |
-
-
- | 79 |
- BXD42 |
- F |
- 100 |
- R0742F1 |
- Feb05 |
- UAB |
-
-
- | 80 |
- BXD42 |
- M |
- 97 |
- R0936F1 |
- Jan04 |
- UMemphis |
-
-
- | 81 |
- BXD42 |
- M |
- 105 |
- R0937F1 |
- Feb05 |
- UMemphis |
-
-
- | 82 |
- BXD43 |
- M |
- 63 |
- R1047F1 |
- Feb05 |
- UTM RW |
-
-
- | 83 |
- BXD44 |
- F |
- 57 |
- R1069F1 |
- Feb05 |
- UTM RW |
-
-
- | 84 |
- BXD44 |
- M |
- 58 |
- R1072F1 |
- Feb05 |
- UTM RW |
-
-
- | 85 |
- BXD45 |
- F |
- 58 |
- R1398F1 |
- Feb05 |
- UTM RW |
-
-
- | 86 |
- BXD48 |
- F |
- 59 |
- R0946F1 |
- Feb05 |
- UTM RW |
-
-
- | 87 |
- BXD48 |
- M |
- 64 |
- R0970F1 |
- Feb05 |
- UTM RW |
-
-
- | 88 |
- BXD51 |
- F |
- 63 |
- R1430F1 |
- Feb05 |
- UTM RW |
-
-
- | 89 |
- BXD51 |
- M |
- 65 |
- R1001F1 |
- Feb05 |
- UTM RW |
-
-
- | 90 |
- BXD60 |
- F |
- 64 |
- R0976F1 |
- Feb05 |
- UTM RW |
-
-
- | 91 |
- BXD60 |
- M |
- 59 |
- R1075F1 |
- Feb05 |
- UTM RW |
-
-
- | 92 |
- BXD62 |
- F |
- 59 |
- R1033F1 |
- Feb05 |
- UTM RW |
-
-
- | 93 |
- BXD62 |
- M |
- 58 |
- R1027F1 |
- Feb05 |
- UTM RW |
-
-
- | 94 |
- BXD69 |
- F |
- 60 |
- R1438F1 |
- Feb05 |
- UTM RW |
-
-
- | 95 |
- BXD69 |
- M |
- 64 |
- R1193F1 |
- Feb05 |
- UTM RW |
-
-
- | 96 |
- BXD73 |
- F |
- 60 |
- R1275F1 |
- Feb05 |
- UTM RW |
-
-
- | 97 |
- BXD73 |
- M |
- 76 |
- R1442F1 |
- Feb05 |
- UTM RW |
-
-
- | 98 |
- BXD77 |
- M |
- 61 |
- R1426F1 |
- Feb05 |
- UTM RW |
-
-
- | 99 |
- BXD86 |
- F |
- 77 |
- R1414F1 |
- Feb05 |
- UTM RW |
-
-
- | 100 |
- BXD86 |
- M |
- 77 |
- R1418F1 |
- Feb05 |
- UTM RW |
-
-
- | 101 |
- BXD87 |
- F |
- 89 |
- R1713F1 |
- Feb05 |
- UTM RW |
-
-
- | 102 |
- BXD87 |
- M |
- 84 |
- R1709F1 |
- Feb05 |
- UTM RW |
-
-
- | 103 |
- BXD90 |
- M |
- 61 |
- R1452F |
- Feb05 |
- UTM RW |
-
-
- | 104 |
- BXD92 |
- F |
- 58 |
- R1299F1 |
- Feb05 |
- UTM RW |
-
-
- | 105 |
- BXD92 |
- M |
- 59 |
- R1307F1 |
- Feb05 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/IBR_M_0606_R/acknowledgment.rtf b/general/datasets/IBR_M_0606_R/acknowledgment.rtf
deleted file mode 100644
index a1563a6..0000000
--- a/general/datasets/IBR_M_0606_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_0606_R/cases.rtf b/general/datasets/IBR_M_0606_R/cases.rtf
deleted file mode 100644
index 8794b88..0000000
--- a/general/datasets/IBR_M_0606_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues
-
-
-All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).
-
diff --git a/general/datasets/IBR_M_0606_R/notes.rtf b/general/datasets/IBR_M_0606_R/notes.rtf
deleted file mode 100644
index 72bad83..0000000
--- a/general/datasets/IBR_M_0606_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.
-
diff --git a/general/datasets/IBR_M_0606_R/platform.rtf b/general/datasets/IBR_M_0606_R/platform.rtf
deleted file mode 100644
index 028fe23..0000000
--- a/general/datasets/IBR_M_0606_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0
diff --git a/general/datasets/IBR_M_0606_R/processing.rtf b/general/datasets/IBR_M_0606_R/processing.rtf
deleted file mode 100644
index 243e5c0..0000000
--- a/general/datasets/IBR_M_0606_R/processing.rtf
+++ /dev/null
@@ -1,20 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
- - Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
- - Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/IBR_M_0606_R/summary.rtf b/general/datasets/IBR_M_0606_R/summary.rtf
deleted file mode 100644
index 6fe94b1..0000000
--- a/general/datasets/IBR_M_0606_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This April 2005 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 45 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 42 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 105 Affymetrix M430A and B array pairs. This particular data set was processed using the RMA protocol. To simplify comparisons among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
-
diff --git a/general/datasets/IBR_M_0606_R/tissue.rtf b/general/datasets/IBR_M_0606_R/tissue.rtf
deleted file mode 100644
index 841d879..0000000
--- a/general/datasets/IBR_M_0606_R/tissue.rtf
+++ /dev/null
@@ -1,977 +0,0 @@
-The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis.
-
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).
-
-Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.
-
-The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.
-
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Age |
- Sample_name |
- Result date |
- Source |
-
-
- | 1 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Nov03 |
- UTM RW |
-
-
- | 2 |
- C57BL/6J |
- F |
- 65 |
- R0903F1 |
- Jan04 |
- UTM RW |
-
-
- | 3 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Nov03 |
- UTM RW |
-
-
- | 4 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Jan04 |
- UTM RW |
-
-
- | 5 |
- C57BL/6J |
- M |
- 66 |
- R0906F1 |
- Feb05 |
- UTM RW |
-
-
- | 6 |
- C57BL/6J |
- M |
- 76 |
- R0997F1 |
- Feb05 |
- UTM RW |
-
-
- | 7 |
- D2B6F1 |
- F |
- 57 |
- R1066F1 |
- Feb05 |
- UTM RW |
-
-
- | 8 |
- D2B6F1 |
- M |
- 59 |
- R1381F1 |
- Feb05 |
- UTM RW |
-
-
- | 9 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Nov03 |
- UTM RW |
-
-
- | 10 |
- DBA/2J |
- F |
- 60 |
- R0917F1 |
- Feb05 |
- UTM RW |
-
-
- | 11 |
- DBA/2J |
- F |
- 60 |
- R0917F2 |
- Jan04 |
- UTM RW |
-
-
- | 12 |
- DBA/2J |
- F |
- 64 |
- R1123F1 |
- Feb05 |
- UTM RW |
-
-
- | 13 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Nov03 |
- UTM RW |
-
-
- | 14 |
- DBA/2J |
- M |
- 60 |
- R0918F1 |
- Jan04 |
- UTM RW |
-
-
- | 15 |
- DBA/2J |
- M |
- 73 |
- R1009F1 |
- Feb05 |
- UTM RW |
-
-
- | 16 |
- B6D2F1 |
- F |
- 127 |
- R0919F1 |
- Jan04 |
- UTM JB |
-
-
- | 17 |
- B6D2F1 |
- F |
- 127 |
- R0919F2 |
- Jan04 |
- UTM JB |
-
-
- | 18 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 19 |
- B6D2F1 |
- F |
- 64 |
- R1053F1 |
- Feb05 |
- UTM RW |
-
-
- | 20 |
- B6D2F1 |
- M |
- 127 |
- R0920F1 |
- Jan04 |
- UTM JB |
-
-
- | 21 |
- B6D2F1 |
- M |
- 127 |
- R0920F2 |
- Jan04 |
- UTM JB |
-
-
- | 22 |
- B6D2F1 |
- M |
- 66 |
- R1057F1 |
- Feb05 |
- UTM RW |
-
-
- | 23 |
- BXD1 |
- M |
- 181 |
- R0956F1 |
- Feb05 |
- UTM JB |
-
-
- | 24 |
- BXD1 |
- F |
- 95 |
- R0895F1 |
- Jan04 |
- UMemphis |
-
-
- | 25 |
- BXD2 |
- F |
- 142 |
- R0907F1 |
- Feb05 |
- UAB |
-
-
- | 26 |
- BXD5 |
- F |
- 56 |
- R0744F1 |
- Feb05 |
- UMemphis |
-
-
- | 27 |
- BXD5 |
- M |
- 71 |
- R0728F1 |
- Jan04 |
- UMemphis |
-
-
- | 28 |
- BXD6 |
- F |
- 57 |
- R1711F1 |
- Feb05 |
- JAX |
-
-
- | 29 |
- BXD6 |
- F |
- 92 |
- R0901F1 |
- Feb05 |
- UMemphis |
-
-
- | 30 |
- BXD6 |
- M |
- 92 |
- R0902F1 |
- Jan04 |
- UMemphis |
-
-
- | 31 |
- BXD8 |
- F |
- 72 |
- R0167F1 |
- Jan04 |
- UAB |
-
-
- | 32 |
- BXD9 |
- F |
- 86 |
- R0908F1 |
- Feb05 |
- UMemphis |
-
-
- | 33 |
- BXD9 |
- M |
- 86 |
- R0909F1 |
- Jan04 |
- UMemphis |
-
-
- | 34 |
- BXD11 |
- F |
- 97 |
- R0745F1 |
- Feb05 |
- UAB |
-
-
- | 35 |
- BXD11 |
- M |
- 92 |
- R0666F1 |
- Feb05 |
- UMemphis |
-
-
- | 36 |
- BXD12 |
- F |
- 64 |
- R0896F1 |
- Feb05 |
- UMemphis |
-
-
- | 37 |
- BXD12 |
- M |
- 64 |
- R0897F1 |
- Jan04 |
- UMemphis |
-
-
- | 38 |
- BXD13 |
- F |
- 86 |
- R0730F1 |
- Feb05 |
- UMemphis |
-
-
- | 39 |
- BXD13 |
- F |
- 86 |
- R0748F1 |
- Jan04 |
- UMemphis |
-
-
- | 40 |
- BXD13 |
- M |
- 76 |
- R0929F1 |
- Feb05 |
- UMemphis |
-
-
- | 41 |
- BXD14 |
- M |
- 91 |
- R0912F1 |
- Jan04 |
- UMemphis |
-
-
- | 42 |
- BXD14 |
- M |
- 68 |
- R1051F1 |
- Feb05 |
- UTM RW |
-
-
- | 43 |
- BXD15 |
- F |
- 80 |
- R0928F1 |
- Feb05 |
- UMemphis |
-
-
- | 44 |
- BXD18 |
- F |
- 108 |
- R0771F1 |
- Jan04 |
- UAB |
-
-
- | 45 |
- BXD19 |
- M |
- 157 |
- R1229F1 |
- Feb05 |
- UTM JB |
-
-
- | 46 |
- BXD19 |
- F |
- 56 |
- R0236F1 |
- Jan04 |
- UAB |
-
-
- | 47 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Jan04 |
- UAB |
-
-
- | 48 |
- BXD21 |
- F |
- 67 |
- R0740F1 |
- Feb05 |
- UAB |
-
-
- | 49 |
- BXD23 |
- F |
- 66 |
- R1035F1 |
- Feb05 |
- UTM RW |
-
-
- | 50 |
- BXD23 |
- M |
- 66 |
- R1037F1 |
- Feb05 |
- UTM RW |
-
-
- | 51 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Jan04 |
- UAB |
-
-
- | 52 |
- BXD23 |
- F |
- 88 |
- R0815F1 |
- Feb05 |
- UAB |
-
-
- | 53 |
- BXD24 |
- F |
- 71 |
- R0914F1 |
- Feb05 |
- UMemphis |
-
-
- | 54 |
- BXD24 |
- M |
- 71 |
- R0913F1 |
- Jan04 |
- UMemphis |
-
-
- | 55 |
- BXD25 |
- F |
- 74 |
- R0373F1 |
- Jan04 |
- UTM RW |
-
-
- | 56 |
- BXD28 |
- F |
- 79 |
- R0910F1 |
- Jan04 |
- UMemphis |
-
-
- | 57 |
- BXD28 |
- M |
- 79 |
- R0911F1 |
- Feb05 |
- UMemphis |
-
-
- | 58 |
- BXD28 |
- F |
- 113 |
- R0892F1 |
- Feb05 |
- UTM RW |
-
-
- | 59 |
- BXD29 |
- F |
- 76 |
- R0693F1 |
- Jan04 |
- UMemphis |
-
-
- | 60 |
- BXD31 |
- F |
- 61 |
- R1199F1 |
- Feb05 |
- UTM RW |
-
-
- | 61 |
- BXD31 |
- M |
- 61 |
- R1141F1 |
- Feb05 |
- UTM RW |
-
-
- | 62 |
- BXD32 |
- F |
- 93 |
- R0898F1 |
- Jan04 |
- UAB |
-
-
- | 63 |
- BXD32 |
- F |
- 76 |
- R1214F1 |
- Feb05 |
- UMemphis |
-
-
- | 64 |
- BXD32 |
- M |
- 65 |
- R1478F1 |
- Feb05 |
- UMemphis |
-
-
- | 65 |
- BXD33 |
- M |
- 77 |
- R0915F1 |
- Jan04 |
- UMemphis |
-
-
- | 66 |
- BXD34 |
- F |
- 92 |
- R0900F1 |
- Feb05 |
- UMemphis |
-
-
- | 67 |
- BXD34 |
- M |
- 56 |
- R0617F1 |
- Feb05 |
- UMemphis |
-
-
- | 68 |
- BXD34 |
- M |
- 72 |
- R0916F1 |
- Jan04 |
- UMemphis |
-
-
- | 69 |
- BXD36 |
- F |
- 61 |
- R1145F1 |
- Feb05 |
- UTM RW |
-
-
- | 70 |
- BXD36 |
- M |
- 77 |
- R0926F1 |
- Jan04 |
- UMemphis |
-
-
- | 71 |
- BXD36 |
- M |
- 61 |
- R1211F1 |
- Feb05 |
- UMemphis |
-
-
- | 72 |
- BXD38 |
- M |
- 83 |
- R1208F1 |
- Feb05 |
- UMemphis |
-
-
- | 73 |
- BXD38 |
- F |
- 69 |
- R0729F1 |
- Feb05 |
- UMemphis |
-
-
- | 74 |
- BXD38 |
- M |
- 69 |
- R0731F1 |
- Jan04 |
- UMemphis |
-
-
- | 75 |
- BXD39 |
- F |
- 76 |
- R1712F1 |
- Feb05 |
- JAX |
-
-
- | 76 |
- BXD39 |
- M |
- 71 |
- R0602F1 |
- Feb05 |
- UAB |
-
-
- | 77 |
- BXD40 |
- F |
- 184 |
- R0741F1 |
- Feb05 |
- UAB |
-
-
- | 78 |
- BXD40 |
- M |
- 56 |
- R0894F1 |
- Feb05 |
- UMemphis |
-
-
- | 79 |
- BXD42 |
- F |
- 100 |
- R0742F1 |
- Feb05 |
- UAB |
-
-
- | 80 |
- BXD42 |
- M |
- 97 |
- R0936F1 |
- Jan04 |
- UMemphis |
-
-
- | 81 |
- BXD42 |
- M |
- 105 |
- R0937F1 |
- Feb05 |
- UMemphis |
-
-
- | 82 |
- BXD43 |
- M |
- 63 |
- R1047F1 |
- Feb05 |
- UTM RW |
-
-
- | 83 |
- BXD44 |
- F |
- 57 |
- R1069F1 |
- Feb05 |
- UTM RW |
-
-
- | 84 |
- BXD44 |
- M |
- 58 |
- R1072F1 |
- Feb05 |
- UTM RW |
-
-
- | 85 |
- BXD45 |
- F |
- 58 |
- R1398F1 |
- Feb05 |
- UTM RW |
-
-
- | 86 |
- BXD48 |
- F |
- 59 |
- R0946F1 |
- Feb05 |
- UTM RW |
-
-
- | 87 |
- BXD48 |
- M |
- 64 |
- R0970F1 |
- Feb05 |
- UTM RW |
-
-
- | 88 |
- BXD51 |
- F |
- 63 |
- R1430F1 |
- Feb05 |
- UTM RW |
-
-
- | 89 |
- BXD51 |
- M |
- 65 |
- R1001F1 |
- Feb05 |
- UTM RW |
-
-
- | 90 |
- BXD60 |
- F |
- 64 |
- R0976F1 |
- Feb05 |
- UTM RW |
-
-
- | 91 |
- BXD60 |
- M |
- 59 |
- R1075F1 |
- Feb05 |
- UTM RW |
-
-
- | 92 |
- BXD62 |
- F |
- 59 |
- R1033F1 |
- Feb05 |
- UTM RW |
-
-
- | 93 |
- BXD62 |
- M |
- 58 |
- R1027F1 |
- Feb05 |
- UTM RW |
-
-
- | 94 |
- BXD69 |
- F |
- 60 |
- R1438F1 |
- Feb05 |
- UTM RW |
-
-
- | 95 |
- BXD69 |
- M |
- 64 |
- R1193F1 |
- Feb05 |
- UTM RW |
-
-
- | 96 |
- BXD73 |
- F |
- 60 |
- R1275F1 |
- Feb05 |
- UTM RW |
-
-
- | 97 |
- BXD73 |
- M |
- 76 |
- R1442F1 |
- Feb05 |
- UTM RW |
-
-
- | 98 |
- BXD77 |
- M |
- 61 |
- R1426F1 |
- Feb05 |
- UTM RW |
-
-
- | 99 |
- BXD86 |
- F |
- 77 |
- R1414F1 |
- Feb05 |
- UTM RW |
-
-
- | 100 |
- BXD86 |
- M |
- 77 |
- R1418F1 |
- Feb05 |
- UTM RW |
-
-
- | 101 |
- BXD87 |
- F |
- 89 |
- R1713F1 |
- Feb05 |
- UTM RW |
-
-
- | 102 |
- BXD87 |
- M |
- 84 |
- R1709F1 |
- Feb05 |
- UTM RW |
-
-
- | 103 |
- BXD90 |
- M |
- 61 |
- R1452F |
- Feb05 |
- UTM RW |
-
-
- | 104 |
- BXD92 |
- F |
- 58 |
- R1299F1 |
- Feb05 |
- UTM RW |
-
-
- | 105 |
- BXD92 |
- M |
- 59 |
- R1307F1 |
- Feb05 |
- UTM RW |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/IBR_M_1004_M/acknowledgment.rtf b/general/datasets/IBR_M_1004_M/acknowledgment.rtf
deleted file mode 100644
index 7b62a11..0000000
--- a/general/datasets/IBR_M_1004_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data for the microarrays were generously provided by support from NIAAA INIA grants to RWW and Thomas Sutter. Support for sample acquistion and WebQTL have been provided by NIMH Human Brain Project, and the Dunavant Chair of Excellence, University of Tennessee Health Science Center. All arrays were processed at the University of Memphis by Dr. Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_1004_M/cases.rtf b/general/datasets/IBR_M_1004_M/cases.rtf
deleted file mode 100644
index 9dc5cbe..0000000
--- a/general/datasets/IBR_M_1004_M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B) and DBA/2J (D). Both B and D strains have been almost fully sequence (8x coverage for B by a public consortium and approximately 1.5x coverage for D by Celera).
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
diff --git a/general/datasets/IBR_M_1004_M/notes.rtf b/general/datasets/IBR_M_1004_M/notes.rtf
deleted file mode 100644
index f3ea488..0000000
--- a/general/datasets/IBR_M_1004_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004.
diff --git a/general/datasets/IBR_M_1004_M/platform.rtf b/general/datasets/IBR_M_1004_M/platform.rtf
deleted file mode 100644
index 51cbff2..0000000
--- a/general/datasets/IBR_M_1004_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 430A and 430B GeneChip Set: Expression data were generated using 430AB array pairs. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on either the Verify UCSC and Verify Ensembl links in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/IBR_M_1004_M/processing.rtf b/general/datasets/IBR_M_1004_M/processing.rtf
deleted file mode 100644
index 4663b88..0000000
--- a/general/datasets/IBR_M_1004_M/processing.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: We corrected for technical variance introduced by two batches. Means separated by the first batch for each gene are corrected same as means of the second batch.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-
-
-
-Probe set data: The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
-
-PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
-
-When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
-
-
-About the array probe sets names:
-
-
-Most probe sets on the mouse 430A and 430B arrays consist of a total of 22 probes, divided into 11 perfect match(PM) probes and 11 mismatch (MM) controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, several suffix characters that highlight design features, a a final A or B character to specify the array pair member. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene.
-
diff --git a/general/datasets/IBR_M_1004_M/summary.rtf b/general/datasets/IBR_M_1004_M/summary.rtf
deleted file mode 100644
index c32676a..0000000
--- a/general/datasets/IBR_M_1004_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This October 2004 data freeze provides initial estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix M430AB microarrays. In contast to the U74Av2 array, this new data set provides broader coverage (~45,000 transcripts) but does not include replicates or as many strains (25 vs 35). Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Data were processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
diff --git a/general/datasets/IBR_M_1004_M/tissue.rtf b/general/datasets/IBR_M_1004_M/tissue.rtf
deleted file mode 100644
index cac878a..0000000
--- a/general/datasets/IBR_M_1004_M/tissue.rtf
+++ /dev/null
@@ -1,261 +0,0 @@
-The data set consists of a single batch of Affymetrix mouse expression 430A and 430B GeneChip array pairs. Each AB pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter and colleagues at the University of Memphis. Before running the main batch of 30 pairs of array, we ran four "test" samples (one male and one female pool from each of the two parental strains, C57BL/6J and DBA/2J). The main set of 30 array pairs includes the same four samples (in other words we have four technical replicates), two F1 hybrid sample (each run two times for a within-batch technical replication), and 22 BXD strains. The data set therefore consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. We should note that the four technical replicates between batches were eventually combined with a correction for a highly significant batch effect. This was done at both the probe and probe set levels to "align" the test batch values with the two main batches. (The ratio of the probe average in the four test arrays to the average of the same probe in the four corresponding main batch arrays was used as a correction factor.) The F1 within-batch technical replicates were simply averaged. In the next batch we will reverse the sex of the BXD samples to achieve a balance with at least 22 BXD strains with one male and one female sample each.
-
-The table below lists the arrays by strain, sex, age, sample identifier, and data results were obtained from the Bioanalytical Core at the University of Memphis. Each array was hybridized to a pool of mRNA from three mice.
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Date |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F2 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F2 |
- Jan04 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F2 |
- Jan03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F2 |
- Jan04 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F1 |
- Nov03 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F2 |
- Jan04 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F1 |
- Nov03 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F2 |
- Jan04 |
-
-
- | BXD1 |
- F |
- 95 |
- 895-F1 |
- Jan04 |
-
-
- | BXD5 |
- M |
- 71 |
- 728-F1 |
- Jan04 |
-
-
- | BXD6 |
- M |
- 92 |
- 902-F1 |
- Jan04 |
-
-
- | BXD8 |
- F |
- 72 |
- S167-F1 |
- Jan04 |
-
-
- | BXD9 |
- M |
- 86 |
- 909-F1 |
- Jan04 |
-
-
- | BXD12 |
- M |
- 64 |
- 897-F1 |
- Jan04 |
-
-
- | BXD13 |
- F |
- 86 |
- 748-F1 |
- Jan04 |
-
-
- | BXD14 |
- M |
- 91 |
- 912-F1 |
- Jan04 |
-
-
- | BXD18 |
- F |
- 108 |
- 771-F1 |
- Jan04 |
-
-
- | BXD19 |
- F |
- 56 |
- S236-F1 |
- Jan04 |
-
-
- | BXD21 |
- F |
- 67 |
- 740-F1 |
- Jan04 |
-
-
- | BXD23 |
- F |
- 88 |
- 815-F1 |
- Jan04 |
-
-
- | BXD24 |
- M |
- 71 |
- 913-F1 |
- Jan04 |
-
-
- | BXD25 |
- F |
- 74 |
- S373-F1 |
- Jan04 |
-
-
- | BXD28 |
- F |
- 79 |
- 910-F1 |
- Jan04 |
-
-
- | BXD29 |
- F |
- 76 |
- 693-F1 |
- Jan04 |
-
-
- | BXD32 |
- F |
- 93 |
- 898-F1 |
- Jan04 |
-
-
- | BXD33 |
- M |
- 77 |
- 915-F1 |
- Jan04 |
-
-
- | BXD34 |
- M |
- 72 |
- 916-F1 |
- Jan04 |
-
-
- | BXD36 |
- M |
- 77 |
- 926-F1 |
- Jan04 |
-
-
- | BXD38 |
- M |
- 69 |
- 731-F1 |
- Jan04 |
-
-
- | BXD42 |
- M |
- 97 |
- 936-F1 |
- Jan04 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/IBR_M_1004_P/acknowledgment.rtf b/general/datasets/IBR_M_1004_P/acknowledgment.rtf
deleted file mode 100644
index 7b62a11..0000000
--- a/general/datasets/IBR_M_1004_P/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data for the microarrays were generously provided by support from NIAAA INIA grants to RWW and Thomas Sutter. Support for sample acquistion and WebQTL have been provided by NIMH Human Brain Project, and the Dunavant Chair of Excellence, University of Tennessee Health Science Center. All arrays were processed at the University of Memphis by Dr. Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_1004_P/cases.rtf b/general/datasets/IBR_M_1004_P/cases.rtf
deleted file mode 100644
index 9dc5cbe..0000000
--- a/general/datasets/IBR_M_1004_P/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B) and DBA/2J (D). Both B and D strains have been almost fully sequence (8x coverage for B by a public consortium and approximately 1.5x coverage for D by Celera).
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
diff --git a/general/datasets/IBR_M_1004_P/notes.rtf b/general/datasets/IBR_M_1004_P/notes.rtf
deleted file mode 100644
index f3ea488..0000000
--- a/general/datasets/IBR_M_1004_P/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004.
diff --git a/general/datasets/IBR_M_1004_P/platform.rtf b/general/datasets/IBR_M_1004_P/platform.rtf
deleted file mode 100644
index 51cbff2..0000000
--- a/general/datasets/IBR_M_1004_P/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 430A and 430B GeneChip Set: Expression data were generated using 430AB array pairs. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on either the Verify UCSC and Verify Ensembl links in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/IBR_M_1004_P/processing.rtf b/general/datasets/IBR_M_1004_P/processing.rtf
deleted file mode 100644
index 4663b88..0000000
--- a/general/datasets/IBR_M_1004_P/processing.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: We corrected for technical variance introduced by two batches. Means separated by the first batch for each gene are corrected same as means of the second batch.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-
-
-
-Probe set data: The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
-
-PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
-
-When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
-
-
-About the array probe sets names:
-
-
-Most probe sets on the mouse 430A and 430B arrays consist of a total of 22 probes, divided into 11 perfect match(PM) probes and 11 mismatch (MM) controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, several suffix characters that highlight design features, a a final A or B character to specify the array pair member. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene.
-
diff --git a/general/datasets/IBR_M_1004_P/summary.rtf b/general/datasets/IBR_M_1004_P/summary.rtf
deleted file mode 100644
index c32676a..0000000
--- a/general/datasets/IBR_M_1004_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This October 2004 data freeze provides initial estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix M430AB microarrays. In contast to the U74Av2 array, this new data set provides broader coverage (~45,000 transcripts) but does not include replicates or as many strains (25 vs 35). Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Data were processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
diff --git a/general/datasets/IBR_M_1004_P/tissue.rtf b/general/datasets/IBR_M_1004_P/tissue.rtf
deleted file mode 100644
index cac878a..0000000
--- a/general/datasets/IBR_M_1004_P/tissue.rtf
+++ /dev/null
@@ -1,261 +0,0 @@
-The data set consists of a single batch of Affymetrix mouse expression 430A and 430B GeneChip array pairs. Each AB pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter and colleagues at the University of Memphis. Before running the main batch of 30 pairs of array, we ran four "test" samples (one male and one female pool from each of the two parental strains, C57BL/6J and DBA/2J). The main set of 30 array pairs includes the same four samples (in other words we have four technical replicates), two F1 hybrid sample (each run two times for a within-batch technical replication), and 22 BXD strains. The data set therefore consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. We should note that the four technical replicates between batches were eventually combined with a correction for a highly significant batch effect. This was done at both the probe and probe set levels to "align" the test batch values with the two main batches. (The ratio of the probe average in the four test arrays to the average of the same probe in the four corresponding main batch arrays was used as a correction factor.) The F1 within-batch technical replicates were simply averaged. In the next batch we will reverse the sex of the BXD samples to achieve a balance with at least 22 BXD strains with one male and one female sample each.
-
-The table below lists the arrays by strain, sex, age, sample identifier, and data results were obtained from the Bioanalytical Core at the University of Memphis. Each array was hybridized to a pool of mRNA from three mice.
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Date |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F2 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F2 |
- Jan04 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F2 |
- Jan03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F2 |
- Jan04 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F1 |
- Nov03 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F2 |
- Jan04 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F1 |
- Nov03 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F2 |
- Jan04 |
-
-
- | BXD1 |
- F |
- 95 |
- 895-F1 |
- Jan04 |
-
-
- | BXD5 |
- M |
- 71 |
- 728-F1 |
- Jan04 |
-
-
- | BXD6 |
- M |
- 92 |
- 902-F1 |
- Jan04 |
-
-
- | BXD8 |
- F |
- 72 |
- S167-F1 |
- Jan04 |
-
-
- | BXD9 |
- M |
- 86 |
- 909-F1 |
- Jan04 |
-
-
- | BXD12 |
- M |
- 64 |
- 897-F1 |
- Jan04 |
-
-
- | BXD13 |
- F |
- 86 |
- 748-F1 |
- Jan04 |
-
-
- | BXD14 |
- M |
- 91 |
- 912-F1 |
- Jan04 |
-
-
- | BXD18 |
- F |
- 108 |
- 771-F1 |
- Jan04 |
-
-
- | BXD19 |
- F |
- 56 |
- S236-F1 |
- Jan04 |
-
-
- | BXD21 |
- F |
- 67 |
- 740-F1 |
- Jan04 |
-
-
- | BXD23 |
- F |
- 88 |
- 815-F1 |
- Jan04 |
-
-
- | BXD24 |
- M |
- 71 |
- 913-F1 |
- Jan04 |
-
-
- | BXD25 |
- F |
- 74 |
- S373-F1 |
- Jan04 |
-
-
- | BXD28 |
- F |
- 79 |
- 910-F1 |
- Jan04 |
-
-
- | BXD29 |
- F |
- 76 |
- 693-F1 |
- Jan04 |
-
-
- | BXD32 |
- F |
- 93 |
- 898-F1 |
- Jan04 |
-
-
- | BXD33 |
- M |
- 77 |
- 915-F1 |
- Jan04 |
-
-
- | BXD34 |
- M |
- 72 |
- 916-F1 |
- Jan04 |
-
-
- | BXD36 |
- M |
- 77 |
- 926-F1 |
- Jan04 |
-
-
- | BXD38 |
- M |
- 69 |
- 731-F1 |
- Jan04 |
-
-
- | BXD42 |
- M |
- 97 |
- 936-F1 |
- Jan04 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/IBR_M_1004_R/acknowledgment.rtf b/general/datasets/IBR_M_1004_R/acknowledgment.rtf
deleted file mode 100644
index 7b62a11..0000000
--- a/general/datasets/IBR_M_1004_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data for the microarrays were generously provided by support from NIAAA INIA grants to RWW and Thomas Sutter. Support for sample acquistion and WebQTL have been provided by NIMH Human Brain Project, and the Dunavant Chair of Excellence, University of Tennessee Health Science Center. All arrays were processed at the University of Memphis by Dr. Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.
diff --git a/general/datasets/IBR_M_1004_R/cases.rtf b/general/datasets/IBR_M_1004_R/cases.rtf
deleted file mode 100644
index 9dc5cbe..0000000
--- a/general/datasets/IBR_M_1004_R/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We have exploited a set of BXD recombinant inbred strains. The parental strains from which all BXD lines are derived are C57BL/6J (B) and DBA/2J (D). Both B and D strains have been almost fully sequence (8x coverage for B by a public consortium and approximately 1.5x coverage for D by Celera).
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
diff --git a/general/datasets/IBR_M_1004_R/notes.rtf b/general/datasets/IBR_M_1004_R/notes.rtf
deleted file mode 100644
index f3ea488..0000000
--- a/general/datasets/IBR_M_1004_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004.
diff --git a/general/datasets/IBR_M_1004_R/platform.rtf b/general/datasets/IBR_M_1004_R/platform.rtf
deleted file mode 100644
index 51cbff2..0000000
--- a/general/datasets/IBR_M_1004_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix 430A and 430B GeneChip Set: Expression data were generated using 430AB array pairs. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on either the Verify UCSC and Verify Ensembl links in the Trait Data and Editing Form (right side of the Location line).
diff --git a/general/datasets/IBR_M_1004_R/processing.rtf b/general/datasets/IBR_M_1004_R/processing.rtf
deleted file mode 100644
index 4663b88..0000000
--- a/general/datasets/IBR_M_1004_R/processing.rtf
+++ /dev/null
@@ -1,29 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
- - Step 7: We corrected for technical variance introduced by two batches. Means separated by the first batch for each gene are corrected same as means of the second batch.
- - Step 8: Finally, we compute the arithmetic mean of the values for the set of microarrays for each strain. In this data set we have modest numbers of replicates and for this reason we do not yet provide error terms for transcripts or probes. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We expect to add statistical controls and adjustments for these variables in subsequent versions of WebQTL.
-
-
-
-
-Probe set data: The original expression values in the Affymetrix CEL files were read into PerfectMatch to generate the normalized PDNN data set.
-
-PDNN values of each array were subsequently normalized to a achieve a mean value of 8 units and a variance of 2 units.
-
-When necessary, we computed the arithmetic mean for technical replicates and treated these as single samples. We then computed the arithmetic mean for the set of 2 to 5 biological replicates for each strain.
-
-
-About the array probe sets names:
-
-
-Most probe sets on the mouse 430A and 430B arrays consist of a total of 22 probes, divided into 11 perfect match(PM) probes and 11 mismatch (MM) controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, several suffix characters that highlight design features, a a final A or B character to specify the array pair member. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene.
-
diff --git a/general/datasets/IBR_M_1004_R/summary.rtf b/general/datasets/IBR_M_1004_R/summary.rtf
deleted file mode 100644
index c32676a..0000000
--- a/general/datasets/IBR_M_1004_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This October 2004 data freeze provides initial estimates of mRNA expression in brains of adult BXD recombinant inbred mice measured using Affymetrix M430AB microarrays. In contast to the U74Av2 array, this new data set provides broader coverage (~45,000 transcripts) but does not include replicates or as many strains (25 vs 35). Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Data were processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units.
diff --git a/general/datasets/IBR_M_1004_R/tissue.rtf b/general/datasets/IBR_M_1004_R/tissue.rtf
deleted file mode 100644
index cac878a..0000000
--- a/general/datasets/IBR_M_1004_R/tissue.rtf
+++ /dev/null
@@ -1,261 +0,0 @@
-The data set consists of a single batch of Affymetrix mouse expression 430A and 430B GeneChip array pairs. Each AB pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter and colleagues at the University of Memphis. Before running the main batch of 30 pairs of array, we ran four "test" samples (one male and one female pool from each of the two parental strains, C57BL/6J and DBA/2J). The main set of 30 array pairs includes the same four samples (in other words we have four technical replicates), two F1 hybrid sample (each run two times for a within-batch technical replication), and 22 BXD strains. The data set therefore consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. We should note that the four technical replicates between batches were eventually combined with a correction for a highly significant batch effect. This was done at both the probe and probe set levels to "align" the test batch values with the two main batches. (The ratio of the probe average in the four test arrays to the average of the same probe in the four corresponding main batch arrays was used as a correction factor.) The F1 within-batch technical replicates were simply averaged. In the next batch we will reverse the sex of the BXD samples to achieve a balance with at least 22 BXD strains with one male and one female sample each.
-
-The table below lists the arrays by strain, sex, age, sample identifier, and data results were obtained from the Bioanalytical Core at the University of Memphis. Each array was hybridized to a pool of mRNA from three mice.
-
-
-
-
-
-
-
-
- | Strain |
- Sex |
- Age |
- SampleID |
- Date |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- F |
- 127 |
- 919-F2 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F1 |
- Jan04 |
-
-
- | B6D2F1 |
- M |
- 127 |
- 920-F2 |
- Jan04 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- F |
- 65 |
- 903-F2 |
- Jan03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F1 |
- Nov03 |
-
-
- | C57BL/6J |
- M |
- 66 |
- 906-F2 |
- Jan04 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F1 |
- Nov03 |
-
-
- | DBA/2J |
- F |
- 60 |
- 917-F2 |
- Jan04 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F1 |
- Nov03 |
-
-
- | DBA/2J |
- M |
- 60 |
- 918-F2 |
- Jan04 |
-
-
- | BXD1 |
- F |
- 95 |
- 895-F1 |
- Jan04 |
-
-
- | BXD5 |
- M |
- 71 |
- 728-F1 |
- Jan04 |
-
-
- | BXD6 |
- M |
- 92 |
- 902-F1 |
- Jan04 |
-
-
- | BXD8 |
- F |
- 72 |
- S167-F1 |
- Jan04 |
-
-
- | BXD9 |
- M |
- 86 |
- 909-F1 |
- Jan04 |
-
-
- | BXD12 |
- M |
- 64 |
- 897-F1 |
- Jan04 |
-
-
- | BXD13 |
- F |
- 86 |
- 748-F1 |
- Jan04 |
-
-
- | BXD14 |
- M |
- 91 |
- 912-F1 |
- Jan04 |
-
-
- | BXD18 |
- F |
- 108 |
- 771-F1 |
- Jan04 |
-
-
- | BXD19 |
- F |
- 56 |
- S236-F1 |
- Jan04 |
-
-
- | BXD21 |
- F |
- 67 |
- 740-F1 |
- Jan04 |
-
-
- | BXD23 |
- F |
- 88 |
- 815-F1 |
- Jan04 |
-
-
- | BXD24 |
- M |
- 71 |
- 913-F1 |
- Jan04 |
-
-
- | BXD25 |
- F |
- 74 |
- S373-F1 |
- Jan04 |
-
-
- | BXD28 |
- F |
- 79 |
- 910-F1 |
- Jan04 |
-
-
- | BXD29 |
- F |
- 76 |
- 693-F1 |
- Jan04 |
-
-
- | BXD32 |
- F |
- 93 |
- 898-F1 |
- Jan04 |
-
-
- | BXD33 |
- M |
- 77 |
- 915-F1 |
- Jan04 |
-
-
- | BXD34 |
- M |
- 72 |
- 916-F1 |
- Jan04 |
-
-
- | BXD36 |
- M |
- 77 |
- 926-F1 |
- Jan04 |
-
-
- | BXD38 |
- M |
- 69 |
- 731-F1 |
- Jan04 |
-
-
- | BXD42 |
- M |
- 97 |
- 936-F1 |
- Jan04 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/INIA_AmgCoh_0311/cases.rtf b/general/datasets/INIA_AmgCoh_0311/cases.rtf
deleted file mode 100644
index b02b19a..0000000
--- a/general/datasets/INIA_AmgCoh_0311/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 58 strains, including 54 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1) were analyzed. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by K. Mozhui. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. Fifty strains have matched male and female samples. Five strains have male only samples (BXD5, 13, 16, 100 and 103). Three strains have only female samples (BXD44, 70, and 87.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/INIA_AmgCoh_0311/experiment-design.rtf b/general/datasets/INIA_AmgCoh_0311/experiment-design.rtf
deleted file mode 100644
index 126d431..0000000
--- a/general/datasets/INIA_AmgCoh_0311/experiment-design.rtf
+++ /dev/null
@@ -1,1152 +0,0 @@
-Data Evaluation Summary
-
-
- - eQLTs with LOD >10 (LRS>46.1): n = 525
- - eQTL with high LOD and LRS: Trait ID 10513604 (Hdhd3) LOD = 39.8, LRS = 183.5
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6853BL |
- BLA |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6861BL |
- BLA |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6851BL |
- BLA |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6859BL |
- BLA |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6863BL |
- BLA |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6865BL |
- BLA |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6857BL |
- BLA |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6855BL |
- BLA |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6799BL |
- BLA |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6795BL |
- BLA |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6787BL |
- BLA |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6785BL |
- BLA |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6819BL |
- BLA |
- BXD12 |
- 78 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 14 |
- R6789BL |
- BLA |
- BXD12 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 15 |
- R6805BL |
- BLA |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6291BL |
- BLA |
- BXD13 |
- N/A |
- M |
- 6/11/09 |
- N/A |
-
-
- | 17 |
- R6811BL |
- BLA |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 18 |
- R6825BL |
- BLA |
- BXD14 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 19 |
- R6657BL |
- BLA |
- BXD16 |
- N/A |
- M |
- 1/8/08 |
- N/A |
-
-
- | 20 |
- R6054BL |
- BLA |
- BXD19 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 21 |
- R6052BL |
- BLA |
- BXD19 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 22 |
- R6803BL |
- BLA |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 23 |
- R6817BL |
- BLA |
- BXD24 |
- 86 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6063BL |
- BLA |
- BXD25 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 25 |
- R6062BL |
- BLA |
- BXD25 |
- N/A |
- M |
- 3/12/08 |
- N/A |
-
-
- | 26 |
- R6659BL |
- BLA |
- BXD27 |
- N/A |
- F |
- 1/8/08 |
- N/A |
-
-
- | 27 |
- R6791BL |
- BLA |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 28 |
- R6797BL |
- BLA |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 29 |
- R6793BL |
- BLA |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 30 |
- R6815BL |
- BLA |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 31 |
- R6801BL |
- BLA |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 32 |
- R6915BL |
- BLA |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 33 |
- R6845BL |
- BLA |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 34 |
- R6821BL |
- BLA |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 35 |
- R6807BL |
- BLA |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 36 |
- R6057BL |
- BLA |
- BXD38 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 37 |
- R6056BL |
- BLA |
- BXD38 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 38 |
- R6827BL |
- BLA |
- BXD39 |
- 79 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 39 |
- R6813BL |
- BLA |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 40 |
- R6847BL |
- BLA |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 41 |
- R6849BL |
- BLA |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 42 |
- R6809BL |
- BLA |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 43 |
- R6823BL |
- BLA |
- BXD42 |
- 87 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 44 |
- R6759BL |
- BLA |
- BXD43 |
- 81 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 45 |
- R6757BL |
- BLA |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 46 |
- R6745BL |
- BLA |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 47 |
- R6763BL |
- BLA |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 48 |
- R6761BL |
- BLA |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 49 |
- R6879BL |
- BLA |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6881BL |
- BLA |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6751BL |
- BLA |
- BXD49 |
- 84 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 52 |
- R6747BL |
- BLA |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 53 |
- R6104BL |
- BLA |
- BXD5 |
- N/A |
- f |
- 10/23/09 |
- N/A |
-
-
- | 54 |
- R6103BL |
- BLA |
- BXD5 |
- N/A |
- M |
- 10/23/09 |
- N/A |
-
-
- | 55 |
- R6889BL |
- BLA |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6891BL |
- BLA |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6074BL |
- BLA |
- BXD51 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 58 |
- R6699BL |
- BLA |
- BXD51 |
- N/A |
- M |
- 4/30/09 |
- N/A |
-
-
- | 59 |
- R6917BL |
- BLA |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 60 |
- R6893BL |
- BLA |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 61 |
- R6769BL |
- BLA |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 62 |
- R6771BL |
- BLA |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6655BL |
- BLA |
- BXD61 |
- N/A |
- F |
- 1/29/08 |
- N/A |
-
-
- | 64 |
- R6653BL |
- BLA |
- BXD61 |
- N/A |
- M |
- 1/29/08 |
- N/A |
-
-
- | 65 |
- R6835BL |
- BLA |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 66 |
- R6843BL |
- BLA |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6887BL |
- BLA |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6885BL |
- BLA |
- BXD63 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6877BL |
- BLA |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6873BL |
- BLA |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6929BL |
- BLA |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6931BL |
- BLA |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6775BL |
- BLA |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 74 |
- R6773BL |
- BLA |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 75 |
- R6925BL |
- BLA |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6921BL |
- BLA |
- BXD70 |
- 76 |
- M |
- 8/17/06 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6869BL |
- BLA |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6871BL |
- BLA |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 79 |
- R6777BL |
- BLA |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 80 |
- R6779BL |
- BLA |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 81 |
- R6837BL |
- BLA |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 82 |
- R6829BL |
- BLA |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 83 |
- R6933BL |
- BLA |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 84 |
- R6935BL |
- BLA |
- BXD79 |
- 87 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 85 |
- R6781BL |
- BLA |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 86 |
- R6783BL |
- BLA |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 87 |
- R6913BL |
- BLA |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 88 |
- R6911BL |
- BLA |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 89 |
- R6841BL |
- BLA |
- BXD84 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 90 |
- R6833BL |
- BLA |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 91 |
- R6937BL |
- BLA |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 92 |
- R6939BL |
- BLA |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 93 |
- R6909BL |
- BLA |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 94 |
- R6895BL |
- BLA |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 95 |
- R6897BL |
- BLA |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 96 |
- R6903BL |
- BLA |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 97 |
- R6905BL |
- BLA |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 98 |
- R6923BL |
- BLA |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 99 |
- R6927BL |
- BLA |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 100 |
- R6919BL |
- BLA |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 101 |
- R6867BL |
- BLA |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 102 |
- R6899BL |
- BLA |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 103 |
- R6901BL |
- BLA |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 104 |
- R6875BL |
- BLA |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 105 |
- R6883BL |
- BLA |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 106 |
- R6831BL |
- BLA |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 107 |
- R6943BL |
- BLA |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 108 |
- R6941BL |
- BLA |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 109 |
- R6753BL |
- BLA |
- BXD102 |
- 88 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 110 |
- R6755BL |
- BLA |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 111 |
- R6765BL |
- BLA |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/INIA_AmgCoh_0311/platform.rtf b/general/datasets/INIA_AmgCoh_0311/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_AmgCoh_0311/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_AmgCoh_0311/processing.rtf b/general/datasets/INIA_AmgCoh_0311/processing.rtf
deleted file mode 100644
index a2a6c30..0000000
--- a/general/datasets/INIA_AmgCoh_0311/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required no initial correction for batch effects and the data in this initial release do not incorporate any additional corrections. However, there are several confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Dissection variation: examine and use probe sets for Ttr as a correction for the inclusion of choroid plexus and non-parenchmymal tissue in samples. Transthyretin is only expressed in the choroid plexus (PMID 16698124
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the 54 probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases (58) in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest 54 probe sets in this amygdala data set accounts of 42% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the amygdala data set can be map as a trait. It is not associated with any QLTs that are even suggestive, and the highest LRS is about 10 on chromosomes 18 and 19. The second principal component trait, which accounts for only 5% of the "noise" variance, has a suggestive QTL (LRS of 12, high B allele) on chromosome 4 at about 90 Mb. We therefore do not think that there is significant risk of major false trans eQTL bands in this data set.
-
-
-Data Release. This data set was first uploaded into GeneNetwork November 25, 2010 and made accessible without a password to all users on December 1, 2010. The data set was orginally entered with two strain identification errors that were fixed Dec 10, 2010 by KM Mozhui and A Centeno (array R6659BL was originally listed as BXD16 but is BXD27; R6789BL was original listed as BXD27 is BXD12). The current data release has no known errors of sex or strain assignment.
-
-Data Status and Use. The data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/INIA_AmgCoh_0311/summary.rtf b/general/datasets/INIA_AmgCoh_0311/summary.rtf
deleted file mode 100644
index 41311b7..0000000
--- a/general/datasets/INIA_AmgCoh_0311/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/INIA_AmgCoh_0311/tissue.rtf b/general/datasets/INIA_AmgCoh_0311/tissue.rtf
deleted file mode 100644
index ea556c7..0000000
--- a/general/datasets/INIA_AmgCoh_0311/tissue.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Dissection Protocol
-
-
- - Animals were sacrificed by cervical dislocation and brains were immediately dissected from the head and stored in RNAlater (www.ambion.com) for 2 to 3 days at 4 deg C in a refrigerator.
- - Brains were placed with ventral side up on a cutting surface and a partial coronal cut was made with a surgical blade at a level that corresponds approximately to the -2.5 mm behind the stereotaxic Bregma point (this cut is just a little rostral from the pontine fibres when viewed from the ventral side).
- - Brains were placed in a coronal matrix (egg-style slicer) and a 2-mm thick coronal slab was taken just rostral to the initial cut.
- - The 2-mm thick slab was placed on a clean glass slide and the hypothalamus was cut out and placed in a tube on dry ice.
- - To dissect the BLA, the temporal lobes were detached by placing a scalpel in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then cut out and placed in a tube on dry ice.
- - Tissue from two mice (right and left sides) and from the same strain and sex (an usually the same litter) were pooled. The only exceptions are BLA samples from strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue was obtained from only one animal per array).
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/cases.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/cases.rtf
deleted file mode 100644
index b02b19a..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 58 strains, including 54 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1) were analyzed. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by K. Mozhui. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. Fifty strains have matched male and female samples. Five strains have male only samples (BXD5, 13, 16, 100 and 103). Three strains have only female samples (BXD44, 70, and 87.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/experiment-design.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/experiment-design.rtf
deleted file mode 100644
index 126d431..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/experiment-design.rtf
+++ /dev/null
@@ -1,1152 +0,0 @@
-Data Evaluation Summary
-
-
- - eQLTs with LOD >10 (LRS>46.1): n = 525
- - eQTL with high LOD and LRS: Trait ID 10513604 (Hdhd3) LOD = 39.8, LRS = 183.5
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6853BL |
- BLA |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6861BL |
- BLA |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6851BL |
- BLA |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6859BL |
- BLA |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6863BL |
- BLA |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6865BL |
- BLA |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6857BL |
- BLA |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6855BL |
- BLA |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6799BL |
- BLA |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6795BL |
- BLA |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6787BL |
- BLA |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6785BL |
- BLA |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6819BL |
- BLA |
- BXD12 |
- 78 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 14 |
- R6789BL |
- BLA |
- BXD12 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 15 |
- R6805BL |
- BLA |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6291BL |
- BLA |
- BXD13 |
- N/A |
- M |
- 6/11/09 |
- N/A |
-
-
- | 17 |
- R6811BL |
- BLA |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 18 |
- R6825BL |
- BLA |
- BXD14 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 19 |
- R6657BL |
- BLA |
- BXD16 |
- N/A |
- M |
- 1/8/08 |
- N/A |
-
-
- | 20 |
- R6054BL |
- BLA |
- BXD19 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 21 |
- R6052BL |
- BLA |
- BXD19 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 22 |
- R6803BL |
- BLA |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 23 |
- R6817BL |
- BLA |
- BXD24 |
- 86 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6063BL |
- BLA |
- BXD25 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 25 |
- R6062BL |
- BLA |
- BXD25 |
- N/A |
- M |
- 3/12/08 |
- N/A |
-
-
- | 26 |
- R6659BL |
- BLA |
- BXD27 |
- N/A |
- F |
- 1/8/08 |
- N/A |
-
-
- | 27 |
- R6791BL |
- BLA |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 28 |
- R6797BL |
- BLA |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 29 |
- R6793BL |
- BLA |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 30 |
- R6815BL |
- BLA |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 31 |
- R6801BL |
- BLA |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 32 |
- R6915BL |
- BLA |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 33 |
- R6845BL |
- BLA |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 34 |
- R6821BL |
- BLA |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 35 |
- R6807BL |
- BLA |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 36 |
- R6057BL |
- BLA |
- BXD38 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 37 |
- R6056BL |
- BLA |
- BXD38 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 38 |
- R6827BL |
- BLA |
- BXD39 |
- 79 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 39 |
- R6813BL |
- BLA |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 40 |
- R6847BL |
- BLA |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 41 |
- R6849BL |
- BLA |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 42 |
- R6809BL |
- BLA |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 43 |
- R6823BL |
- BLA |
- BXD42 |
- 87 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 44 |
- R6759BL |
- BLA |
- BXD43 |
- 81 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 45 |
- R6757BL |
- BLA |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 46 |
- R6745BL |
- BLA |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 47 |
- R6763BL |
- BLA |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 48 |
- R6761BL |
- BLA |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 49 |
- R6879BL |
- BLA |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6881BL |
- BLA |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6751BL |
- BLA |
- BXD49 |
- 84 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 52 |
- R6747BL |
- BLA |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 53 |
- R6104BL |
- BLA |
- BXD5 |
- N/A |
- f |
- 10/23/09 |
- N/A |
-
-
- | 54 |
- R6103BL |
- BLA |
- BXD5 |
- N/A |
- M |
- 10/23/09 |
- N/A |
-
-
- | 55 |
- R6889BL |
- BLA |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6891BL |
- BLA |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6074BL |
- BLA |
- BXD51 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 58 |
- R6699BL |
- BLA |
- BXD51 |
- N/A |
- M |
- 4/30/09 |
- N/A |
-
-
- | 59 |
- R6917BL |
- BLA |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 60 |
- R6893BL |
- BLA |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 61 |
- R6769BL |
- BLA |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 62 |
- R6771BL |
- BLA |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6655BL |
- BLA |
- BXD61 |
- N/A |
- F |
- 1/29/08 |
- N/A |
-
-
- | 64 |
- R6653BL |
- BLA |
- BXD61 |
- N/A |
- M |
- 1/29/08 |
- N/A |
-
-
- | 65 |
- R6835BL |
- BLA |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 66 |
- R6843BL |
- BLA |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6887BL |
- BLA |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6885BL |
- BLA |
- BXD63 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6877BL |
- BLA |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6873BL |
- BLA |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6929BL |
- BLA |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6931BL |
- BLA |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6775BL |
- BLA |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 74 |
- R6773BL |
- BLA |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 75 |
- R6925BL |
- BLA |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6921BL |
- BLA |
- BXD70 |
- 76 |
- M |
- 8/17/06 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6869BL |
- BLA |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6871BL |
- BLA |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 79 |
- R6777BL |
- BLA |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 80 |
- R6779BL |
- BLA |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 81 |
- R6837BL |
- BLA |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 82 |
- R6829BL |
- BLA |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 83 |
- R6933BL |
- BLA |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 84 |
- R6935BL |
- BLA |
- BXD79 |
- 87 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 85 |
- R6781BL |
- BLA |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 86 |
- R6783BL |
- BLA |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 87 |
- R6913BL |
- BLA |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 88 |
- R6911BL |
- BLA |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 89 |
- R6841BL |
- BLA |
- BXD84 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 90 |
- R6833BL |
- BLA |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 91 |
- R6937BL |
- BLA |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 92 |
- R6939BL |
- BLA |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 93 |
- R6909BL |
- BLA |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 94 |
- R6895BL |
- BLA |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 95 |
- R6897BL |
- BLA |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 96 |
- R6903BL |
- BLA |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 97 |
- R6905BL |
- BLA |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 98 |
- R6923BL |
- BLA |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 99 |
- R6927BL |
- BLA |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 100 |
- R6919BL |
- BLA |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 101 |
- R6867BL |
- BLA |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 102 |
- R6899BL |
- BLA |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 103 |
- R6901BL |
- BLA |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 104 |
- R6875BL |
- BLA |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 105 |
- R6883BL |
- BLA |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 106 |
- R6831BL |
- BLA |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 107 |
- R6943BL |
- BLA |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 108 |
- R6941BL |
- BLA |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 109 |
- R6753BL |
- BLA |
- BXD102 |
- 88 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 110 |
- R6755BL |
- BLA |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 111 |
- R6765BL |
- BLA |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/platform.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/processing.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/processing.rtf
deleted file mode 100644
index a2a6c30..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required no initial correction for batch effects and the data in this initial release do not incorporate any additional corrections. However, there are several confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Dissection variation: examine and use probe sets for Ttr as a correction for the inclusion of choroid plexus and non-parenchmymal tissue in samples. Transthyretin is only expressed in the choroid plexus (PMID 16698124
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the 54 probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases (58) in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest 54 probe sets in this amygdala data set accounts of 42% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the amygdala data set can be map as a trait. It is not associated with any QLTs that are even suggestive, and the highest LRS is about 10 on chromosomes 18 and 19. The second principal component trait, which accounts for only 5% of the "noise" variance, has a suggestive QTL (LRS of 12, high B allele) on chromosome 4 at about 90 Mb. We therefore do not think that there is significant risk of major false trans eQTL bands in this data set.
-
-
-Data Release. This data set was first uploaded into GeneNetwork November 25, 2010 and made accessible without a password to all users on December 1, 2010. The data set was orginally entered with two strain identification errors that were fixed Dec 10, 2010 by KM Mozhui and A Centeno (array R6659BL was originally listed as BXD16 but is BXD27; R6789BL was original listed as BXD27 is BXD12). The current data release has no known errors of sex or strain assignment.
-
-Data Status and Use. The data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/specifics.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/specifics.rtf
deleted file mode 100644
index 2400c03..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Exon Level
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/summary.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/summary.rtf
deleted file mode 100644
index 41311b7..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/tissue.rtf b/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/tissue.rtf
deleted file mode 100644
index ea556c7..0000000
--- a/general/datasets/INIA_Amg_BLA_Ex-RMA_1110/tissue.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Dissection Protocol
-
-
- - Animals were sacrificed by cervical dislocation and brains were immediately dissected from the head and stored in RNAlater (www.ambion.com) for 2 to 3 days at 4 deg C in a refrigerator.
- - Brains were placed with ventral side up on a cutting surface and a partial coronal cut was made with a surgical blade at a level that corresponds approximately to the -2.5 mm behind the stereotaxic Bregma point (this cut is just a little rostral from the pontine fibres when viewed from the ventral side).
- - Brains were placed in a coronal matrix (egg-style slicer) and a 2-mm thick coronal slab was taken just rostral to the initial cut.
- - The 2-mm thick slab was placed on a clean glass slide and the hypothalamus was cut out and placed in a tube on dry ice.
- - To dissect the BLA, the temporal lobes were detached by placing a scalpel in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then cut out and placed in a tube on dry ice.
- - Tissue from two mice (right and left sides) and from the same strain and sex (an usually the same litter) were pooled. The only exceptions are BLA samples from strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue was obtained from only one animal per array).
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/cases.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/cases.rtf
deleted file mode 100644
index b02b19a..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 58 strains, including 54 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1) were analyzed. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by K. Mozhui. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. Fifty strains have matched male and female samples. Five strains have male only samples (BXD5, 13, 16, 100 and 103). Three strains have only female samples (BXD44, 70, and 87.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/experiment-design.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/experiment-design.rtf
deleted file mode 100644
index 126d431..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/experiment-design.rtf
+++ /dev/null
@@ -1,1152 +0,0 @@
-Data Evaluation Summary
-
-
- - eQLTs with LOD >10 (LRS>46.1): n = 525
- - eQTL with high LOD and LRS: Trait ID 10513604 (Hdhd3) LOD = 39.8, LRS = 183.5
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6853BL |
- BLA |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6861BL |
- BLA |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6851BL |
- BLA |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6859BL |
- BLA |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6863BL |
- BLA |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6865BL |
- BLA |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6857BL |
- BLA |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6855BL |
- BLA |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6799BL |
- BLA |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6795BL |
- BLA |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6787BL |
- BLA |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6785BL |
- BLA |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6819BL |
- BLA |
- BXD12 |
- 78 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 14 |
- R6789BL |
- BLA |
- BXD12 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 15 |
- R6805BL |
- BLA |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6291BL |
- BLA |
- BXD13 |
- N/A |
- M |
- 6/11/09 |
- N/A |
-
-
- | 17 |
- R6811BL |
- BLA |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 18 |
- R6825BL |
- BLA |
- BXD14 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 19 |
- R6657BL |
- BLA |
- BXD16 |
- N/A |
- M |
- 1/8/08 |
- N/A |
-
-
- | 20 |
- R6054BL |
- BLA |
- BXD19 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 21 |
- R6052BL |
- BLA |
- BXD19 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 22 |
- R6803BL |
- BLA |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 23 |
- R6817BL |
- BLA |
- BXD24 |
- 86 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6063BL |
- BLA |
- BXD25 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 25 |
- R6062BL |
- BLA |
- BXD25 |
- N/A |
- M |
- 3/12/08 |
- N/A |
-
-
- | 26 |
- R6659BL |
- BLA |
- BXD27 |
- N/A |
- F |
- 1/8/08 |
- N/A |
-
-
- | 27 |
- R6791BL |
- BLA |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 28 |
- R6797BL |
- BLA |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 29 |
- R6793BL |
- BLA |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 30 |
- R6815BL |
- BLA |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 31 |
- R6801BL |
- BLA |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 32 |
- R6915BL |
- BLA |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 33 |
- R6845BL |
- BLA |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 34 |
- R6821BL |
- BLA |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 35 |
- R6807BL |
- BLA |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 36 |
- R6057BL |
- BLA |
- BXD38 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 37 |
- R6056BL |
- BLA |
- BXD38 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 38 |
- R6827BL |
- BLA |
- BXD39 |
- 79 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 39 |
- R6813BL |
- BLA |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 40 |
- R6847BL |
- BLA |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 41 |
- R6849BL |
- BLA |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 42 |
- R6809BL |
- BLA |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 43 |
- R6823BL |
- BLA |
- BXD42 |
- 87 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 44 |
- R6759BL |
- BLA |
- BXD43 |
- 81 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 45 |
- R6757BL |
- BLA |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 46 |
- R6745BL |
- BLA |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 47 |
- R6763BL |
- BLA |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 48 |
- R6761BL |
- BLA |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 49 |
- R6879BL |
- BLA |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6881BL |
- BLA |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6751BL |
- BLA |
- BXD49 |
- 84 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 52 |
- R6747BL |
- BLA |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 53 |
- R6104BL |
- BLA |
- BXD5 |
- N/A |
- f |
- 10/23/09 |
- N/A |
-
-
- | 54 |
- R6103BL |
- BLA |
- BXD5 |
- N/A |
- M |
- 10/23/09 |
- N/A |
-
-
- | 55 |
- R6889BL |
- BLA |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6891BL |
- BLA |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6074BL |
- BLA |
- BXD51 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 58 |
- R6699BL |
- BLA |
- BXD51 |
- N/A |
- M |
- 4/30/09 |
- N/A |
-
-
- | 59 |
- R6917BL |
- BLA |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 60 |
- R6893BL |
- BLA |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 61 |
- R6769BL |
- BLA |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 62 |
- R6771BL |
- BLA |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6655BL |
- BLA |
- BXD61 |
- N/A |
- F |
- 1/29/08 |
- N/A |
-
-
- | 64 |
- R6653BL |
- BLA |
- BXD61 |
- N/A |
- M |
- 1/29/08 |
- N/A |
-
-
- | 65 |
- R6835BL |
- BLA |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 66 |
- R6843BL |
- BLA |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6887BL |
- BLA |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6885BL |
- BLA |
- BXD63 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6877BL |
- BLA |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6873BL |
- BLA |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6929BL |
- BLA |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6931BL |
- BLA |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6775BL |
- BLA |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 74 |
- R6773BL |
- BLA |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 75 |
- R6925BL |
- BLA |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6921BL |
- BLA |
- BXD70 |
- 76 |
- M |
- 8/17/06 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6869BL |
- BLA |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6871BL |
- BLA |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 79 |
- R6777BL |
- BLA |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 80 |
- R6779BL |
- BLA |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 81 |
- R6837BL |
- BLA |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 82 |
- R6829BL |
- BLA |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 83 |
- R6933BL |
- BLA |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 84 |
- R6935BL |
- BLA |
- BXD79 |
- 87 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 85 |
- R6781BL |
- BLA |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 86 |
- R6783BL |
- BLA |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 87 |
- R6913BL |
- BLA |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 88 |
- R6911BL |
- BLA |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 89 |
- R6841BL |
- BLA |
- BXD84 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 90 |
- R6833BL |
- BLA |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 91 |
- R6937BL |
- BLA |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 92 |
- R6939BL |
- BLA |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 93 |
- R6909BL |
- BLA |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 94 |
- R6895BL |
- BLA |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 95 |
- R6897BL |
- BLA |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 96 |
- R6903BL |
- BLA |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 97 |
- R6905BL |
- BLA |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 98 |
- R6923BL |
- BLA |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 99 |
- R6927BL |
- BLA |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 100 |
- R6919BL |
- BLA |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 101 |
- R6867BL |
- BLA |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 102 |
- R6899BL |
- BLA |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 103 |
- R6901BL |
- BLA |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 104 |
- R6875BL |
- BLA |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 105 |
- R6883BL |
- BLA |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 106 |
- R6831BL |
- BLA |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 107 |
- R6943BL |
- BLA |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 108 |
- R6941BL |
- BLA |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 109 |
- R6753BL |
- BLA |
- BXD102 |
- 88 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 110 |
- R6755BL |
- BLA |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 111 |
- R6765BL |
- BLA |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/platform.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/processing.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/processing.rtf
deleted file mode 100644
index a2a6c30..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required no initial correction for batch effects and the data in this initial release do not incorporate any additional corrections. However, there are several confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Dissection variation: examine and use probe sets for Ttr as a correction for the inclusion of choroid plexus and non-parenchmymal tissue in samples. Transthyretin is only expressed in the choroid plexus (PMID 16698124
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the 54 probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases (58) in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest 54 probe sets in this amygdala data set accounts of 42% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the amygdala data set can be map as a trait. It is not associated with any QLTs that are even suggestive, and the highest LRS is about 10 on chromosomes 18 and 19. The second principal component trait, which accounts for only 5% of the "noise" variance, has a suggestive QTL (LRS of 12, high B allele) on chromosome 4 at about 90 Mb. We therefore do not think that there is significant risk of major false trans eQTL bands in this data set.
-
-
-Data Release. This data set was first uploaded into GeneNetwork November 25, 2010 and made accessible without a password to all users on December 1, 2010. The data set was orginally entered with two strain identification errors that were fixed Dec 10, 2010 by KM Mozhui and A Centeno (array R6659BL was originally listed as BXD16 but is BXD27; R6789BL was original listed as BXD27 is BXD12). The current data release has no known errors of sex or strain assignment.
-
-Data Status and Use. The data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/specifics.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/specifics.rtf
deleted file mode 100644
index d877bcf..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Gene Level
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/summary.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/summary.rtf
deleted file mode 100644
index 41311b7..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/INIA_Amg_BLA_RMA_1110/tissue.rtf b/general/datasets/INIA_Amg_BLA_RMA_1110/tissue.rtf
deleted file mode 100644
index ea556c7..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_1110/tissue.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Dissection Protocol
-
-
- - Animals were sacrificed by cervical dislocation and brains were immediately dissected from the head and stored in RNAlater (www.ambion.com) for 2 to 3 days at 4 deg C in a refrigerator.
- - Brains were placed with ventral side up on a cutting surface and a partial coronal cut was made with a surgical blade at a level that corresponds approximately to the -2.5 mm behind the stereotaxic Bregma point (this cut is just a little rostral from the pontine fibres when viewed from the ventral side).
- - Brains were placed in a coronal matrix (egg-style slicer) and a 2-mm thick coronal slab was taken just rostral to the initial cut.
- - The 2-mm thick slab was placed on a clean glass slide and the hypothalamus was cut out and placed in a tube on dry ice.
- - To dissect the BLA, the temporal lobes were detached by placing a scalpel in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then cut out and placed in a tube on dry ice.
- - Tissue from two mice (right and left sides) and from the same strain and sex (an usually the same litter) were pooled. The only exceptions are BLA samples from strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue was obtained from only one animal per array).
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_RMA_F_1110/cases.rtf b/general/datasets/INIA_Amg_BLA_RMA_F_1110/cases.rtf
deleted file mode 100644
index b02b19a..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_F_1110/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 58 strains, including 54 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1) were analyzed. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by K. Mozhui. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. Fifty strains have matched male and female samples. Five strains have male only samples (BXD5, 13, 16, 100 and 103). Three strains have only female samples (BXD44, 70, and 87.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/INIA_Amg_BLA_RMA_F_1110/experiment-design.rtf b/general/datasets/INIA_Amg_BLA_RMA_F_1110/experiment-design.rtf
deleted file mode 100644
index 126d431..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_F_1110/experiment-design.rtf
+++ /dev/null
@@ -1,1152 +0,0 @@
-Data Evaluation Summary
-
-
- - eQLTs with LOD >10 (LRS>46.1): n = 525
- - eQTL with high LOD and LRS: Trait ID 10513604 (Hdhd3) LOD = 39.8, LRS = 183.5
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6853BL |
- BLA |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6861BL |
- BLA |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6851BL |
- BLA |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6859BL |
- BLA |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6863BL |
- BLA |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6865BL |
- BLA |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6857BL |
- BLA |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6855BL |
- BLA |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6799BL |
- BLA |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6795BL |
- BLA |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6787BL |
- BLA |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6785BL |
- BLA |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6819BL |
- BLA |
- BXD12 |
- 78 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 14 |
- R6789BL |
- BLA |
- BXD12 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 15 |
- R6805BL |
- BLA |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6291BL |
- BLA |
- BXD13 |
- N/A |
- M |
- 6/11/09 |
- N/A |
-
-
- | 17 |
- R6811BL |
- BLA |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 18 |
- R6825BL |
- BLA |
- BXD14 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 19 |
- R6657BL |
- BLA |
- BXD16 |
- N/A |
- M |
- 1/8/08 |
- N/A |
-
-
- | 20 |
- R6054BL |
- BLA |
- BXD19 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 21 |
- R6052BL |
- BLA |
- BXD19 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 22 |
- R6803BL |
- BLA |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 23 |
- R6817BL |
- BLA |
- BXD24 |
- 86 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6063BL |
- BLA |
- BXD25 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 25 |
- R6062BL |
- BLA |
- BXD25 |
- N/A |
- M |
- 3/12/08 |
- N/A |
-
-
- | 26 |
- R6659BL |
- BLA |
- BXD27 |
- N/A |
- F |
- 1/8/08 |
- N/A |
-
-
- | 27 |
- R6791BL |
- BLA |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 28 |
- R6797BL |
- BLA |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 29 |
- R6793BL |
- BLA |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 30 |
- R6815BL |
- BLA |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 31 |
- R6801BL |
- BLA |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 32 |
- R6915BL |
- BLA |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 33 |
- R6845BL |
- BLA |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 34 |
- R6821BL |
- BLA |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 35 |
- R6807BL |
- BLA |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 36 |
- R6057BL |
- BLA |
- BXD38 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 37 |
- R6056BL |
- BLA |
- BXD38 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 38 |
- R6827BL |
- BLA |
- BXD39 |
- 79 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 39 |
- R6813BL |
- BLA |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 40 |
- R6847BL |
- BLA |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 41 |
- R6849BL |
- BLA |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 42 |
- R6809BL |
- BLA |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 43 |
- R6823BL |
- BLA |
- BXD42 |
- 87 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 44 |
- R6759BL |
- BLA |
- BXD43 |
- 81 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 45 |
- R6757BL |
- BLA |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 46 |
- R6745BL |
- BLA |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 47 |
- R6763BL |
- BLA |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 48 |
- R6761BL |
- BLA |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 49 |
- R6879BL |
- BLA |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6881BL |
- BLA |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6751BL |
- BLA |
- BXD49 |
- 84 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 52 |
- R6747BL |
- BLA |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 53 |
- R6104BL |
- BLA |
- BXD5 |
- N/A |
- f |
- 10/23/09 |
- N/A |
-
-
- | 54 |
- R6103BL |
- BLA |
- BXD5 |
- N/A |
- M |
- 10/23/09 |
- N/A |
-
-
- | 55 |
- R6889BL |
- BLA |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6891BL |
- BLA |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6074BL |
- BLA |
- BXD51 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 58 |
- R6699BL |
- BLA |
- BXD51 |
- N/A |
- M |
- 4/30/09 |
- N/A |
-
-
- | 59 |
- R6917BL |
- BLA |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 60 |
- R6893BL |
- BLA |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 61 |
- R6769BL |
- BLA |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 62 |
- R6771BL |
- BLA |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6655BL |
- BLA |
- BXD61 |
- N/A |
- F |
- 1/29/08 |
- N/A |
-
-
- | 64 |
- R6653BL |
- BLA |
- BXD61 |
- N/A |
- M |
- 1/29/08 |
- N/A |
-
-
- | 65 |
- R6835BL |
- BLA |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 66 |
- R6843BL |
- BLA |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6887BL |
- BLA |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6885BL |
- BLA |
- BXD63 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6877BL |
- BLA |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6873BL |
- BLA |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6929BL |
- BLA |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6931BL |
- BLA |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6775BL |
- BLA |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 74 |
- R6773BL |
- BLA |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 75 |
- R6925BL |
- BLA |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6921BL |
- BLA |
- BXD70 |
- 76 |
- M |
- 8/17/06 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6869BL |
- BLA |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6871BL |
- BLA |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 79 |
- R6777BL |
- BLA |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 80 |
- R6779BL |
- BLA |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 81 |
- R6837BL |
- BLA |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 82 |
- R6829BL |
- BLA |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 83 |
- R6933BL |
- BLA |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 84 |
- R6935BL |
- BLA |
- BXD79 |
- 87 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 85 |
- R6781BL |
- BLA |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 86 |
- R6783BL |
- BLA |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 87 |
- R6913BL |
- BLA |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 88 |
- R6911BL |
- BLA |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 89 |
- R6841BL |
- BLA |
- BXD84 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 90 |
- R6833BL |
- BLA |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 91 |
- R6937BL |
- BLA |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 92 |
- R6939BL |
- BLA |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 93 |
- R6909BL |
- BLA |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 94 |
- R6895BL |
- BLA |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 95 |
- R6897BL |
- BLA |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 96 |
- R6903BL |
- BLA |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 97 |
- R6905BL |
- BLA |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 98 |
- R6923BL |
- BLA |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 99 |
- R6927BL |
- BLA |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 100 |
- R6919BL |
- BLA |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 101 |
- R6867BL |
- BLA |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 102 |
- R6899BL |
- BLA |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 103 |
- R6901BL |
- BLA |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 104 |
- R6875BL |
- BLA |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 105 |
- R6883BL |
- BLA |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 106 |
- R6831BL |
- BLA |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 107 |
- R6943BL |
- BLA |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 108 |
- R6941BL |
- BLA |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 109 |
- R6753BL |
- BLA |
- BXD102 |
- 88 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 110 |
- R6755BL |
- BLA |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 111 |
- R6765BL |
- BLA |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_RMA_F_1110/platform.rtf b/general/datasets/INIA_Amg_BLA_RMA_F_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_F_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Amg_BLA_RMA_F_1110/processing.rtf b/general/datasets/INIA_Amg_BLA_RMA_F_1110/processing.rtf
deleted file mode 100644
index a2a6c30..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_F_1110/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required no initial correction for batch effects and the data in this initial release do not incorporate any additional corrections. However, there are several confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Dissection variation: examine and use probe sets for Ttr as a correction for the inclusion of choroid plexus and non-parenchmymal tissue in samples. Transthyretin is only expressed in the choroid plexus (PMID 16698124
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the 54 probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases (58) in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest 54 probe sets in this amygdala data set accounts of 42% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the amygdala data set can be map as a trait. It is not associated with any QLTs that are even suggestive, and the highest LRS is about 10 on chromosomes 18 and 19. The second principal component trait, which accounts for only 5% of the "noise" variance, has a suggestive QTL (LRS of 12, high B allele) on chromosome 4 at about 90 Mb. We therefore do not think that there is significant risk of major false trans eQTL bands in this data set.
-
-
-Data Release. This data set was first uploaded into GeneNetwork November 25, 2010 and made accessible without a password to all users on December 1, 2010. The data set was orginally entered with two strain identification errors that were fixed Dec 10, 2010 by KM Mozhui and A Centeno (array R6659BL was originally listed as BXD16 but is BXD27; R6789BL was original listed as BXD27 is BXD12). The current data release has no known errors of sex or strain assignment.
-
-Data Status and Use. The data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/INIA_Amg_BLA_RMA_F_1110/summary.rtf b/general/datasets/INIA_Amg_BLA_RMA_F_1110/summary.rtf
deleted file mode 100644
index 41311b7..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_F_1110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/INIA_Amg_BLA_RMA_F_1110/tissue.rtf b/general/datasets/INIA_Amg_BLA_RMA_F_1110/tissue.rtf
deleted file mode 100644
index ea556c7..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_F_1110/tissue.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Dissection Protocol
-
-
- - Animals were sacrificed by cervical dislocation and brains were immediately dissected from the head and stored in RNAlater (www.ambion.com) for 2 to 3 days at 4 deg C in a refrigerator.
- - Brains were placed with ventral side up on a cutting surface and a partial coronal cut was made with a surgical blade at a level that corresponds approximately to the -2.5 mm behind the stereotaxic Bregma point (this cut is just a little rostral from the pontine fibres when viewed from the ventral side).
- - Brains were placed in a coronal matrix (egg-style slicer) and a 2-mm thick coronal slab was taken just rostral to the initial cut.
- - The 2-mm thick slab was placed on a clean glass slide and the hypothalamus was cut out and placed in a tube on dry ice.
- - To dissect the BLA, the temporal lobes were detached by placing a scalpel in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then cut out and placed in a tube on dry ice.
- - Tissue from two mice (right and left sides) and from the same strain and sex (an usually the same litter) were pooled. The only exceptions are BLA samples from strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue was obtained from only one animal per array).
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/cases.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/cases.rtf
deleted file mode 100644
index b02b19a..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 58 strains, including 54 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1) were analyzed. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by K. Mozhui. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. Fifty strains have matched male and female samples. Five strains have male only samples (BXD5, 13, 16, 100 and 103). Three strains have only female samples (BXD44, 70, and 87.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/experiment-design.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/experiment-design.rtf
deleted file mode 100644
index 126d431..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/experiment-design.rtf
+++ /dev/null
@@ -1,1152 +0,0 @@
-Data Evaluation Summary
-
-
- - eQLTs with LOD >10 (LRS>46.1): n = 525
- - eQTL with high LOD and LRS: Trait ID 10513604 (Hdhd3) LOD = 39.8, LRS = 183.5
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6853BL |
- BLA |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6861BL |
- BLA |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6851BL |
- BLA |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6859BL |
- BLA |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6863BL |
- BLA |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6865BL |
- BLA |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6857BL |
- BLA |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6855BL |
- BLA |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6799BL |
- BLA |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6795BL |
- BLA |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6787BL |
- BLA |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6785BL |
- BLA |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6819BL |
- BLA |
- BXD12 |
- 78 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 14 |
- R6789BL |
- BLA |
- BXD12 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 15 |
- R6805BL |
- BLA |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6291BL |
- BLA |
- BXD13 |
- N/A |
- M |
- 6/11/09 |
- N/A |
-
-
- | 17 |
- R6811BL |
- BLA |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 18 |
- R6825BL |
- BLA |
- BXD14 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 19 |
- R6657BL |
- BLA |
- BXD16 |
- N/A |
- M |
- 1/8/08 |
- N/A |
-
-
- | 20 |
- R6054BL |
- BLA |
- BXD19 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 21 |
- R6052BL |
- BLA |
- BXD19 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 22 |
- R6803BL |
- BLA |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 23 |
- R6817BL |
- BLA |
- BXD24 |
- 86 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6063BL |
- BLA |
- BXD25 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 25 |
- R6062BL |
- BLA |
- BXD25 |
- N/A |
- M |
- 3/12/08 |
- N/A |
-
-
- | 26 |
- R6659BL |
- BLA |
- BXD27 |
- N/A |
- F |
- 1/8/08 |
- N/A |
-
-
- | 27 |
- R6791BL |
- BLA |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 28 |
- R6797BL |
- BLA |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 29 |
- R6793BL |
- BLA |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 30 |
- R6815BL |
- BLA |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 31 |
- R6801BL |
- BLA |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 32 |
- R6915BL |
- BLA |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 33 |
- R6845BL |
- BLA |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 34 |
- R6821BL |
- BLA |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 35 |
- R6807BL |
- BLA |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 36 |
- R6057BL |
- BLA |
- BXD38 |
- N/A |
- F |
- 2/26/08 |
- N/A |
-
-
- | 37 |
- R6056BL |
- BLA |
- BXD38 |
- N/A |
- M |
- 2/26/08 |
- N/A |
-
-
- | 38 |
- R6827BL |
- BLA |
- BXD39 |
- 79 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 39 |
- R6813BL |
- BLA |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 40 |
- R6847BL |
- BLA |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 41 |
- R6849BL |
- BLA |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 42 |
- R6809BL |
- BLA |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 43 |
- R6823BL |
- BLA |
- BXD42 |
- 87 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 44 |
- R6759BL |
- BLA |
- BXD43 |
- 81 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 45 |
- R6757BL |
- BLA |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 46 |
- R6745BL |
- BLA |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 47 |
- R6763BL |
- BLA |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 48 |
- R6761BL |
- BLA |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 49 |
- R6879BL |
- BLA |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6881BL |
- BLA |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6751BL |
- BLA |
- BXD49 |
- 84 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 52 |
- R6747BL |
- BLA |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 53 |
- R6104BL |
- BLA |
- BXD5 |
- N/A |
- f |
- 10/23/09 |
- N/A |
-
-
- | 54 |
- R6103BL |
- BLA |
- BXD5 |
- N/A |
- M |
- 10/23/09 |
- N/A |
-
-
- | 55 |
- R6889BL |
- BLA |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6891BL |
- BLA |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6074BL |
- BLA |
- BXD51 |
- N/A |
- F |
- 3/12/08 |
- N/A |
-
-
- | 58 |
- R6699BL |
- BLA |
- BXD51 |
- N/A |
- M |
- 4/30/09 |
- N/A |
-
-
- | 59 |
- R6917BL |
- BLA |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 60 |
- R6893BL |
- BLA |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 61 |
- R6769BL |
- BLA |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 62 |
- R6771BL |
- BLA |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6655BL |
- BLA |
- BXD61 |
- N/A |
- F |
- 1/29/08 |
- N/A |
-
-
- | 64 |
- R6653BL |
- BLA |
- BXD61 |
- N/A |
- M |
- 1/29/08 |
- N/A |
-
-
- | 65 |
- R6835BL |
- BLA |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 66 |
- R6843BL |
- BLA |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6887BL |
- BLA |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6885BL |
- BLA |
- BXD63 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6877BL |
- BLA |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6873BL |
- BLA |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6929BL |
- BLA |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6931BL |
- BLA |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6775BL |
- BLA |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 74 |
- R6773BL |
- BLA |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 75 |
- R6925BL |
- BLA |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6921BL |
- BLA |
- BXD70 |
- 76 |
- M |
- 8/17/06 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6869BL |
- BLA |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6871BL |
- BLA |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 79 |
- R6777BL |
- BLA |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 80 |
- R6779BL |
- BLA |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 81 |
- R6837BL |
- BLA |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 82 |
- R6829BL |
- BLA |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 83 |
- R6933BL |
- BLA |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 84 |
- R6935BL |
- BLA |
- BXD79 |
- 87 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 85 |
- R6781BL |
- BLA |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 86 |
- R6783BL |
- BLA |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 87 |
- R6913BL |
- BLA |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 88 |
- R6911BL |
- BLA |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 89 |
- R6841BL |
- BLA |
- BXD84 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 90 |
- R6833BL |
- BLA |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 91 |
- R6937BL |
- BLA |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 92 |
- R6939BL |
- BLA |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 93 |
- R6909BL |
- BLA |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 94 |
- R6895BL |
- BLA |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 95 |
- R6897BL |
- BLA |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 96 |
- R6903BL |
- BLA |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 97 |
- R6905BL |
- BLA |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 98 |
- R6923BL |
- BLA |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 99 |
- R6927BL |
- BLA |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 100 |
- R6919BL |
- BLA |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 101 |
- R6867BL |
- BLA |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 102 |
- R6899BL |
- BLA |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 103 |
- R6901BL |
- BLA |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 104 |
- R6875BL |
- BLA |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 105 |
- R6883BL |
- BLA |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 106 |
- R6831BL |
- BLA |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 107 |
- R6943BL |
- BLA |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 108 |
- R6941BL |
- BLA |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 109 |
- R6753BL |
- BLA |
- BXD102 |
- 88 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 110 |
- R6755BL |
- BLA |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 111 |
- R6765BL |
- BLA |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/platform.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/processing.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/processing.rtf
deleted file mode 100644
index a2a6c30..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/processing.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required no initial correction for batch effects and the data in this initial release do not incorporate any additional corrections. However, there are several confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Dissection variation: examine and use probe sets for Ttr as a correction for the inclusion of choroid plexus and non-parenchmymal tissue in samples. Transthyretin is only expressed in the choroid plexus (PMID 16698124
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the 54 probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases (58) in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest 54 probe sets in this amygdala data set accounts of 42% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the amygdala data set can be map as a trait. It is not associated with any QLTs that are even suggestive, and the highest LRS is about 10 on chromosomes 18 and 19. The second principal component trait, which accounts for only 5% of the "noise" variance, has a suggestive QTL (LRS of 12, high B allele) on chromosome 4 at about 90 Mb. We therefore do not think that there is significant risk of major false trans eQTL bands in this data set.
-
-
-Data Release. This data set was first uploaded into GeneNetwork November 25, 2010 and made accessible without a password to all users on December 1, 2010. The data set was orginally entered with two strain identification errors that were fixed Dec 10, 2010 by KM Mozhui and A Centeno (array R6659BL was originally listed as BXD16 but is BXD27; R6789BL was original listed as BXD27 is BXD12). The current data release has no known errors of sex or strain assignment.
-
-Data Status and Use. The data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/specifics.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/specifics.rtf
deleted file mode 100644
index 8c3a60b..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Male samples only
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/summary.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/summary.rtf
deleted file mode 100644
index 41311b7..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/INIA_Amg_BLA_RMA_M_1110/tissue.rtf b/general/datasets/INIA_Amg_BLA_RMA_M_1110/tissue.rtf
deleted file mode 100644
index ea556c7..0000000
--- a/general/datasets/INIA_Amg_BLA_RMA_M_1110/tissue.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Dissection Protocol
-
-
- - Animals were sacrificed by cervical dislocation and brains were immediately dissected from the head and stored in RNAlater (www.ambion.com) for 2 to 3 days at 4 deg C in a refrigerator.
- - Brains were placed with ventral side up on a cutting surface and a partial coronal cut was made with a surgical blade at a level that corresponds approximately to the -2.5 mm behind the stereotaxic Bregma point (this cut is just a little rostral from the pontine fibres when viewed from the ventral side).
- - Brains were placed in a coronal matrix (egg-style slicer) and a 2-mm thick coronal slab was taken just rostral to the initial cut.
- - The 2-mm thick slab was placed on a clean glass slide and the hypothalamus was cut out and placed in a tube on dry ice.
- - To dissect the BLA, the temporal lobes were detached by placing a scalpel in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then cut out and placed in a tube on dry ice.
- - Tissue from two mice (right and left sides) and from the same strain and sex (an usually the same litter) were pooled. The only exceptions are BLA samples from strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue was obtained from only one animal per array).
-
-
-
diff --git a/general/datasets/INIA_Hyp_F_RMA_1110/acknowledgment.rtf b/general/datasets/INIA_Hyp_F_RMA_1110/acknowledgment.rtf
deleted file mode 100644
index 2c3f2bd..0000000
--- a/general/datasets/INIA_Hyp_F_RMA_1110/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported by Integrative Neuroscience Initiative on Alcoholism grants U01AA13499, U01AA017590, U01AA0016662. The authors are also grateful to Arthur Centeno and Lorne Rose, and the Molecular Resource Center at UTHSC.
diff --git a/general/datasets/INIA_Hyp_F_RMA_1110/cases.rtf b/general/datasets/INIA_Hyp_F_RMA_1110/cases.rtf
deleted file mode 100644
index f19e9c8..0000000
--- a/general/datasets/INIA_Hyp_F_RMA_1110/cases.rtf
+++ /dev/null
@@ -1,916 +0,0 @@
-The BXD recombinant inbred strains are derived from crossing the C57BL/6J (B6) and DBA/2J (D2) parental strains and inbreeding for over 20 generations (Taylor et al., 1999; Peirce et al., 2004). All mice used in this study were born and housed at the University of Tennessee Health Science Center. Mice were kept at an average of 3–4 per cage in a temperature-controlled vivarium (22 deg C) and maintained at a 12 h light/dark cycle. All animal protocols were approved by the Animal Care and Use Committee. We studied a total of 50 BXD strains, but only acquired matched male–female data pairs for 39 strains (35 BXD strains, parental B6 and D2, and two reciprocal F1 hybrids, B6D2F1 and D2B6F1). The average age of mice was 78 days. We provide more detail on the experimen-tal design and precise age and time of sacriï¬ce of all cases at stored in 4 deg C for 2–3 days. To dissect the hypothalamus, the brain was placed with the ventral side facing up in a coronal "brain cutting" matrix. Using the medial mammillary body as landmark, a vertical cut was made right along the posterior boundary of the hypothala-mus. A second vertical cut was made 2 mm from the ï¬rst cut. This edge lies slightly caudal to the optic chiasm and cuts through the retrochiasmatic nucleus. The hypothalamus was then sliced out from this 2 mm thick section. Each of the 39 mouse strains is represented by male and female samples (total of 78 microarray samples). Each individual sample consisted of tissue pooled from two mice of the same strain and sex that are usually littermates. The total number of mice used was 78 females and 78 males. RNA was puriï¬ed using the RNAeasy micro kit on the QIAcube system (Qiagen)2. RNA purity and concen-tration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6854HYP |
- Hyp |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6862HYP |
- Hyp |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6852HYP |
- Hyp |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6860HYP |
- Hyp |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6864HYP |
- Hyp |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6866HYP |
- Hyp |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6858HYP |
- Hyp |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6856HYP |
- Hyp |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6800HYP |
- Hyp |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6796HYP |
- Hyp |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6788HYP |
- Hyp |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6786HYP |
- Hyp |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6806HYP |
- Hyp |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 14 |
- R6812HYP |
- Hyp |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 15 |
- R6804HYP |
- Hyp |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6792HYP |
- Hyp |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 17 |
- R6790HYP |
- Hyp |
- BXD27 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 18 |
- R6798HYP |
- Hyp |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 19 |
- R6794HYP |
- Hyp |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 20 |
- R6816HYP |
- Hyp |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 21 |
- R6802HYP |
- Hyp |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 22 |
- R6916HYP |
- Hyp |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 23 |
- R6846HYP |
- Hyp |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6822HYP |
- Hyp |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 25 |
- R6808HYP |
- Hyp |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 26 |
- R6814HYP |
- Hyp |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 27 |
- R6848HYP |
- Hyp |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 28 |
- R6850HYP |
- Hyp |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 29 |
- R6810HYP |
- Hyp |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 30 |
- R6758HYP |
- Hyp |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 31 |
- R6746HYP |
- Hyp |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 32 |
- R6750HYP |
- Hyp |
- BXD44 |
- 83 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 33 |
- R6764HYP |
- Hyp |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 34 |
- R6762HYP |
- Hyp |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 35 |
- R6880HYP |
- Hyp |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 36 |
- R6882HYP |
- Hyp |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 37 |
- R6748HYP |
- Hyp |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 38 |
- R6890HYP |
- Hyp |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 39 |
- R6892HYP |
- Hyp |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 40 |
- R6918HYP |
- Hyp |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 41 |
- R6894HYP |
- Hyp |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 42 |
- R6770HYP |
- Hyp |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 43 |
- R6772HYP |
- Hyp |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 44 |
- R6836HYP |
- Hyp |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 45 |
- R6844HYP |
- Hyp |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 46 |
- R6888HYP |
- Hyp |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 47 |
- R6878HYP |
- Hyp |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 48 |
- R6874HYP |
- Hyp |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 49 |
- R6930HYP |
- Hyp |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6932HYP |
- Hyp |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6776HYP |
- Hyp |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 52 |
- R6774HYP |
- Hyp |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 53 |
- R6926HYP |
- Hyp |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 54 |
- R6922HYP |
- Hyp |
- BXD70 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 55 |
- R6870HYP |
- Hyp |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6872HYP |
- Hyp |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6778HYP |
- Hyp |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 58 |
- R6780HYP |
- Hyp |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 59 |
- R6838HYP |
- Hyp |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 60 |
- R6830HYP |
- Hyp |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 61 |
- R6934HYP |
- Hyp |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 62 |
- R6782HYP |
- Hyp |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6784HYP |
- Hyp |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 64 |
- R6914HYP |
- Hyp |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 65 |
- R6912HYP |
- Hyp |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 66 |
- R6834HYP |
- Hyp |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6938HYP |
- Hyp |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6940HYP |
- Hyp |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6910HYP |
- Hyp |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6908HYP |
- Hyp |
- BXD87 |
- 83 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6896HYP |
- Hyp |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6898HYP |
- Hyp |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6904HYP |
- Hyp |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 74 |
- R6906HYP |
- Hyp |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 75 |
- R6924HYP |
- Hyp |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6928HYP |
- Hyp |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6920HYP |
- Hyp |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6868HYP |
- Hyp |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 79 |
- R6900HYP |
- Hyp |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 80 |
- R6902HYP |
- Hyp |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 81 |
- R6876HYP |
- Hyp |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 82 |
- R6884HYP |
- Hyp |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 83 |
- R6840HYP |
- Hyp |
- BXD100 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 84 |
- R6832HYP |
- Hyp |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 85 |
- R6944HYP |
- Hyp |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 86 |
- R6942HYP |
- Hyp |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 87 |
- R6756HYP |
- Hyp |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 88 |
- R6768HYP |
- Hyp |
- BXD103 |
- 78 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 89 |
- R6766HYP |
- Hyp |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/INIA_Hyp_F_RMA_1110/experiment-design.rtf b/general/datasets/INIA_Hyp_F_RMA_1110/experiment-design.rtf
deleted file mode 100644
index 443af4a..0000000
--- a/general/datasets/INIA_Hyp_F_RMA_1110/experiment-design.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Hypothalamus was dissected from adult male and female mice and process for expression analysis.
-
-RNA isolation
-Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-This preliminary data set is associated with 430 eQTLs with LOD scores above 10. Peak LRS is 146 for Trait ID 10513604 (Hdhd3).
diff --git a/general/datasets/INIA_Hyp_F_RMA_1110/platform.rtf b/general/datasets/INIA_Hyp_F_RMA_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Hyp_F_RMA_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Hyp_F_RMA_1110/processing.rtf b/general/datasets/INIA_Hyp_F_RMA_1110/processing.rtf
deleted file mode 100644
index b3e8689..0000000
--- a/general/datasets/INIA_Hyp_F_RMA_1110/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Total RNA was processed using standard protocols and hybridized to the Affymetrix Mouse Gene 1.0 ST arrays4. This array contains 34,700 probe sets that target ∼29,000 well-deï¬ned transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive cov-erage of transcripts from a single gene. Male and female samples were interleaved and processed together to avoid batch confounds. Details on the strain, age, and sex of each sample can be obtained from the information available for the INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) data set on www.genenetwork.org. Probe set level intensity values were extracted from the CEL ï¬les using the Affymetrix GeneChip Operating Software. Data nor-malization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units. The entire data set can be down-loaded from www.genenetwork.org using the accession number GN281 (http://www.genenetwork.org/webqtl/main.py?FormID = sharinginfo&GN_AccessionId = 281) and also from the NIH Gene Expression Omnibus5 using the GEO accession number GSE36674. For this study we used a subset of cases that were repre-sented by both male and female samples – 78 sex-balanced arrays. Statistical power provided by this sample size (N = 39 strains) was estimated using the R function power.t.test6 with the SD set at 0.17, which is the average value. Only transcripts with above aver-age expression (minimum expression value above 8.5 on a log2 scale) were included for further analysis (17,192 probe sets). We used a two-tailed paired t -test to identify transcripts with signiï¬-cant expression difference between males and females. We applied the Benjamini and Hochberg false discovery rate (FDR) method and selected differentially expressed transcripts using a 10% FDR criterion.
diff --git a/general/datasets/INIA_Hyp_F_RMA_1110/summary.rtf b/general/datasets/INIA_Hyp_F_RMA_1110/summary.rtf
deleted file mode 100644
index 02671d5..0000000
--- a/general/datasets/INIA_Hyp_F_RMA_1110/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.
-
-Data released initially Nov 25, 2010, updated March 7, 2011 by A. Centeno and K. Mozhui to add two additional arrays. Data appear to be error-free in terms of sex and strain assignments shown in the table below.
-
-Dissection protocol:
-
-
- - Animals were sacrificed by quick cervical dislocation and brains were removed and stored in RNAlater (www.ambion.com) for 2 to 3 days
- - Brain was placed with ventral side up and a partial cut was made with a blade at -2.5 from Bregma (just a little rostral from the pontine fibres when viewed from the ventral side)
- - The brain was then place in a coronal matrix and a 2 mm section was made rostral to the first cut
- - The 2mm Section was placed on a clean glass slide and hypothalamus was sliced out and placed in a tube on dry ice.
- - To dissect out the BLA, the temporal lobes were detached by placing a scalple in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then sliced out and placed in a tube on dry ice.
- - Tissues from two mice of the same strain and sex were pooled. The only exceptions to this are the BLA samples for strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue from only one animal).
-
-
-The hypothalamus contains nuclei and cell populations that are critical in reproduction and that differ signiï¬cantly between the sexes in structure and function. To examine the molecular and genetic basis for these differences, we quantiï¬ed gene expression in the hypothalamus of 39 pairs of adult male and female mice belonging to the BXD strains. This experimental design enabled us to deï¬ne hypothalamic gene coexpression networks and provided robust estimates of absolute expression differences. As expected, sex has the strongest effect on the expression of genes on the X and Y chromosomes (e.g., Uty, Xist, Kdm6a).Transcripts associated with the endocrine system and neuropeptide signaling also differ signiï¬cantly. Sex-differentiated transcripts often have well delimited expression within speciï¬c hypothalamic nuclei that have roles in reproduction. For instance, the estro-gen receptor (Esr1) and neurokinin B (Tac2) genes have intense expression in the medial preoptic and arcuate nuclei and comparatively high expression in females. Despite the strong effect of sex on single transcripts, the global pattern of covariance among transcripts is well preserved, and consequently, males and females have well matched coexpression modules. However, there are sex-speciï¬c hub genes in functionally equivalent modules. For example, only in males is the Y-linked gene, Uty, a highly connected transcript in a network that regulates chromatin modiï¬cation and gene transcription. In females, the X chromo-some paralog, Kdm6a, takes the place of Uty in the same network. We also ï¬nd signiï¬cant effect of sex on genetic regulation and the same network in males and females can be associated with markedly different regulatory loci. With the exception of a few sex-speciï¬c modules, our analysis reveals a system in which sets of functionally related transcripts are organized into stable sex-independent networks that are controlled at a higher level by sex-speciï¬c modulators.
diff --git a/general/datasets/INIA_Hyp_M_RMA_1110/acknowledgment.rtf b/general/datasets/INIA_Hyp_M_RMA_1110/acknowledgment.rtf
deleted file mode 100644
index 2c3f2bd..0000000
--- a/general/datasets/INIA_Hyp_M_RMA_1110/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported by Integrative Neuroscience Initiative on Alcoholism grants U01AA13499, U01AA017590, U01AA0016662. The authors are also grateful to Arthur Centeno and Lorne Rose, and the Molecular Resource Center at UTHSC.
diff --git a/general/datasets/INIA_Hyp_M_RMA_1110/cases.rtf b/general/datasets/INIA_Hyp_M_RMA_1110/cases.rtf
deleted file mode 100644
index f19e9c8..0000000
--- a/general/datasets/INIA_Hyp_M_RMA_1110/cases.rtf
+++ /dev/null
@@ -1,916 +0,0 @@
-The BXD recombinant inbred strains are derived from crossing the C57BL/6J (B6) and DBA/2J (D2) parental strains and inbreeding for over 20 generations (Taylor et al., 1999; Peirce et al., 2004). All mice used in this study were born and housed at the University of Tennessee Health Science Center. Mice were kept at an average of 3–4 per cage in a temperature-controlled vivarium (22 deg C) and maintained at a 12 h light/dark cycle. All animal protocols were approved by the Animal Care and Use Committee. We studied a total of 50 BXD strains, but only acquired matched male–female data pairs for 39 strains (35 BXD strains, parental B6 and D2, and two reciprocal F1 hybrids, B6D2F1 and D2B6F1). The average age of mice was 78 days. We provide more detail on the experimen-tal design and precise age and time of sacriï¬ce of all cases at stored in 4 deg C for 2–3 days. To dissect the hypothalamus, the brain was placed with the ventral side facing up in a coronal "brain cutting" matrix. Using the medial mammillary body as landmark, a vertical cut was made right along the posterior boundary of the hypothala-mus. A second vertical cut was made 2 mm from the ï¬rst cut. This edge lies slightly caudal to the optic chiasm and cuts through the retrochiasmatic nucleus. The hypothalamus was then sliced out from this 2 mm thick section. Each of the 39 mouse strains is represented by male and female samples (total of 78 microarray samples). Each individual sample consisted of tissue pooled from two mice of the same strain and sex that are usually littermates. The total number of mice used was 78 females and 78 males. RNA was puriï¬ed using the RNAeasy micro kit on the QIAcube system (Qiagen)2. RNA purity and concen-tration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6854HYP |
- Hyp |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6862HYP |
- Hyp |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6852HYP |
- Hyp |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6860HYP |
- Hyp |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6864HYP |
- Hyp |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6866HYP |
- Hyp |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6858HYP |
- Hyp |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6856HYP |
- Hyp |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6800HYP |
- Hyp |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6796HYP |
- Hyp |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6788HYP |
- Hyp |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6786HYP |
- Hyp |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6806HYP |
- Hyp |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 14 |
- R6812HYP |
- Hyp |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 15 |
- R6804HYP |
- Hyp |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6792HYP |
- Hyp |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 17 |
- R6790HYP |
- Hyp |
- BXD27 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 18 |
- R6798HYP |
- Hyp |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 19 |
- R6794HYP |
- Hyp |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 20 |
- R6816HYP |
- Hyp |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 21 |
- R6802HYP |
- Hyp |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 22 |
- R6916HYP |
- Hyp |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 23 |
- R6846HYP |
- Hyp |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6822HYP |
- Hyp |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 25 |
- R6808HYP |
- Hyp |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 26 |
- R6814HYP |
- Hyp |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 27 |
- R6848HYP |
- Hyp |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 28 |
- R6850HYP |
- Hyp |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 29 |
- R6810HYP |
- Hyp |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 30 |
- R6758HYP |
- Hyp |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 31 |
- R6746HYP |
- Hyp |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 32 |
- R6750HYP |
- Hyp |
- BXD44 |
- 83 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 33 |
- R6764HYP |
- Hyp |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 34 |
- R6762HYP |
- Hyp |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 35 |
- R6880HYP |
- Hyp |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 36 |
- R6882HYP |
- Hyp |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 37 |
- R6748HYP |
- Hyp |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 38 |
- R6890HYP |
- Hyp |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 39 |
- R6892HYP |
- Hyp |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 40 |
- R6918HYP |
- Hyp |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 41 |
- R6894HYP |
- Hyp |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 42 |
- R6770HYP |
- Hyp |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 43 |
- R6772HYP |
- Hyp |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 44 |
- R6836HYP |
- Hyp |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 45 |
- R6844HYP |
- Hyp |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 46 |
- R6888HYP |
- Hyp |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 47 |
- R6878HYP |
- Hyp |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 48 |
- R6874HYP |
- Hyp |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 49 |
- R6930HYP |
- Hyp |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6932HYP |
- Hyp |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6776HYP |
- Hyp |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 52 |
- R6774HYP |
- Hyp |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 53 |
- R6926HYP |
- Hyp |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 54 |
- R6922HYP |
- Hyp |
- BXD70 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 55 |
- R6870HYP |
- Hyp |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6872HYP |
- Hyp |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6778HYP |
- Hyp |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 58 |
- R6780HYP |
- Hyp |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 59 |
- R6838HYP |
- Hyp |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 60 |
- R6830HYP |
- Hyp |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 61 |
- R6934HYP |
- Hyp |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 62 |
- R6782HYP |
- Hyp |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6784HYP |
- Hyp |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 64 |
- R6914HYP |
- Hyp |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 65 |
- R6912HYP |
- Hyp |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 66 |
- R6834HYP |
- Hyp |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6938HYP |
- Hyp |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6940HYP |
- Hyp |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6910HYP |
- Hyp |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6908HYP |
- Hyp |
- BXD87 |
- 83 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6896HYP |
- Hyp |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6898HYP |
- Hyp |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6904HYP |
- Hyp |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 74 |
- R6906HYP |
- Hyp |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 75 |
- R6924HYP |
- Hyp |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6928HYP |
- Hyp |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6920HYP |
- Hyp |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6868HYP |
- Hyp |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 79 |
- R6900HYP |
- Hyp |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 80 |
- R6902HYP |
- Hyp |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 81 |
- R6876HYP |
- Hyp |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 82 |
- R6884HYP |
- Hyp |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 83 |
- R6840HYP |
- Hyp |
- BXD100 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 84 |
- R6832HYP |
- Hyp |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 85 |
- R6944HYP |
- Hyp |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 86 |
- R6942HYP |
- Hyp |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 87 |
- R6756HYP |
- Hyp |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 88 |
- R6768HYP |
- Hyp |
- BXD103 |
- 78 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 89 |
- R6766HYP |
- Hyp |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/INIA_Hyp_M_RMA_1110/experiment-design.rtf b/general/datasets/INIA_Hyp_M_RMA_1110/experiment-design.rtf
deleted file mode 100644
index 443af4a..0000000
--- a/general/datasets/INIA_Hyp_M_RMA_1110/experiment-design.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Hypothalamus was dissected from adult male and female mice and process for expression analysis.
-
-RNA isolation
-Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-This preliminary data set is associated with 430 eQTLs with LOD scores above 10. Peak LRS is 146 for Trait ID 10513604 (Hdhd3).
diff --git a/general/datasets/INIA_Hyp_M_RMA_1110/platform.rtf b/general/datasets/INIA_Hyp_M_RMA_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Hyp_M_RMA_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Hyp_M_RMA_1110/processing.rtf b/general/datasets/INIA_Hyp_M_RMA_1110/processing.rtf
deleted file mode 100644
index b3e8689..0000000
--- a/general/datasets/INIA_Hyp_M_RMA_1110/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Total RNA was processed using standard protocols and hybridized to the Affymetrix Mouse Gene 1.0 ST arrays4. This array contains 34,700 probe sets that target ∼29,000 well-deï¬ned transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive cov-erage of transcripts from a single gene. Male and female samples were interleaved and processed together to avoid batch confounds. Details on the strain, age, and sex of each sample can be obtained from the information available for the INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) data set on www.genenetwork.org. Probe set level intensity values were extracted from the CEL ï¬les using the Affymetrix GeneChip Operating Software. Data nor-malization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units. The entire data set can be down-loaded from www.genenetwork.org using the accession number GN281 (http://www.genenetwork.org/webqtl/main.py?FormID = sharinginfo&GN_AccessionId = 281) and also from the NIH Gene Expression Omnibus5 using the GEO accession number GSE36674. For this study we used a subset of cases that were repre-sented by both male and female samples – 78 sex-balanced arrays. Statistical power provided by this sample size (N = 39 strains) was estimated using the R function power.t.test6 with the SD set at 0.17, which is the average value. Only transcripts with above aver-age expression (minimum expression value above 8.5 on a log2 scale) were included for further analysis (17,192 probe sets). We used a two-tailed paired t -test to identify transcripts with signiï¬-cant expression difference between males and females. We applied the Benjamini and Hochberg false discovery rate (FDR) method and selected differentially expressed transcripts using a 10% FDR criterion.
diff --git a/general/datasets/INIA_Hyp_M_RMA_1110/summary.rtf b/general/datasets/INIA_Hyp_M_RMA_1110/summary.rtf
deleted file mode 100644
index 02671d5..0000000
--- a/general/datasets/INIA_Hyp_M_RMA_1110/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.
-
-Data released initially Nov 25, 2010, updated March 7, 2011 by A. Centeno and K. Mozhui to add two additional arrays. Data appear to be error-free in terms of sex and strain assignments shown in the table below.
-
-Dissection protocol:
-
-
- - Animals were sacrificed by quick cervical dislocation and brains were removed and stored in RNAlater (www.ambion.com) for 2 to 3 days
- - Brain was placed with ventral side up and a partial cut was made with a blade at -2.5 from Bregma (just a little rostral from the pontine fibres when viewed from the ventral side)
- - The brain was then place in a coronal matrix and a 2 mm section was made rostral to the first cut
- - The 2mm Section was placed on a clean glass slide and hypothalamus was sliced out and placed in a tube on dry ice.
- - To dissect out the BLA, the temporal lobes were detached by placing a scalple in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then sliced out and placed in a tube on dry ice.
- - Tissues from two mice of the same strain and sex were pooled. The only exceptions to this are the BLA samples for strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue from only one animal).
-
-
-The hypothalamus contains nuclei and cell populations that are critical in reproduction and that differ signiï¬cantly between the sexes in structure and function. To examine the molecular and genetic basis for these differences, we quantiï¬ed gene expression in the hypothalamus of 39 pairs of adult male and female mice belonging to the BXD strains. This experimental design enabled us to deï¬ne hypothalamic gene coexpression networks and provided robust estimates of absolute expression differences. As expected, sex has the strongest effect on the expression of genes on the X and Y chromosomes (e.g., Uty, Xist, Kdm6a).Transcripts associated with the endocrine system and neuropeptide signaling also differ signiï¬cantly. Sex-differentiated transcripts often have well delimited expression within speciï¬c hypothalamic nuclei that have roles in reproduction. For instance, the estro-gen receptor (Esr1) and neurokinin B (Tac2) genes have intense expression in the medial preoptic and arcuate nuclei and comparatively high expression in females. Despite the strong effect of sex on single transcripts, the global pattern of covariance among transcripts is well preserved, and consequently, males and females have well matched coexpression modules. However, there are sex-speciï¬c hub genes in functionally equivalent modules. For example, only in males is the Y-linked gene, Uty, a highly connected transcript in a network that regulates chromatin modiï¬cation and gene transcription. In females, the X chromo-some paralog, Kdm6a, takes the place of Uty in the same network. We also ï¬nd signiï¬cant effect of sex on genetic regulation and the same network in males and females can be associated with markedly different regulatory loci. With the exception of a few sex-speciï¬c modules, our analysis reveals a system in which sets of functionally related transcripts are organized into stable sex-independent networks that are controlled at a higher level by sex-speciï¬c modulators.
diff --git a/general/datasets/INIA_Hyp_PCA_0813_v4/acknowledgment.rtf b/general/datasets/INIA_Hyp_PCA_0813_v4/acknowledgment.rtf
deleted file mode 100644
index 2c3f2bd..0000000
--- a/general/datasets/INIA_Hyp_PCA_0813_v4/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported by Integrative Neuroscience Initiative on Alcoholism grants U01AA13499, U01AA017590, U01AA0016662. The authors are also grateful to Arthur Centeno and Lorne Rose, and the Molecular Resource Center at UTHSC.
diff --git a/general/datasets/INIA_Hyp_PCA_0813_v4/cases.rtf b/general/datasets/INIA_Hyp_PCA_0813_v4/cases.rtf
deleted file mode 100644
index f19e9c8..0000000
--- a/general/datasets/INIA_Hyp_PCA_0813_v4/cases.rtf
+++ /dev/null
@@ -1,916 +0,0 @@
-The BXD recombinant inbred strains are derived from crossing the C57BL/6J (B6) and DBA/2J (D2) parental strains and inbreeding for over 20 generations (Taylor et al., 1999; Peirce et al., 2004). All mice used in this study were born and housed at the University of Tennessee Health Science Center. Mice were kept at an average of 3–4 per cage in a temperature-controlled vivarium (22 deg C) and maintained at a 12 h light/dark cycle. All animal protocols were approved by the Animal Care and Use Committee. We studied a total of 50 BXD strains, but only acquired matched male–female data pairs for 39 strains (35 BXD strains, parental B6 and D2, and two reciprocal F1 hybrids, B6D2F1 and D2B6F1). The average age of mice was 78 days. We provide more detail on the experimen-tal design and precise age and time of sacriï¬ce of all cases at stored in 4 deg C for 2–3 days. To dissect the hypothalamus, the brain was placed with the ventral side facing up in a coronal "brain cutting" matrix. Using the medial mammillary body as landmark, a vertical cut was made right along the posterior boundary of the hypothala-mus. A second vertical cut was made 2 mm from the ï¬rst cut. This edge lies slightly caudal to the optic chiasm and cuts through the retrochiasmatic nucleus. The hypothalamus was then sliced out from this 2 mm thick section. Each of the 39 mouse strains is represented by male and female samples (total of 78 microarray samples). Each individual sample consisted of tissue pooled from two mice of the same strain and sex that are usually littermates. The total number of mice used was 78 females and 78 males. RNA was puriï¬ed using the RNAeasy micro kit on the QIAcube system (Qiagen)2. RNA purity and concen-tration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6854HYP |
- Hyp |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6862HYP |
- Hyp |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6852HYP |
- Hyp |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6860HYP |
- Hyp |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6864HYP |
- Hyp |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6866HYP |
- Hyp |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6858HYP |
- Hyp |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6856HYP |
- Hyp |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6800HYP |
- Hyp |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6796HYP |
- Hyp |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6788HYP |
- Hyp |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6786HYP |
- Hyp |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6806HYP |
- Hyp |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 14 |
- R6812HYP |
- Hyp |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 15 |
- R6804HYP |
- Hyp |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6792HYP |
- Hyp |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 17 |
- R6790HYP |
- Hyp |
- BXD27 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 18 |
- R6798HYP |
- Hyp |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 19 |
- R6794HYP |
- Hyp |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 20 |
- R6816HYP |
- Hyp |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 21 |
- R6802HYP |
- Hyp |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 22 |
- R6916HYP |
- Hyp |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 23 |
- R6846HYP |
- Hyp |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6822HYP |
- Hyp |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 25 |
- R6808HYP |
- Hyp |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 26 |
- R6814HYP |
- Hyp |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 27 |
- R6848HYP |
- Hyp |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 28 |
- R6850HYP |
- Hyp |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 29 |
- R6810HYP |
- Hyp |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 30 |
- R6758HYP |
- Hyp |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 31 |
- R6746HYP |
- Hyp |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 32 |
- R6750HYP |
- Hyp |
- BXD44 |
- 83 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 33 |
- R6764HYP |
- Hyp |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 34 |
- R6762HYP |
- Hyp |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 35 |
- R6880HYP |
- Hyp |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 36 |
- R6882HYP |
- Hyp |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 37 |
- R6748HYP |
- Hyp |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 38 |
- R6890HYP |
- Hyp |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 39 |
- R6892HYP |
- Hyp |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 40 |
- R6918HYP |
- Hyp |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 41 |
- R6894HYP |
- Hyp |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 42 |
- R6770HYP |
- Hyp |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 43 |
- R6772HYP |
- Hyp |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 44 |
- R6836HYP |
- Hyp |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 45 |
- R6844HYP |
- Hyp |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 46 |
- R6888HYP |
- Hyp |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 47 |
- R6878HYP |
- Hyp |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 48 |
- R6874HYP |
- Hyp |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 49 |
- R6930HYP |
- Hyp |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6932HYP |
- Hyp |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6776HYP |
- Hyp |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 52 |
- R6774HYP |
- Hyp |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 53 |
- R6926HYP |
- Hyp |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 54 |
- R6922HYP |
- Hyp |
- BXD70 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 55 |
- R6870HYP |
- Hyp |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6872HYP |
- Hyp |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6778HYP |
- Hyp |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 58 |
- R6780HYP |
- Hyp |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 59 |
- R6838HYP |
- Hyp |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 60 |
- R6830HYP |
- Hyp |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 61 |
- R6934HYP |
- Hyp |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 62 |
- R6782HYP |
- Hyp |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6784HYP |
- Hyp |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 64 |
- R6914HYP |
- Hyp |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 65 |
- R6912HYP |
- Hyp |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 66 |
- R6834HYP |
- Hyp |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6938HYP |
- Hyp |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6940HYP |
- Hyp |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6910HYP |
- Hyp |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6908HYP |
- Hyp |
- BXD87 |
- 83 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6896HYP |
- Hyp |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6898HYP |
- Hyp |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6904HYP |
- Hyp |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 74 |
- R6906HYP |
- Hyp |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 75 |
- R6924HYP |
- Hyp |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6928HYP |
- Hyp |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6920HYP |
- Hyp |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6868HYP |
- Hyp |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 79 |
- R6900HYP |
- Hyp |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 80 |
- R6902HYP |
- Hyp |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 81 |
- R6876HYP |
- Hyp |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 82 |
- R6884HYP |
- Hyp |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 83 |
- R6840HYP |
- Hyp |
- BXD100 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 84 |
- R6832HYP |
- Hyp |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 85 |
- R6944HYP |
- Hyp |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 86 |
- R6942HYP |
- Hyp |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 87 |
- R6756HYP |
- Hyp |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 88 |
- R6768HYP |
- Hyp |
- BXD103 |
- 78 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 89 |
- R6766HYP |
- Hyp |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/INIA_Hyp_PCA_0813_v4/experiment-design.rtf b/general/datasets/INIA_Hyp_PCA_0813_v4/experiment-design.rtf
deleted file mode 100644
index 443af4a..0000000
--- a/general/datasets/INIA_Hyp_PCA_0813_v4/experiment-design.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Hypothalamus was dissected from adult male and female mice and process for expression analysis.
-
-RNA isolation
-Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-This preliminary data set is associated with 430 eQTLs with LOD scores above 10. Peak LRS is 146 for Trait ID 10513604 (Hdhd3).
diff --git a/general/datasets/INIA_Hyp_PCA_0813_v4/platform.rtf b/general/datasets/INIA_Hyp_PCA_0813_v4/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Hyp_PCA_0813_v4/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Hyp_PCA_0813_v4/processing.rtf b/general/datasets/INIA_Hyp_PCA_0813_v4/processing.rtf
deleted file mode 100644
index b3e8689..0000000
--- a/general/datasets/INIA_Hyp_PCA_0813_v4/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Total RNA was processed using standard protocols and hybridized to the Affymetrix Mouse Gene 1.0 ST arrays4. This array contains 34,700 probe sets that target ∼29,000 well-deï¬ned transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive cov-erage of transcripts from a single gene. Male and female samples were interleaved and processed together to avoid batch confounds. Details on the strain, age, and sex of each sample can be obtained from the information available for the INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) data set on www.genenetwork.org. Probe set level intensity values were extracted from the CEL ï¬les using the Affymetrix GeneChip Operating Software. Data nor-malization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units. The entire data set can be down-loaded from www.genenetwork.org using the accession number GN281 (http://www.genenetwork.org/webqtl/main.py?FormID = sharinginfo&GN_AccessionId = 281) and also from the NIH Gene Expression Omnibus5 using the GEO accession number GSE36674. For this study we used a subset of cases that were repre-sented by both male and female samples – 78 sex-balanced arrays. Statistical power provided by this sample size (N = 39 strains) was estimated using the R function power.t.test6 with the SD set at 0.17, which is the average value. Only transcripts with above aver-age expression (minimum expression value above 8.5 on a log2 scale) were included for further analysis (17,192 probe sets). We used a two-tailed paired t -test to identify transcripts with signiï¬-cant expression difference between males and females. We applied the Benjamini and Hochberg false discovery rate (FDR) method and selected differentially expressed transcripts using a 10% FDR criterion.
diff --git a/general/datasets/INIA_Hyp_PCA_0813_v4/summary.rtf b/general/datasets/INIA_Hyp_PCA_0813_v4/summary.rtf
deleted file mode 100644
index 02671d5..0000000
--- a/general/datasets/INIA_Hyp_PCA_0813_v4/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.
-
-Data released initially Nov 25, 2010, updated March 7, 2011 by A. Centeno and K. Mozhui to add two additional arrays. Data appear to be error-free in terms of sex and strain assignments shown in the table below.
-
-Dissection protocol:
-
-
- - Animals were sacrificed by quick cervical dislocation and brains were removed and stored in RNAlater (www.ambion.com) for 2 to 3 days
- - Brain was placed with ventral side up and a partial cut was made with a blade at -2.5 from Bregma (just a little rostral from the pontine fibres when viewed from the ventral side)
- - The brain was then place in a coronal matrix and a 2 mm section was made rostral to the first cut
- - The 2mm Section was placed on a clean glass slide and hypothalamus was sliced out and placed in a tube on dry ice.
- - To dissect out the BLA, the temporal lobes were detached by placing a scalple in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then sliced out and placed in a tube on dry ice.
- - Tissues from two mice of the same strain and sex were pooled. The only exceptions to this are the BLA samples for strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue from only one animal).
-
-
-The hypothalamus contains nuclei and cell populations that are critical in reproduction and that differ signiï¬cantly between the sexes in structure and function. To examine the molecular and genetic basis for these differences, we quantiï¬ed gene expression in the hypothalamus of 39 pairs of adult male and female mice belonging to the BXD strains. This experimental design enabled us to deï¬ne hypothalamic gene coexpression networks and provided robust estimates of absolute expression differences. As expected, sex has the strongest effect on the expression of genes on the X and Y chromosomes (e.g., Uty, Xist, Kdm6a).Transcripts associated with the endocrine system and neuropeptide signaling also differ signiï¬cantly. Sex-differentiated transcripts often have well delimited expression within speciï¬c hypothalamic nuclei that have roles in reproduction. For instance, the estro-gen receptor (Esr1) and neurokinin B (Tac2) genes have intense expression in the medial preoptic and arcuate nuclei and comparatively high expression in females. Despite the strong effect of sex on single transcripts, the global pattern of covariance among transcripts is well preserved, and consequently, males and females have well matched coexpression modules. However, there are sex-speciï¬c hub genes in functionally equivalent modules. For example, only in males is the Y-linked gene, Uty, a highly connected transcript in a network that regulates chromatin modiï¬cation and gene transcription. In females, the X chromo-some paralog, Kdm6a, takes the place of Uty in the same network. We also ï¬nd signiï¬cant effect of sex on genetic regulation and the same network in males and females can be associated with markedly different regulatory loci. With the exception of a few sex-speciï¬c modules, our analysis reveals a system in which sets of functionally related transcripts are organized into stable sex-independent networks that are controlled at a higher level by sex-speciï¬c modulators.
diff --git a/general/datasets/INIA_Hyp_RMA_1110/acknowledgment.rtf b/general/datasets/INIA_Hyp_RMA_1110/acknowledgment.rtf
deleted file mode 100644
index 2c3f2bd..0000000
--- a/general/datasets/INIA_Hyp_RMA_1110/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported by Integrative Neuroscience Initiative on Alcoholism grants U01AA13499, U01AA017590, U01AA0016662. The authors are also grateful to Arthur Centeno and Lorne Rose, and the Molecular Resource Center at UTHSC.
diff --git a/general/datasets/INIA_Hyp_RMA_1110/cases.rtf b/general/datasets/INIA_Hyp_RMA_1110/cases.rtf
deleted file mode 100644
index f19e9c8..0000000
--- a/general/datasets/INIA_Hyp_RMA_1110/cases.rtf
+++ /dev/null
@@ -1,916 +0,0 @@
-The BXD recombinant inbred strains are derived from crossing the C57BL/6J (B6) and DBA/2J (D2) parental strains and inbreeding for over 20 generations (Taylor et al., 1999; Peirce et al., 2004). All mice used in this study were born and housed at the University of Tennessee Health Science Center. Mice were kept at an average of 3–4 per cage in a temperature-controlled vivarium (22 deg C) and maintained at a 12 h light/dark cycle. All animal protocols were approved by the Animal Care and Use Committee. We studied a total of 50 BXD strains, but only acquired matched male–female data pairs for 39 strains (35 BXD strains, parental B6 and D2, and two reciprocal F1 hybrids, B6D2F1 and D2B6F1). The average age of mice was 78 days. We provide more detail on the experimen-tal design and precise age and time of sacriï¬ce of all cases at stored in 4 deg C for 2–3 days. To dissect the hypothalamus, the brain was placed with the ventral side facing up in a coronal "brain cutting" matrix. Using the medial mammillary body as landmark, a vertical cut was made right along the posterior boundary of the hypothala-mus. A second vertical cut was made 2 mm from the ï¬rst cut. This edge lies slightly caudal to the optic chiasm and cuts through the retrochiasmatic nucleus. The hypothalamus was then sliced out from this 2 mm thick section. Each of the 39 mouse strains is represented by male and female samples (total of 78 microarray samples). Each individual sample consisted of tissue pooled from two mice of the same strain and sex that are usually littermates. The total number of mice used was 78 females and 78 males. RNA was puriï¬ed using the RNAeasy micro kit on the QIAcube system (Qiagen)2. RNA purity and concen-tration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6854HYP |
- Hyp |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6862HYP |
- Hyp |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6852HYP |
- Hyp |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6860HYP |
- Hyp |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6864HYP |
- Hyp |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6866HYP |
- Hyp |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6858HYP |
- Hyp |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6856HYP |
- Hyp |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6800HYP |
- Hyp |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6796HYP |
- Hyp |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6788HYP |
- Hyp |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6786HYP |
- Hyp |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6806HYP |
- Hyp |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 14 |
- R6812HYP |
- Hyp |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 15 |
- R6804HYP |
- Hyp |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6792HYP |
- Hyp |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 17 |
- R6790HYP |
- Hyp |
- BXD27 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 18 |
- R6798HYP |
- Hyp |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 19 |
- R6794HYP |
- Hyp |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 20 |
- R6816HYP |
- Hyp |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 21 |
- R6802HYP |
- Hyp |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 22 |
- R6916HYP |
- Hyp |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 23 |
- R6846HYP |
- Hyp |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6822HYP |
- Hyp |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 25 |
- R6808HYP |
- Hyp |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 26 |
- R6814HYP |
- Hyp |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 27 |
- R6848HYP |
- Hyp |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 28 |
- R6850HYP |
- Hyp |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 29 |
- R6810HYP |
- Hyp |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 30 |
- R6758HYP |
- Hyp |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 31 |
- R6746HYP |
- Hyp |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 32 |
- R6750HYP |
- Hyp |
- BXD44 |
- 83 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 33 |
- R6764HYP |
- Hyp |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 34 |
- R6762HYP |
- Hyp |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 35 |
- R6880HYP |
- Hyp |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 36 |
- R6882HYP |
- Hyp |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 37 |
- R6748HYP |
- Hyp |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 38 |
- R6890HYP |
- Hyp |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 39 |
- R6892HYP |
- Hyp |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 40 |
- R6918HYP |
- Hyp |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 41 |
- R6894HYP |
- Hyp |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 42 |
- R6770HYP |
- Hyp |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 43 |
- R6772HYP |
- Hyp |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 44 |
- R6836HYP |
- Hyp |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 45 |
- R6844HYP |
- Hyp |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 46 |
- R6888HYP |
- Hyp |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 47 |
- R6878HYP |
- Hyp |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 48 |
- R6874HYP |
- Hyp |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 49 |
- R6930HYP |
- Hyp |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6932HYP |
- Hyp |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6776HYP |
- Hyp |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 52 |
- R6774HYP |
- Hyp |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 53 |
- R6926HYP |
- Hyp |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 54 |
- R6922HYP |
- Hyp |
- BXD70 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 55 |
- R6870HYP |
- Hyp |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6872HYP |
- Hyp |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6778HYP |
- Hyp |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 58 |
- R6780HYP |
- Hyp |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 59 |
- R6838HYP |
- Hyp |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 60 |
- R6830HYP |
- Hyp |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 61 |
- R6934HYP |
- Hyp |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 62 |
- R6782HYP |
- Hyp |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6784HYP |
- Hyp |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 64 |
- R6914HYP |
- Hyp |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 65 |
- R6912HYP |
- Hyp |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 66 |
- R6834HYP |
- Hyp |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6938HYP |
- Hyp |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6940HYP |
- Hyp |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6910HYP |
- Hyp |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6908HYP |
- Hyp |
- BXD87 |
- 83 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6896HYP |
- Hyp |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6898HYP |
- Hyp |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6904HYP |
- Hyp |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 74 |
- R6906HYP |
- Hyp |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 75 |
- R6924HYP |
- Hyp |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6928HYP |
- Hyp |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6920HYP |
- Hyp |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6868HYP |
- Hyp |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 79 |
- R6900HYP |
- Hyp |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 80 |
- R6902HYP |
- Hyp |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 81 |
- R6876HYP |
- Hyp |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 82 |
- R6884HYP |
- Hyp |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 83 |
- R6840HYP |
- Hyp |
- BXD100 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 84 |
- R6832HYP |
- Hyp |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 85 |
- R6944HYP |
- Hyp |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 86 |
- R6942HYP |
- Hyp |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 87 |
- R6756HYP |
- Hyp |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 88 |
- R6768HYP |
- Hyp |
- BXD103 |
- 78 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 89 |
- R6766HYP |
- Hyp |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/INIA_Hyp_RMA_1110/experiment-design.rtf b/general/datasets/INIA_Hyp_RMA_1110/experiment-design.rtf
deleted file mode 100644
index 443af4a..0000000
--- a/general/datasets/INIA_Hyp_RMA_1110/experiment-design.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Hypothalamus was dissected from adult male and female mice and process for expression analysis.
-
-RNA isolation
-Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-This preliminary data set is associated with 430 eQTLs with LOD scores above 10. Peak LRS is 146 for Trait ID 10513604 (Hdhd3).
diff --git a/general/datasets/INIA_Hyp_RMA_1110/platform.rtf b/general/datasets/INIA_Hyp_RMA_1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Hyp_RMA_1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Hyp_RMA_1110/processing.rtf b/general/datasets/INIA_Hyp_RMA_1110/processing.rtf
deleted file mode 100644
index b3e8689..0000000
--- a/general/datasets/INIA_Hyp_RMA_1110/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Total RNA was processed using standard protocols and hybridized to the Affymetrix Mouse Gene 1.0 ST arrays4. This array contains 34,700 probe sets that target ∼29,000 well-deï¬ned transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive cov-erage of transcripts from a single gene. Male and female samples were interleaved and processed together to avoid batch confounds. Details on the strain, age, and sex of each sample can be obtained from the information available for the INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) data set on www.genenetwork.org. Probe set level intensity values were extracted from the CEL ï¬les using the Affymetrix GeneChip Operating Software. Data nor-malization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units. The entire data set can be down-loaded from www.genenetwork.org using the accession number GN281 (http://www.genenetwork.org/webqtl/main.py?FormID = sharinginfo&GN_AccessionId = 281) and also from the NIH Gene Expression Omnibus5 using the GEO accession number GSE36674. For this study we used a subset of cases that were repre-sented by both male and female samples – 78 sex-balanced arrays. Statistical power provided by this sample size (N = 39 strains) was estimated using the R function power.t.test6 with the SD set at 0.17, which is the average value. Only transcripts with above aver-age expression (minimum expression value above 8.5 on a log2 scale) were included for further analysis (17,192 probe sets). We used a two-tailed paired t -test to identify transcripts with signiï¬-cant expression difference between males and females. We applied the Benjamini and Hochberg false discovery rate (FDR) method and selected differentially expressed transcripts using a 10% FDR criterion.
diff --git a/general/datasets/INIA_Hyp_RMA_1110/summary.rtf b/general/datasets/INIA_Hyp_RMA_1110/summary.rtf
deleted file mode 100644
index 02671d5..0000000
--- a/general/datasets/INIA_Hyp_RMA_1110/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.
-
-Data released initially Nov 25, 2010, updated March 7, 2011 by A. Centeno and K. Mozhui to add two additional arrays. Data appear to be error-free in terms of sex and strain assignments shown in the table below.
-
-Dissection protocol:
-
-
- - Animals were sacrificed by quick cervical dislocation and brains were removed and stored in RNAlater (www.ambion.com) for 2 to 3 days
- - Brain was placed with ventral side up and a partial cut was made with a blade at -2.5 from Bregma (just a little rostral from the pontine fibres when viewed from the ventral side)
- - The brain was then place in a coronal matrix and a 2 mm section was made rostral to the first cut
- - The 2mm Section was placed on a clean glass slide and hypothalamus was sliced out and placed in a tube on dry ice.
- - To dissect out the BLA, the temporal lobes were detached by placing a scalple in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then sliced out and placed in a tube on dry ice.
- - Tissues from two mice of the same strain and sex were pooled. The only exceptions to this are the BLA samples for strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue from only one animal).
-
-
-The hypothalamus contains nuclei and cell populations that are critical in reproduction and that differ signiï¬cantly between the sexes in structure and function. To examine the molecular and genetic basis for these differences, we quantiï¬ed gene expression in the hypothalamus of 39 pairs of adult male and female mice belonging to the BXD strains. This experimental design enabled us to deï¬ne hypothalamic gene coexpression networks and provided robust estimates of absolute expression differences. As expected, sex has the strongest effect on the expression of genes on the X and Y chromosomes (e.g., Uty, Xist, Kdm6a).Transcripts associated with the endocrine system and neuropeptide signaling also differ signiï¬cantly. Sex-differentiated transcripts often have well delimited expression within speciï¬c hypothalamic nuclei that have roles in reproduction. For instance, the estro-gen receptor (Esr1) and neurokinin B (Tac2) genes have intense expression in the medial preoptic and arcuate nuclei and comparatively high expression in females. Despite the strong effect of sex on single transcripts, the global pattern of covariance among transcripts is well preserved, and consequently, males and females have well matched coexpression modules. However, there are sex-speciï¬c hub genes in functionally equivalent modules. For example, only in males is the Y-linked gene, Uty, a highly connected transcript in a network that regulates chromatin modiï¬cation and gene transcription. In females, the X chromo-some paralog, Kdm6a, takes the place of Uty in the same network. We also ï¬nd signiï¬cant effect of sex on genetic regulation and the same network in males and females can be associated with markedly different regulatory loci. With the exception of a few sex-speciï¬c modules, our analysis reveals a system in which sets of functionally related transcripts are organized into stable sex-independent networks that are controlled at a higher level by sex-speciï¬c modulators.
diff --git a/general/datasets/INIA_Hyp_RMA_Ex-1110/acknowledgment.rtf b/general/datasets/INIA_Hyp_RMA_Ex-1110/acknowledgment.rtf
deleted file mode 100644
index 2c3f2bd..0000000
--- a/general/datasets/INIA_Hyp_RMA_Ex-1110/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported by Integrative Neuroscience Initiative on Alcoholism grants U01AA13499, U01AA017590, U01AA0016662. The authors are also grateful to Arthur Centeno and Lorne Rose, and the Molecular Resource Center at UTHSC.
diff --git a/general/datasets/INIA_Hyp_RMA_Ex-1110/cases.rtf b/general/datasets/INIA_Hyp_RMA_Ex-1110/cases.rtf
deleted file mode 100644
index f19e9c8..0000000
--- a/general/datasets/INIA_Hyp_RMA_Ex-1110/cases.rtf
+++ /dev/null
@@ -1,916 +0,0 @@
-The BXD recombinant inbred strains are derived from crossing the C57BL/6J (B6) and DBA/2J (D2) parental strains and inbreeding for over 20 generations (Taylor et al., 1999; Peirce et al., 2004). All mice used in this study were born and housed at the University of Tennessee Health Science Center. Mice were kept at an average of 3–4 per cage in a temperature-controlled vivarium (22 deg C) and maintained at a 12 h light/dark cycle. All animal protocols were approved by the Animal Care and Use Committee. We studied a total of 50 BXD strains, but only acquired matched male–female data pairs for 39 strains (35 BXD strains, parental B6 and D2, and two reciprocal F1 hybrids, B6D2F1 and D2B6F1). The average age of mice was 78 days. We provide more detail on the experimen-tal design and precise age and time of sacriï¬ce of all cases at stored in 4 deg C for 2–3 days. To dissect the hypothalamus, the brain was placed with the ventral side facing up in a coronal "brain cutting" matrix. Using the medial mammillary body as landmark, a vertical cut was made right along the posterior boundary of the hypothala-mus. A second vertical cut was made 2 mm from the ï¬rst cut. This edge lies slightly caudal to the optic chiasm and cuts through the retrochiasmatic nucleus. The hypothalamus was then sliced out from this 2 mm thick section. Each of the 39 mouse strains is represented by male and female samples (total of 78 microarray samples). Each individual sample consisted of tissue pooled from two mice of the same strain and sex that are usually littermates. The total number of mice used was 78 females and 78 males. RNA was puriï¬ed using the RNAeasy micro kit on the QIAcube system (Qiagen)2. RNA purity and concen-tration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tissue |
- Strain |
- Age |
- Sex |
- Date sacrifice |
- Time sacrifice |
-
-
- | 1 |
- R6854HYP |
- Hyp |
- C57BL/6J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 2 |
- R6862HYP |
- Hyp |
- C57BL/6J |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 3 |
- R6852HYP |
- Hyp |
- D2B6F1 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 4 |
- R6860HYP |
- Hyp |
- D2B6F1 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 5 |
- R6864HYP |
- Hyp |
- DBA/2J |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 6 |
- R6866HYP |
- Hyp |
- DBA/2J |
- 68 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 7 |
- R6858HYP |
- Hyp |
- B6D2F1 |
- 69 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 8 |
- R6856HYP |
- Hyp |
- B6D2F1 |
- 69 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 9 |
- R6800HYP |
- Hyp |
- BXD1 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 10 |
- R6796HYP |
- Hyp |
- BXD1 |
- 85 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 11 |
- R6788HYP |
- Hyp |
- BXD11 |
- 87 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 12 |
- R6786HYP |
- Hyp |
- BXD11 |
- 76 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 13 |
- R6806HYP |
- Hyp |
- BXD12 |
- 77 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 14 |
- R6812HYP |
- Hyp |
- BXD14 |
- 81 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 15 |
- R6804HYP |
- Hyp |
- BXD24 |
- 85 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 16 |
- R6792HYP |
- Hyp |
- BXD27 |
- 75 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 17 |
- R6790HYP |
- Hyp |
- BXD27 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 18 |
- R6798HYP |
- Hyp |
- BXD29 |
- 71 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 19 |
- R6794HYP |
- Hyp |
- BXD29 |
- 71 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 20 |
- R6816HYP |
- Hyp |
- BXD31 |
- 74 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 21 |
- R6802HYP |
- Hyp |
- BXD31 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 22 |
- R6916HYP |
- Hyp |
- BXD32 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 23 |
- R6846HYP |
- Hyp |
- BXD32 |
- 81 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 24 |
- R6822HYP |
- Hyp |
- BXD34 |
- 77 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 25 |
- R6808HYP |
- Hyp |
- BXD34 |
- 77 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 26 |
- R6814HYP |
- Hyp |
- BXD39 |
- 79 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 27 |
- R6848HYP |
- Hyp |
- BXD40 |
- 85 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 28 |
- R6850HYP |
- Hyp |
- BXD40 |
- 85 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 29 |
- R6810HYP |
- Hyp |
- BXD42 |
- 87 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 30 |
- R6758HYP |
- Hyp |
- BXD43 |
- 81 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 31 |
- R6746HYP |
- Hyp |
- BXD44 |
- 83 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 32 |
- R6750HYP |
- Hyp |
- BXD44 |
- 83 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 33 |
- R6764HYP |
- Hyp |
- BXD45 |
- 77 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 34 |
- R6762HYP |
- Hyp |
- BXD45 |
- 77 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 35 |
- R6880HYP |
- Hyp |
- BXD48 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 36 |
- R6882HYP |
- Hyp |
- BXD48 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 37 |
- R6748HYP |
- Hyp |
- BXD49 |
- 84 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 38 |
- R6890HYP |
- Hyp |
- BXD50 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 39 |
- R6892HYP |
- Hyp |
- BXD50 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 40 |
- R6918HYP |
- Hyp |
- BXD56 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 41 |
- R6894HYP |
- Hyp |
- BXD56 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 42 |
- R6770HYP |
- Hyp |
- BXD60 |
- 70 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 43 |
- R6772HYP |
- Hyp |
- BXD60 |
- 70 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 44 |
- R6836HYP |
- Hyp |
- BXD62 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 45 |
- R6844HYP |
- Hyp |
- BXD62 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 46 |
- R6888HYP |
- Hyp |
- BXD63 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 47 |
- R6878HYP |
- Hyp |
- BXD65 |
- 84 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 48 |
- R6874HYP |
- Hyp |
- BXD65 |
- 84 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 49 |
- R6930HYP |
- Hyp |
- BXD68 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 50 |
- R6932HYP |
- Hyp |
- BXD68 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 51 |
- R6776HYP |
- Hyp |
- BXD69 |
- 69 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 52 |
- R6774HYP |
- Hyp |
- BXD69 |
- 80 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 53 |
- R6926HYP |
- Hyp |
- BXD70 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 54 |
- R6922HYP |
- Hyp |
- BXD70 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 55 |
- R6870HYP |
- Hyp |
- BXD71 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 56 |
- R6872HYP |
- Hyp |
- BXD71 |
- 76 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 57 |
- R6778HYP |
- Hyp |
- BXD73 |
- 83 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 58 |
- R6780HYP |
- Hyp |
- BXD73 |
- 83 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 59 |
- R6838HYP |
- Hyp |
- BXD75 |
- 76 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 60 |
- R6830HYP |
- Hyp |
- BXD75 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 61 |
- R6934HYP |
- Hyp |
- BXD79 |
- 87 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 62 |
- R6782HYP |
- Hyp |
- BXD80 |
- 73 |
- F |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 63 |
- R6784HYP |
- Hyp |
- BXD80 |
- 73 |
- M |
- 8/17/10 |
- 1:15 PM to 5 PM |
-
-
- | 64 |
- R6914HYP |
- Hyp |
- BXD83 |
- 81 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 65 |
- R6912HYP |
- Hyp |
- BXD83 |
- 81 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 66 |
- R6834HYP |
- Hyp |
- BXD84 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 67 |
- R6938HYP |
- Hyp |
- BXD85 |
- 74 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 68 |
- R6940HYP |
- Hyp |
- BXD85 |
- 74 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 69 |
- R6910HYP |
- Hyp |
- BXD87 |
- 83 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 70 |
- R6908HYP |
- Hyp |
- BXD87 |
- 83 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 71 |
- R6896HYP |
- Hyp |
- BXD89 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 72 |
- R6898HYP |
- Hyp |
- BXD89 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 73 |
- R6904HYP |
- Hyp |
- BXD90 |
- 82 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 74 |
- R6906HYP |
- Hyp |
- BXD90 |
- 82 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 75 |
- R6924HYP |
- Hyp |
- BXD92 |
- 86 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 76 |
- R6928HYP |
- Hyp |
- BXD92 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 77 |
- R6920HYP |
- Hyp |
- BXD95 |
- 76 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 78 |
- R6868HYP |
- Hyp |
- BXD95 |
- 76 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 79 |
- R6900HYP |
- Hyp |
- BXD97 |
- 71 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 80 |
- R6902HYP |
- Hyp |
- BXD97 |
- 71 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 81 |
- R6876HYP |
- Hyp |
- BXD99 |
- 77 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 82 |
- R6884HYP |
- Hyp |
- BXD99 |
- 77 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 83 |
- R6840HYP |
- Hyp |
- BXD100 |
- 83 |
- F |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 84 |
- R6832HYP |
- Hyp |
- BXD100 |
- 83 |
- M |
- 8/18/10 |
- 8:45AM to 12:30 PM |
-
-
- | 85 |
- R6944HYP |
- Hyp |
- BXD101 |
- 89 |
- F |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 86 |
- R6942HYP |
- Hyp |
- BXD101 |
- 89 |
- M |
- 8/18/10 |
- 1 PM to 6:45 PM |
-
-
- | 87 |
- R6756HYP |
- Hyp |
- BXD102 |
- 88 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 88 |
- R6768HYP |
- Hyp |
- BXD103 |
- 78 |
- F |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
- | 89 |
- R6766HYP |
- Hyp |
- BXD103 |
- 78 |
- M |
- 8/17/10 |
- 9:30 AM to 12:30AM |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/INIA_Hyp_RMA_Ex-1110/experiment-design.rtf b/general/datasets/INIA_Hyp_RMA_Ex-1110/experiment-design.rtf
deleted file mode 100644
index 443af4a..0000000
--- a/general/datasets/INIA_Hyp_RMA_Ex-1110/experiment-design.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-Hypothalamus was dissected from adult male and female mice and process for expression analysis.
-
-RNA isolation
-Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-This preliminary data set is associated with 430 eQTLs with LOD scores above 10. Peak LRS is 146 for Trait ID 10513604 (Hdhd3).
diff --git a/general/datasets/INIA_Hyp_RMA_Ex-1110/platform.rtf b/general/datasets/INIA_Hyp_RMA_Ex-1110/platform.rtf
deleted file mode 100644
index aba2206..0000000
--- a/general/datasets/INIA_Hyp_RMA_Ex-1110/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)
diff --git a/general/datasets/INIA_Hyp_RMA_Ex-1110/processing.rtf b/general/datasets/INIA_Hyp_RMA_Ex-1110/processing.rtf
deleted file mode 100644
index b3e8689..0000000
--- a/general/datasets/INIA_Hyp_RMA_Ex-1110/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Total RNA was processed using standard protocols and hybridized to the Affymetrix Mouse Gene 1.0 ST arrays4. This array contains 34,700 probe sets that target ∼29,000 well-deï¬ned transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive cov-erage of transcripts from a single gene. Male and female samples were interleaved and processed together to avoid batch confounds. Details on the strain, age, and sex of each sample can be obtained from the information available for the INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) data set on www.genenetwork.org. Probe set level intensity values were extracted from the CEL ï¬les using the Affymetrix GeneChip Operating Software. Data nor-malization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units. The entire data set can be down-loaded from www.genenetwork.org using the accession number GN281 (http://www.genenetwork.org/webqtl/main.py?FormID = sharinginfo&GN_AccessionId = 281) and also from the NIH Gene Expression Omnibus5 using the GEO accession number GSE36674. For this study we used a subset of cases that were repre-sented by both male and female samples – 78 sex-balanced arrays. Statistical power provided by this sample size (N = 39 strains) was estimated using the R function power.t.test6 with the SD set at 0.17, which is the average value. Only transcripts with above aver-age expression (minimum expression value above 8.5 on a log2 scale) were included for further analysis (17,192 probe sets). We used a two-tailed paired t -test to identify transcripts with signiï¬-cant expression difference between males and females. We applied the Benjamini and Hochberg false discovery rate (FDR) method and selected differentially expressed transcripts using a 10% FDR criterion.
diff --git a/general/datasets/INIA_Hyp_RMA_Ex-1110/summary.rtf b/general/datasets/INIA_Hyp_RMA_Ex-1110/summary.rtf
deleted file mode 100644
index 02671d5..0000000
--- a/general/datasets/INIA_Hyp_RMA_Ex-1110/summary.rtf
+++ /dev/null
@@ -1,16 +0,0 @@
-These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.
-
-Data released initially Nov 25, 2010, updated March 7, 2011 by A. Centeno and K. Mozhui to add two additional arrays. Data appear to be error-free in terms of sex and strain assignments shown in the table below.
-
-Dissection protocol:
-
-
- - Animals were sacrificed by quick cervical dislocation and brains were removed and stored in RNAlater (www.ambion.com) for 2 to 3 days
- - Brain was placed with ventral side up and a partial cut was made with a blade at -2.5 from Bregma (just a little rostral from the pontine fibres when viewed from the ventral side)
- - The brain was then place in a coronal matrix and a 2 mm section was made rostral to the first cut
- - The 2mm Section was placed on a clean glass slide and hypothalamus was sliced out and placed in a tube on dry ice.
- - To dissect out the BLA, the temporal lobes were detached by placing a scalple in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then sliced out and placed in a tube on dry ice.
- - Tissues from two mice of the same strain and sex were pooled. The only exceptions to this are the BLA samples for strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue from only one animal).
-
-
-The hypothalamus contains nuclei and cell populations that are critical in reproduction and that differ signiï¬cantly between the sexes in structure and function. To examine the molecular and genetic basis for these differences, we quantiï¬ed gene expression in the hypothalamus of 39 pairs of adult male and female mice belonging to the BXD strains. This experimental design enabled us to deï¬ne hypothalamic gene coexpression networks and provided robust estimates of absolute expression differences. As expected, sex has the strongest effect on the expression of genes on the X and Y chromosomes (e.g., Uty, Xist, Kdm6a).Transcripts associated with the endocrine system and neuropeptide signaling also differ signiï¬cantly. Sex-differentiated transcripts often have well delimited expression within speciï¬c hypothalamic nuclei that have roles in reproduction. For instance, the estro-gen receptor (Esr1) and neurokinin B (Tac2) genes have intense expression in the medial preoptic and arcuate nuclei and comparatively high expression in females. Despite the strong effect of sex on single transcripts, the global pattern of covariance among transcripts is well preserved, and consequently, males and females have well matched coexpression modules. However, there are sex-speciï¬c hub genes in functionally equivalent modules. For example, only in males is the Y-linked gene, Uty, a highly connected transcript in a network that regulates chromatin modiï¬cation and gene transcription. In females, the X chromo-some paralog, Kdm6a, takes the place of Uty in the same network. We also ï¬nd signiï¬cant effect of sex on genetic regulation and the same network in males and females can be associated with markedly different regulatory loci. With the exception of a few sex-speciï¬c modules, our analysis reveals a system in which sets of functionally related transcripts are organized into stable sex-independent networks that are controlled at a higher level by sex-speciï¬c modulators.
diff --git a/general/datasets/INIA_MacFas_AMG_RMA_0110/summary.rtf b/general/datasets/INIA_MacFas_AMG_RMA_0110/summary.rtf
deleted file mode 100644
index 42959fa..0000000
--- a/general/datasets/INIA_MacFas_AMG_RMA_0110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 90, Name: INIA Macaca fasicularis Amygdala (Jan10)
\ No newline at end of file
diff --git a/general/datasets/INIA_MacFas_Ac_RMA_0110/summary.rtf b/general/datasets/INIA_MacFas_Ac_RMA_0110/summary.rtf
deleted file mode 100644
index cbfec8d..0000000
--- a/general/datasets/INIA_MacFas_Ac_RMA_0110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 88, Name: INIA Macaca fasicularis Nucleus Accumbens (Jan10)
\ No newline at end of file
diff --git a/general/datasets/INIA_MacFas_Hc_RMA_0110/summary.rtf b/general/datasets/INIA_MacFas_Hc_RMA_0110/summary.rtf
deleted file mode 100644
index f305a05..0000000
--- a/general/datasets/INIA_MacFas_Hc_RMA_0110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 89, Name: INIA Macaca fasicularis Hippocampus (Jan10)
\ No newline at end of file
diff --git a/general/datasets/INIA_MacFas_Pf_RMA_0110/summary.rtf b/general/datasets/INIA_MacFas_Pf_RMA_0110/summary.rtf
deleted file mode 100644
index 06ec6f0..0000000
--- a/general/datasets/INIA_MacFas_Pf_RMA_0110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 87, Name: INIA Macaca fasicularis Prefrontal Cortex (Jan10)
\ No newline at end of file
diff --git a/general/datasets/INIA_MacFas_brain_RMA_0110/notes.rtf b/general/datasets/INIA_MacFas_brain_RMA_0110/notes.rtf
deleted file mode 100644
index 958acba..0000000
--- a/general/datasets/INIA_MacFas_brain_RMA_0110/notes.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-Dr. Miles Note:
-
-The initial 16 animals from INIA cohort 3 are the samples that are in GeneNetwork -- and there we had 4 brain regions x 16 animals -- prefrontal cortex (Brodmann areas 24, 25 and 32 pooled together), nucleus acumen, hippocampus and amygdala.
-
-INIA cohort 3 includes 12 ethanol drinking female cynomolgous Indochinese monkeys and 4 control Indonesian monkeys.
diff --git a/general/datasets/INIA_MacFas_brain_RMA_0110/summary.rtf b/general/datasets/INIA_MacFas_brain_RMA_0110/summary.rtf
deleted file mode 100644
index 103b4c3..0000000
--- a/general/datasets/INIA_MacFas_brain_RMA_0110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 86, Name: INIA Macaca fasicularis Brain (Jan10)
diff --git a/general/datasets/Illum_BXD_PBL_1108/summary.rtf b/general/datasets/Illum_BXD_PBL_1108/summary.rtf
deleted file mode 100644
index 172b4ee..0000000
--- a/general/datasets/Illum_BXD_PBL_1108/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 67, Name: UWA Illumina PBL (Nov08) RSN **
\ No newline at end of file
diff --git a/general/datasets/Illum_BXD_Spl_1108/summary.rtf b/general/datasets/Illum_BXD_Spl_1108/summary.rtf
deleted file mode 100644
index 7b131b7..0000000
--- a/general/datasets/Illum_BXD_Spl_1108/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 65, Name: UWA Illumina Spleen (Nov08) RSN **
\ No newline at end of file
diff --git a/general/datasets/Illum_BXD_Thy_1108/summary.rtf b/general/datasets/Illum_BXD_Thy_1108/summary.rtf
deleted file mode 100644
index f075479..0000000
--- a/general/datasets/Illum_BXD_Thy_1108/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 66, Name: UWA Illumina Thymus (Nov08) RSN **
\ No newline at end of file
diff --git a/general/datasets/Illum_LXS_Hipp_NOE_1008/summary.rtf b/general/datasets/Illum_LXS_Hipp_NOE_1008/summary.rtf
deleted file mode 100644
index f49829f..0000000
--- a/general/datasets/Illum_LXS_Hipp_NOE_1008/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 63, Name: Hippocampus Illumina NOS (Oct08) RankInv beta
\ No newline at end of file
diff --git a/general/datasets/Illum_LXS_Hipp_NON_1008/summary.rtf b/general/datasets/Illum_LXS_Hipp_NON_1008/summary.rtf
deleted file mode 100644
index f49829f..0000000
--- a/general/datasets/Illum_LXS_Hipp_NON_1008/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 63, Name: Hippocampus Illumina NOS (Oct08) RankInv beta
\ No newline at end of file
diff --git a/general/datasets/Illum_LXS_Hipp_NOS_1008/summary.rtf b/general/datasets/Illum_LXS_Hipp_NOS_1008/summary.rtf
deleted file mode 100644
index f49829f..0000000
--- a/general/datasets/Illum_LXS_Hipp_NOS_1008/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 63, Name: Hippocampus Illumina NOS (Oct08) RankInv beta
\ No newline at end of file
diff --git a/general/datasets/Illum_LXS_Hipp_RSE_1008/summary.rtf b/general/datasets/Illum_LXS_Hipp_RSE_1008/summary.rtf
deleted file mode 100644
index f49829f..0000000
--- a/general/datasets/Illum_LXS_Hipp_RSE_1008/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 63, Name: Hippocampus Illumina NOS (Oct08) RankInv beta
\ No newline at end of file
diff --git a/general/datasets/Illum_LXS_Hipp_RSS_1008/summary.rtf b/general/datasets/Illum_LXS_Hipp_RSS_1008/summary.rtf
deleted file mode 100644
index f49829f..0000000
--- a/general/datasets/Illum_LXS_Hipp_RSS_1008/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 63, Name: Hippocampus Illumina NOS (Oct08) RankInv beta
\ No newline at end of file
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/acknowledgment.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/acknowledgment.rtf
deleted file mode 100644
index d8f3e9a..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data source acknowledgment:
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. · Lu Lu, M.D. Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/cases.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/cases.rtf
deleted file mode 100644
index efa4371..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/cases.rtf
+++ /dev/null
@@ -1,2140 +0,0 @@
-Quality Control on Sex Labels: Sex of the samples was validated using sex-specific probe set.
-
-
-
-
- |
- Legend: We evaluated whether or not the sex of samples were labeled correctly by measuring the expression of Xist using probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample.
-
-
-
- Data Table 1:
-
-
- This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
-
- |
-
-
- |
- Downloading all data:
-
- All data links (right-most column above) will be available as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
- |
-
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/experiment-design.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/experiment-design.rtf
deleted file mode 100644
index f477cb7..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/notes.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/notes.rtf
deleted file mode 100644
index 938409b..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/platform.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/platform.rtf
deleted file mode 100644
index 2ac899d..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the array platform:
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/processing.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/processing.rtf
deleted file mode 100644
index c3d0555..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-This data set uses the LOESS with Variance Stabilizing Transform (VST) and Background correction from the lumi package downloaded from Bioconductor (http://www.bioconductor.org/). For the more detailed information, please see the lumi package documentation.
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/summary.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/summary.rtf
deleted file mode 100644
index ebfc03f..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/summary.rtf
+++ /dev/null
@@ -1,33 +0,0 @@
-August 07 ILLUMINA Mouse-6 DATA SET RSN: The LXS Hippocampus Illumina Robust Spline Normalization with No Background correction data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were not included. This particular data set was processed using the Illumina "Robust Spline Normalization with No Background Correction" protocol. Values were log2 transformed and the current data range from 6.481 average (very low or no expression) to 24.852 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Hippocampus Illumina (Aug 07) RSN data set, ### probes have LRS values >46.
-
-In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets:
-
-
- - 1050 for Hippocampus Illumina (Aug07) LOESS
- - 1162 for Hippocampus Illumina (Aug07) LOESS_NB
- - 1129 for Hippocampus Illumina (Aug07) QUANT
- - 1176 for Hippocampus Illumina (Aug07) QUANT_NB
- - NO DATA for Hippocampus Illumina (Aug07) RSN
- - NO DATA for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 1183 for Hippocampus Illumina (May 07) RankInv
- - 1167 for Hippocampus Illumina (Oct06) Rank
- - 1170 for Hippocampus Illumina (Oct06) RankInv
-
-
-The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follow
-
-
- - 338.4 for Hippocampus Illumina (Aug07) LOESS
- - 339.8 for Hippocampus Illumina (Aug07) LOESS_NB
- - 370.2 for Hippocampus Illumina (Aug07) QUANT
- - 363.5 for Hippocampus Illumina (Aug07) QUANT_NB
- - 374.8 for Hippocampus Illumina (Aug07) RSN
- - 363.0 for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 360.3 for Hippocampus Illumina (May 07) RankInv
- - 358.1 for Hippocampus Illumina (Oct06) Rank
- - 358.8 for Hippocampus Illumina (Oct06) RankInv
-
diff --git a/general/datasets/Illum_LXS_Hipp_loess0807/tissue.rtf b/general/datasets/Illum_LXS_Hipp_loess0807/tissue.rtf
deleted file mode 100644
index febccce..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess0807/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-About the animals and tissue used to generate this set of data:
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/acknowledgment.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/acknowledgment.rtf
deleted file mode 100644
index d8f3e9a..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data source acknowledgment:
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. · Lu Lu, M.D. Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/cases.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/cases.rtf
deleted file mode 100644
index efa4371..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/cases.rtf
+++ /dev/null
@@ -1,2140 +0,0 @@
-Quality Control on Sex Labels: Sex of the samples was validated using sex-specific probe set.
-
-
-
-
- |
- Legend: We evaluated whether or not the sex of samples were labeled correctly by measuring the expression of Xist using probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample.
-
-
-
- Data Table 1:
-
-
- This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
-
- |
-
-
- |
- Downloading all data:
-
- All data links (right-most column above) will be available as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
- |
-
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/experiment-design.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/experiment-design.rtf
deleted file mode 100644
index f477cb7..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/notes.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/notes.rtf
deleted file mode 100644
index 938409b..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/platform.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/platform.rtf
deleted file mode 100644
index 2ac899d..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the array platform:
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/processing.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/processing.rtf
deleted file mode 100644
index c3d0555..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-This data set uses the LOESS with Variance Stabilizing Transform (VST) and Background correction from the lumi package downloaded from Bioconductor (http://www.bioconductor.org/). For the more detailed information, please see the lumi package documentation.
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/summary.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/summary.rtf
deleted file mode 100644
index ebfc03f..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/summary.rtf
+++ /dev/null
@@ -1,33 +0,0 @@
-August 07 ILLUMINA Mouse-6 DATA SET RSN: The LXS Hippocampus Illumina Robust Spline Normalization with No Background correction data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were not included. This particular data set was processed using the Illumina "Robust Spline Normalization with No Background Correction" protocol. Values were log2 transformed and the current data range from 6.481 average (very low or no expression) to 24.852 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Hippocampus Illumina (Aug 07) RSN data set, ### probes have LRS values >46.
-
-In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets:
-
-
- - 1050 for Hippocampus Illumina (Aug07) LOESS
- - 1162 for Hippocampus Illumina (Aug07) LOESS_NB
- - 1129 for Hippocampus Illumina (Aug07) QUANT
- - 1176 for Hippocampus Illumina (Aug07) QUANT_NB
- - NO DATA for Hippocampus Illumina (Aug07) RSN
- - NO DATA for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 1183 for Hippocampus Illumina (May 07) RankInv
- - 1167 for Hippocampus Illumina (Oct06) Rank
- - 1170 for Hippocampus Illumina (Oct06) RankInv
-
-
-The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follow
-
-
- - 338.4 for Hippocampus Illumina (Aug07) LOESS
- - 339.8 for Hippocampus Illumina (Aug07) LOESS_NB
- - 370.2 for Hippocampus Illumina (Aug07) QUANT
- - 363.5 for Hippocampus Illumina (Aug07) QUANT_NB
- - 374.8 for Hippocampus Illumina (Aug07) RSN
- - 363.0 for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 360.3 for Hippocampus Illumina (May 07) RankInv
- - 358.1 for Hippocampus Illumina (Oct06) Rank
- - 358.8 for Hippocampus Illumina (Oct06) RankInv
-
diff --git a/general/datasets/Illum_LXS_Hipp_loess_nb0807/tissue.rtf b/general/datasets/Illum_LXS_Hipp_loess_nb0807/tissue.rtf
deleted file mode 100644
index febccce..0000000
--- a/general/datasets/Illum_LXS_Hipp_loess_nb0807/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-About the animals and tissue used to generate this set of data:
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/acknowledgment.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/acknowledgment.rtf
deleted file mode 100644
index d8f3e9a..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data source acknowledgment:
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. · Lu Lu, M.D. Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/cases.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/cases.rtf
deleted file mode 100644
index efa4371..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/cases.rtf
+++ /dev/null
@@ -1,2140 +0,0 @@
-Quality Control on Sex Labels: Sex of the samples was validated using sex-specific probe set.
-
-
-
-
- |
- Legend: We evaluated whether or not the sex of samples were labeled correctly by measuring the expression of Xist using probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample.
-
-
-
- Data Table 1:
-
-
- This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
-
- |
-
-
- |
- Downloading all data:
-
- All data links (right-most column above) will be available as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
- |
-
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/experiment-design.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/experiment-design.rtf
deleted file mode 100644
index f477cb7..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/notes.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/notes.rtf
deleted file mode 100644
index 938409b..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/platform.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/platform.rtf
deleted file mode 100644
index 2ac899d..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the array platform:
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/processing.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/processing.rtf
deleted file mode 100644
index c3d0555..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-This data set uses the LOESS with Variance Stabilizing Transform (VST) and Background correction from the lumi package downloaded from Bioconductor (http://www.bioconductor.org/). For the more detailed information, please see the lumi package documentation.
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/summary.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/summary.rtf
deleted file mode 100644
index ebfc03f..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/summary.rtf
+++ /dev/null
@@ -1,33 +0,0 @@
-August 07 ILLUMINA Mouse-6 DATA SET RSN: The LXS Hippocampus Illumina Robust Spline Normalization with No Background correction data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were not included. This particular data set was processed using the Illumina "Robust Spline Normalization with No Background Correction" protocol. Values were log2 transformed and the current data range from 6.481 average (very low or no expression) to 24.852 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Hippocampus Illumina (Aug 07) RSN data set, ### probes have LRS values >46.
-
-In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets:
-
-
- - 1050 for Hippocampus Illumina (Aug07) LOESS
- - 1162 for Hippocampus Illumina (Aug07) LOESS_NB
- - 1129 for Hippocampus Illumina (Aug07) QUANT
- - 1176 for Hippocampus Illumina (Aug07) QUANT_NB
- - NO DATA for Hippocampus Illumina (Aug07) RSN
- - NO DATA for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 1183 for Hippocampus Illumina (May 07) RankInv
- - 1167 for Hippocampus Illumina (Oct06) Rank
- - 1170 for Hippocampus Illumina (Oct06) RankInv
-
-
-The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follow
-
-
- - 338.4 for Hippocampus Illumina (Aug07) LOESS
- - 339.8 for Hippocampus Illumina (Aug07) LOESS_NB
- - 370.2 for Hippocampus Illumina (Aug07) QUANT
- - 363.5 for Hippocampus Illumina (Aug07) QUANT_NB
- - 374.8 for Hippocampus Illumina (Aug07) RSN
- - 363.0 for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 360.3 for Hippocampus Illumina (May 07) RankInv
- - 358.1 for Hippocampus Illumina (Oct06) Rank
- - 358.8 for Hippocampus Illumina (Oct06) RankInv
-
diff --git a/general/datasets/Illum_LXS_Hipp_quant0807/tissue.rtf b/general/datasets/Illum_LXS_Hipp_quant0807/tissue.rtf
deleted file mode 100644
index febccce..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant0807/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-About the animals and tissue used to generate this set of data:
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/acknowledgment.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/acknowledgment.rtf
deleted file mode 100644
index d8f3e9a..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data source acknowledgment:
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. · Lu Lu, M.D. Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/cases.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/cases.rtf
deleted file mode 100644
index efa4371..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/cases.rtf
+++ /dev/null
@@ -1,2140 +0,0 @@
-Quality Control on Sex Labels: Sex of the samples was validated using sex-specific probe set.
-
-
-
-
- |
- Legend: We evaluated whether or not the sex of samples were labeled correctly by measuring the expression of Xist using probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample.
-
-
-
- Data Table 1:
-
-
- This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
-
- |
-
-
- |
- Downloading all data:
-
- All data links (right-most column above) will be available as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
- |
-
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/experiment-design.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/experiment-design.rtf
deleted file mode 100644
index f477cb7..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/notes.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/notes.rtf
deleted file mode 100644
index 938409b..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/platform.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/platform.rtf
deleted file mode 100644
index 2ac899d..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the array platform:
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/processing.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/processing.rtf
deleted file mode 100644
index c3d0555..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-This data set uses the LOESS with Variance Stabilizing Transform (VST) and Background correction from the lumi package downloaded from Bioconductor (http://www.bioconductor.org/). For the more detailed information, please see the lumi package documentation.
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/summary.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/summary.rtf
deleted file mode 100644
index ebfc03f..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/summary.rtf
+++ /dev/null
@@ -1,33 +0,0 @@
-August 07 ILLUMINA Mouse-6 DATA SET RSN: The LXS Hippocampus Illumina Robust Spline Normalization with No Background correction data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were not included. This particular data set was processed using the Illumina "Robust Spline Normalization with No Background Correction" protocol. Values were log2 transformed and the current data range from 6.481 average (very low or no expression) to 24.852 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Hippocampus Illumina (Aug 07) RSN data set, ### probes have LRS values >46.
-
-In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets:
-
-
- - 1050 for Hippocampus Illumina (Aug07) LOESS
- - 1162 for Hippocampus Illumina (Aug07) LOESS_NB
- - 1129 for Hippocampus Illumina (Aug07) QUANT
- - 1176 for Hippocampus Illumina (Aug07) QUANT_NB
- - NO DATA for Hippocampus Illumina (Aug07) RSN
- - NO DATA for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 1183 for Hippocampus Illumina (May 07) RankInv
- - 1167 for Hippocampus Illumina (Oct06) Rank
- - 1170 for Hippocampus Illumina (Oct06) RankInv
-
-
-The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follow
-
-
- - 338.4 for Hippocampus Illumina (Aug07) LOESS
- - 339.8 for Hippocampus Illumina (Aug07) LOESS_NB
- - 370.2 for Hippocampus Illumina (Aug07) QUANT
- - 363.5 for Hippocampus Illumina (Aug07) QUANT_NB
- - 374.8 for Hippocampus Illumina (Aug07) RSN
- - 363.0 for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 360.3 for Hippocampus Illumina (May 07) RankInv
- - 358.1 for Hippocampus Illumina (Oct06) Rank
- - 358.8 for Hippocampus Illumina (Oct06) RankInv
-
diff --git a/general/datasets/Illum_LXS_Hipp_quant_nb0807/tissue.rtf b/general/datasets/Illum_LXS_Hipp_quant_nb0807/tissue.rtf
deleted file mode 100644
index febccce..0000000
--- a/general/datasets/Illum_LXS_Hipp_quant_nb0807/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-About the animals and tissue used to generate this set of data:
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/acknowledgment.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/acknowledgment.rtf
deleted file mode 100644
index d8f3e9a..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data source acknowledgment:
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. · Lu Lu, M.D. Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/cases.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/cases.rtf
deleted file mode 100644
index efa4371..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/cases.rtf
+++ /dev/null
@@ -1,2140 +0,0 @@
-Quality Control on Sex Labels: Sex of the samples was validated using sex-specific probe set.
-
-
-
-
- |
- Legend: We evaluated whether or not the sex of samples were labeled correctly by measuring the expression of Xist using probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample.
-
-
-
- Data Table 1:
-
-
- This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
-
- |
-
-
- |
- Downloading all data:
-
- All data links (right-most column above) will be available as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
- |
-
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/experiment-design.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/experiment-design.rtf
deleted file mode 100644
index f477cb7..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/notes.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/notes.rtf
deleted file mode 100644
index 938409b..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/platform.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/platform.rtf
deleted file mode 100644
index 2ac899d..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the array platform:
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/processing.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/processing.rtf
deleted file mode 100644
index c3d0555..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-This data set uses the LOESS with Variance Stabilizing Transform (VST) and Background correction from the lumi package downloaded from Bioconductor (http://www.bioconductor.org/). For the more detailed information, please see the lumi package documentation.
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/summary.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/summary.rtf
deleted file mode 100644
index ebfc03f..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/summary.rtf
+++ /dev/null
@@ -1,33 +0,0 @@
-August 07 ILLUMINA Mouse-6 DATA SET RSN: The LXS Hippocampus Illumina Robust Spline Normalization with No Background correction data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were not included. This particular data set was processed using the Illumina "Robust Spline Normalization with No Background Correction" protocol. Values were log2 transformed and the current data range from 6.481 average (very low or no expression) to 24.852 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Hippocampus Illumina (Aug 07) RSN data set, ### probes have LRS values >46.
-
-In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets:
-
-
- - 1050 for Hippocampus Illumina (Aug07) LOESS
- - 1162 for Hippocampus Illumina (Aug07) LOESS_NB
- - 1129 for Hippocampus Illumina (Aug07) QUANT
- - 1176 for Hippocampus Illumina (Aug07) QUANT_NB
- - NO DATA for Hippocampus Illumina (Aug07) RSN
- - NO DATA for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 1183 for Hippocampus Illumina (May 07) RankInv
- - 1167 for Hippocampus Illumina (Oct06) Rank
- - 1170 for Hippocampus Illumina (Oct06) RankInv
-
-
-The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follow
-
-
- - 338.4 for Hippocampus Illumina (Aug07) LOESS
- - 339.8 for Hippocampus Illumina (Aug07) LOESS_NB
- - 370.2 for Hippocampus Illumina (Aug07) QUANT
- - 363.5 for Hippocampus Illumina (Aug07) QUANT_NB
- - 374.8 for Hippocampus Illumina (Aug07) RSN
- - 363.0 for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 360.3 for Hippocampus Illumina (May 07) RankInv
- - 358.1 for Hippocampus Illumina (Oct06) Rank
- - 358.8 for Hippocampus Illumina (Oct06) RankInv
-
diff --git a/general/datasets/Illum_LXS_Hipp_rsn0807/tissue.rtf b/general/datasets/Illum_LXS_Hipp_rsn0807/tissue.rtf
deleted file mode 100644
index febccce..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn0807/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-About the animals and tissue used to generate this set of data:
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/acknowledgment.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/acknowledgment.rtf
deleted file mode 100644
index d8f3e9a..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data source acknowledgment:
-
-Data were generated with funds to Lu Lu, Beth Bennett, Mike Miles, Melloni Cook from INIA. · Lu Lu, M.D. Grant Support: NIH U01AA13499, U24AA13513 (Lu Lu, PI)
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/cases.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/cases.rtf
deleted file mode 100644
index efa4371..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/cases.rtf
+++ /dev/null
@@ -1,2140 +0,0 @@
-Quality Control on Sex Labels: Sex of the samples was validated using sex-specific probe set.
-
-
-
-
- |
- Legend: We evaluated whether or not the sex of samples were labeled correctly by measuring the expression of Xist using probe ILM106520068. In this bar chart the expression of Xist is very low in LXS114 and has a low error term. This is because both arrays are male samples rather than 1 male and 1 female sample.
-
-
-
- Data Table 1:
-
-
- This table lists all arrays by order of strain (index) and includes data on tube ID, strain, age, sex, F generation number, number of animals in each sample pool (pool size), slide ID, slide position (A through F), scan date, and scan batch.
-
-
-
-
-
-
-
-
-
- | index |
- tube ID |
- strain |
- age |
- sex |
- gener-
- ation |
- pool
- size |
- slide
- ID |
- slide
- position |
- batch
- by slide |
- scan
- batch |
-
-
- | 1 |
- R2851H2 |
- ILS |
- 77 |
- F |
- >100 |
- 4 |
- 1523516003 |
- B |
- 1 |
- 1 |
-
-
- | 2 |
- R0595H2 |
- ILS |
- 71 |
- F |
- >100 |
- 2 |
- 1523516030 |
- B |
- 4 |
- 2 |
-
-
- | 3 |
- R2874H2 |
- ILS |
- 78 |
- M |
- >100 |
- 4 |
- 1523516011 |
- B |
- 2 |
- 1 |
-
-
- | 4 |
- R0585H2 |
- ILS |
- 65 |
- M |
- >100 |
- 2 |
- 1523516028 |
- A |
- 3 |
- 2 |
-
-
- | 5 |
- R3281H1 |
- ILSXISSF1 |
- 90 |
- F |
- NA |
- 3 |
- 1562224029 |
- A |
- 28 |
- 13 |
-
-
- | 6 |
- R2857H2 |
- ISS |
- 75 |
- F |
- >100 |
- 4 |
- 1523516011 |
- A |
- 2 |
- 1 |
-
-
- | 7 |
- R0589H2 |
- ISS |
- 73 |
- F |
- >100 |
- 2 |
- 1523516028 |
- B |
- 3 |
- 2 |
-
-
- | 8 |
- R2955H2 |
- ISS |
- 53 |
- M |
- >100 |
- 3 |
- 1523516003 |
- A |
- 1 |
- 1 |
-
-
- | 9 |
- R0578H2 |
- ISS |
- 67 |
- M |
- >100 |
- 2 |
- 1523516030 |
- A |
- 4 |
- 2 |
-
-
- | 10 |
- R3282H1 |
- ISSXILSF1 |
- 97 |
- M |
- NA |
- 3 |
- 1562224029 |
- B |
- 28 |
- 13 |
-
-
- | 11 |
- R2013H2 |
- LXS10 |
- 84 |
- F |
- 27 |
- 2 |
- 1562224049 |
- E |
- 18 |
- 9 |
-
-
- | 12 |
- R1993H2 |
- LXS10 |
- 78 |
- M |
- 27 |
- 2 |
- 1562224036 |
- E |
- 17 |
- 9 |
-
-
- | 13 |
- R1997H2 |
- LXS100 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224049 |
- A |
- 18 |
- 9 |
-
-
- | 14 |
- R1983H2 |
- LXS100 |
- 77 |
- M |
- 25 |
- 2 |
- 1562224047 |
- F |
- 16 |
- 8 |
-
-
- | 15 |
- R2083H2 |
- LXS101 |
- 85 |
- F |
- 28 |
- 2 |
- 1562224050 |
- B |
- 19 |
- 9 |
-
-
- | 16 |
- R2084H2 |
- LXS101 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224050 |
- C |
- 19 |
- 9 |
-
-
- | 17 |
- R2186H2 |
- LXS102 |
- 73 |
- F |
- 29 |
- 2 |
- 1523516001 |
- C |
- 9 |
- 5 |
-
-
- | 18 |
- R2187H2 |
- LXS102 |
- 73 |
- M |
- 29 |
- 2 |
- 1562224053 |
- C |
- 20 |
- 10 |
-
-
- | 19 |
- R2809H2 |
- LXS103 |
- 72 |
- F |
- 26 |
- 2 |
- 1562224034 |
- C |
- 23 |
- 11 |
-
-
- | 20 |
- R2854H1 |
- LXS103 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516006 |
- D |
- 6 |
- 3 |
-
-
- | 21 |
- R2735H2 |
- LXS107 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516028 |
- D |
- 3 |
- 2 |
-
-
- | 22 |
- R2738H2 |
- LXS107 |
- 78 |
- M |
- 26 |
- 2 |
- 1562224054 |
- C |
- 21 |
- 10 |
-
-
- | 23 |
- R2840H2 |
- LXS110 |
- 67 |
- F |
- 25 |
- 2 |
- 1562224037 |
- D |
- 24 |
- 11 |
-
-
- | 24 |
- R2157H2 |
- LXS110 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516033 |
- E |
- 8 |
- 4 |
-
-
- | 25 |
- R2172H2 |
- LXS112 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516001 |
- B |
- 9 |
- 5 |
-
-
- | 26 |
- R2841H2 |
- LXS112 |
- 84 |
- M |
- 27 |
- 2 |
- 1562224042 |
- D |
- 27 |
- 12 |
-
-
- | 27 |
- R2188H2 |
- LXS114 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224053 |
- D |
- 20 |
- 10 |
-
-
- | 28 |
- R2204H2 |
- LXS114 |
- 72 |
- M |
- 28 |
- 2 |
- 1523516001 |
- D |
- 9 |
- 5 |
-
-
- | 29 |
- R2168H2 |
- LXS115 |
- 80 |
- F |
- 27 |
- 2 |
- 1523516001 |
- A |
- 9 |
- 5 |
-
-
- | 30 |
- R2085H2 |
- LXS115 |
- 71 |
- M |
- 27 |
- 2 |
- 1562224050 |
- D |
- 19 |
- 9 |
-
-
- | 31 |
- R2811H2 |
- LXS117 |
- 72 |
- F |
- 28 |
- 2 |
- 1562224034 |
- D |
- 23 |
- 11 |
-
-
- | 32 |
- R2212H2 |
- LXS117 |
- 74 |
- M |
- 27 |
- 2 |
- 1523516001 |
- E |
- 9 |
- 5 |
-
-
- | 33 |
- R1992H2 |
- LXS122 |
- 86 |
- F |
- 26 |
- 2 |
- 1562224036 |
- D |
- 17 |
- 9 |
-
-
- | 34 |
- R2219H2 |
- LXS122 |
- 72 |
- M |
- 26 |
- 2 |
- 1562224054 |
- A |
- 21 |
- 10 |
-
-
- | 35 |
- R2876H2 |
- LXS123 |
- 87 |
- F |
- 28 |
- 2 |
- 1562224038 |
- C |
- 25 |
- 11 |
-
-
- | 36 |
- R2832H1 |
- LXS123 |
- 77 |
- M |
- 27 |
- 2 |
- 1523516011 |
- E |
- 2 |
- 1 |
-
-
- | 37 |
- R2872H1 |
- LXS124 |
- 83 |
- F |
- 28 |
- 2 |
- 1523516006 |
- E |
- 6 |
- 3 |
-
-
- | 38 |
- R2871H2 |
- LXS124 |
- 85 |
- M |
- 28 |
- 2 |
- 1562224042 |
- F |
- 27 |
- 12 |
-
-
- | 39 |
- R1909H2 |
- LXS13 |
- 79 |
- F |
- 25 |
- 2 |
- 1523516024 |
- D |
- 13 |
- 7 |
-
-
- | 40 |
- R1901H2 |
- LXS13 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- D |
- 26 |
- 12 |
-
-
- | 41 |
- R2023H2 |
- LXS14 |
- 86 |
- F |
- 25 |
- 2 |
- 1562224050 |
- A |
- 19 |
- 9 |
-
-
- | 42 |
- R1612H2 |
- LXS14 |
- 85 |
- M |
- 26 |
- 2 |
- 1523516015 |
- A |
- 10 |
- 5 |
-
-
- | 43 |
- R1936H2 |
- LXS16 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516024 |
- E |
- 13 |
- 7 |
-
-
- | 44 |
- R1912H2 |
- LXS16 |
- 81 |
- M |
- 25 |
- 2 |
- 1523516033 |
- B |
- 8 |
- 4 |
-
-
- | 45 |
- R1961H2 |
- LXS19 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516029 |
- F |
- 14 |
- 7 |
-
-
- | 46 |
- R1904H2 |
- LXS19 |
- 66 |
- M |
- 26 |
- 2 |
- 1523516024 |
- B |
- 13 |
- 7 |
-
-
- | 47 |
- R1883H2 |
- LXS2 |
- 71 |
- F |
- 27 |
- 2 |
- 1523516009 |
- F |
- 12 |
- 6 |
-
-
- | 48 |
- R2753H2 |
- LXS2 |
- 74 |
- M |
- 28 |
- 2 |
- 1523516030 |
- E |
- 4 |
- 2 |
-
-
- | 49 |
- R1729H2 |
- LXS22 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516032 |
- E |
- 7 |
- 4 |
-
-
- | 50 |
- R2743H2 |
- LXS22 |
- 79 |
- M |
- 27 |
- 2 |
- 1562224054 |
- D |
- 21 |
- 10 |
-
-
- | 51 |
- R1966H2 |
- LXS23 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224032 |
- D |
- 15 |
- 8 |
-
-
- | 52 |
- R1971H2 |
- LXS23 |
- 73 |
- M |
- 26 |
- 2 |
- 1562224047 |
- A |
- 16 |
- 8 |
-
-
- | 53 |
- R2795H2 |
- LXS24 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516003 |
- C |
- 1 |
- 1 |
-
-
- | 54 |
- R1755H2 |
- LXS24 |
- 56 |
- M |
- 25 |
- 2 |
- 1523516007 |
- A |
- 11 |
- 6 |
-
-
- | 55 |
- R1986H2 |
- LXS25 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224036 |
- A |
- 17 |
- 9 |
-
-
- | 56 |
- R2006H2 |
- LXS25 |
- 75 |
- M |
- 27 |
- 2 |
- 1562224049 |
- C |
- 18 |
- 9 |
-
-
- | 57 |
- R2014H2 |
- LXS26 |
- 82 |
- F |
- 25 |
- 2 |
- 1562224049 |
- F |
- 18 |
- 9 |
-
-
- | 58 |
- R2009H2 |
- LXS26 |
- 82 |
- M |
- 26 |
- 2 |
- 1562224049 |
- D |
- 18 |
- 9 |
-
-
- | 59 |
- R2824H1 |
- LXS28 |
- 67 |
- F |
- 28 |
- 2 |
- 1562224042 |
- A |
- 27 |
- 12 |
-
-
- | 60 |
- R1753H1 |
- LXS28 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224041 |
- F |
- 26 |
- 12 |
-
-
- | 61 |
- R2765H2 |
- LXS3 |
- 63 |
- F |
- 27 |
- 2 |
- 1523516005 |
- B |
- 5 |
- 3 |
-
-
- | 62 |
- R1898H2 |
- LXS3 |
- 81 |
- M |
- 26 |
- 2 |
- 1562224041 |
- C |
- 26 |
- 12 |
-
-
- | 63 |
- R2764H2 |
- LXS31 |
- 73 |
- F |
- 29 |
- 2 |
- 1562224060 |
- C |
- 22 |
- 10 |
-
-
- | 64 |
- R1908H2 |
- LXS31 |
- 80 |
- M |
- 28 |
- 2 |
- 1523516024 |
- C |
- 13 |
- 7 |
-
-
- | 65 |
- R2758H2 |
- LXS32 |
- 70 |
- F |
- 26 |
- 2 |
- 1523516030 |
- F |
- 4 |
- 2 |
-
-
- | 66 |
- R1743H1 |
- LXS32 |
- 67 |
- M |
- 25 |
- 2 |
- 1562224041 |
- E |
- 26 |
- 12 |
-
-
- | 67 |
- R2794H2 |
- LXS34 |
- 75 |
- F |
- 27 |
- 2 |
- 1562224034 |
- B |
- 23 |
- 11 |
-
-
- | 68 |
- R2870H2 |
- LXS34 |
- 78 |
- F |
- 27 |
- 2 |
- 1562224029 |
- C |
- 28 |
- 13 |
-
-
- | 69 |
- R2746H2 |
- LXS35 |
- 80 |
- F |
- 22 |
- 2 |
- 1523516030 |
- C |
- 4 |
- 2 |
-
-
- | 70 |
- R2747H2 |
- LXS35 |
- 81 |
- M |
- 22 |
- 2 |
- 1562224060 |
- A |
- 22 |
- 10 |
-
-
- | 71 |
- R1968H2 |
- LXS36 |
- 76 |
- F |
- 25 |
- 2 |
- 1562224032 |
- E |
- 15 |
- 8 |
-
-
- | 72 |
- R1640H2 |
- LXS36 |
- 76 |
- M |
- 25 |
- 2 |
- 1523516032 |
- C |
- 7 |
- 4 |
-
-
- | 73 |
- R2835H1 |
- LXS38 |
- 67 |
- F |
- 27 |
- 2 |
- 1523516011 |
- F |
- 2 |
- 1 |
-
-
- | 74 |
- R2842H2 |
- LXS38 |
- 67 |
- M |
- 27 |
- 2 |
- 1562224042 |
- E |
- 27 |
- 12 |
-
-
- | 75 |
- R2210H2 |
- LXS39 |
- 81 |
- F |
- 28 |
- 2 |
- 1562224053 |
- E |
- 20 |
- 10 |
-
-
- | 76 |
- R2736H2 |
- LXS39 |
- 75 |
- M |
- 27 |
- 2 |
- 1523516028 |
- E |
- 3 |
- 2 |
-
-
- | 77 |
- R1978H2 |
- LXS41 |
- 78 |
- F |
- 26 |
- 2 |
- 1562224047 |
- C |
- 16 |
- 8 |
-
-
- | 78 |
- R1783H2 |
- LXS41 |
- 56 |
- M |
- 26 |
- 2 |
- 1523516007 |
- D |
- 11 |
- 6 |
-
-
- | 79 |
- R2822H2 |
- LXS42 |
- 66 |
- F |
- 27 |
- 2 |
- 1562224034 |
- F |
- 23 |
- 11 |
-
-
- | 80 |
- R2769H2 |
- LXS42 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224042 |
- B |
- 27 |
- 12 |
-
-
- | 81 |
- R1974H2 |
- LXS43 |
- 84 |
- F |
- 26 |
- 2 |
- 1562224047 |
- B |
- 16 |
- 8 |
-
-
- | 82 |
- R1733H2 |
- LXS43 |
- 72 |
- M |
- 26 |
- 2 |
- 1523516015 |
- C |
- 10 |
- 5 |
-
-
- | 83 |
- R1756H2 |
- LXS46 |
- 56 |
- F |
- 25 |
- 2 |
- 1523516007 |
- B |
- 11 |
- 6 |
-
-
- | 84 |
- R1727H2 |
- LXS46 |
- 70 |
- M |
- 25 |
- 2 |
- 1523516032 |
- D |
- 7 |
- 4 |
-
-
- | 85 |
- R1970H2 |
- LXS48 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224032 |
- F |
- 15 |
- 8 |
-
-
- | 86 |
- R1981H2 |
- LXS48 |
- 72 |
- M |
- 27 |
- 2 |
- 1562224042 |
- C |
- 27 |
- 12 |
-
-
- | 87 |
- R1957H2 |
- LXS49 |
- 72 |
- F |
- 25 |
- 2 |
- 1523516029 |
- C |
- 14 |
- 7 |
-
-
- | 88 |
- R2259H2 |
- LXS49 |
- 72 |
- M |
- 25 |
- 2 |
- 1523516028 |
- C |
- 3 |
- 2 |
-
-
- | 89 |
- R2836H1 |
- LXS5 |
- 68 |
- F |
- 28 |
- 2 |
- 1523516006 |
- A |
- 6 |
- 3 |
-
-
- | 90 |
- R2213H2 |
- LXS5 |
- 80 |
- M |
- 27 |
- 2 |
- 1562224053 |
- F |
- 20 |
- 10 |
-
-
- | 91 |
- R2791H2 |
- LXS50 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224034 |
- A |
- 23 |
- 11 |
-
-
- | 92 |
- R1789H2 |
- LXS50 |
- 57 |
- M |
- 26 |
- 2 |
- 1523516033 |
- A |
- 8 |
- 4 |
-
-
- | 93 |
- R1740H2 |
- LXS51 |
- 68 |
- F |
- 27 |
- 2 |
- 1523516032 |
- F |
- 7 |
- 4 |
-
-
- | 94 |
- R1734H2 |
- LXS51 |
- 68 |
- M |
- 26 |
- 2 |
- 1523516015 |
- D |
- 10 |
- 5 |
-
-
- | 95 |
- R2786H2 |
- LXS52 |
- 61 |
- F |
- 27 |
- 2 |
- 1562224060 |
- D |
- 22 |
- 10 |
-
-
- | 96 |
- R2768H2 |
- LXS52 |
- 61 |
- M |
- 27 |
- 2 |
- 1523516005 |
- C |
- 5 |
- 3 |
-
-
- | 97 |
- R2154H2 |
- LXS54 |
- 70 |
- F |
- 27 |
- 2 |
- 1523516033 |
- D |
- 8 |
- 4 |
-
-
- | 98 |
- R2155H2 |
- LXS54 |
- 70 |
- M |
- 27 |
- 2 |
- 1562224053 |
- A |
- 20 |
- 10 |
-
-
- | 99 |
- R1821H2 |
- LXS55 |
- 77 |
- F |
- 25 |
- 2 |
- 1523516009 |
- C |
- 12 |
- 6 |
-
-
- | 100 |
- R1951H2 |
- LXS55 |
- 74 |
- M |
- 26 |
- 2 |
- 1523516024 |
- F |
- 13 |
- 7 |
-
-
- | 101 |
- R2789H2 |
- LXS56 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516005 |
- F |
- 5 |
- 3 |
-
-
- | 102 |
- R2788H2 |
- LXS56 |
- 71 |
- M |
- 25 |
- 2 |
- 1562224060 |
- F |
- 22 |
- 10 |
-
-
- | 103 |
- R2787H2 |
- LXS59 |
- 66 |
- F |
- 29 |
- 2 |
- 1562224060 |
- E |
- 22 |
- 10 |
-
-
- | 104 |
- R2785H2 |
- LXS59 |
- 62 |
- M |
- 29 |
- 2 |
- 1523516005 |
- E |
- 5 |
- 3 |
-
-
- | 105 |
- R1791H2 |
- LXS60 |
- 58 |
- F |
- 27 |
- 2 |
- 1562224038 |
- D |
- 25 |
- 11 |
-
-
- | 106 |
- R1792H2 |
- LXS60 |
- 64 |
- M |
- 27 |
- 2 |
- 1523516007 |
- E |
- 11 |
- 6 |
-
-
- | 107 |
- R1796H2 |
- LXS62 |
- 58 |
- F |
- 27 |
- 2 |
- 1523516007 |
- F |
- 11 |
- 6 |
-
-
- | 108 |
- R1797H2 |
- LXS62 |
- 58 |
- M |
- 27 |
- 2 |
- 1562224038 |
- E |
- 25 |
- 11 |
-
-
- | 109 |
- R2220H2 |
- LXS64 |
- 71 |
- F |
- 28 |
- 2 |
- 1523516001 |
- F |
- 9 |
- 5 |
-
-
- | 110 |
- R2221H2 |
- LXS64 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- B |
- 21 |
- 10 |
-
-
- | 111 |
- R1989H2 |
- LXS66 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224036 |
- B |
- 17 |
- 9 |
-
-
- | 112 |
- R1843H2 |
- LXS66 |
- 78 |
- M |
- 27 |
- 2 |
- 1523516009 |
- E |
- 12 |
- 6 |
-
-
- | 113 |
- R2820H2 |
- LXS68 |
- 67 |
- F |
- 29 |
- 2 |
- 1523516003 |
- E |
- 1 |
- 1 |
-
-
- | 114 |
- R2819H2 |
- LXS68 |
- 67 |
- M |
- 29 |
- 2 |
- 1562224034 |
- E |
- 23 |
- 11 |
-
-
- | 115 |
- R1963H2 |
- LXS7 |
- 78 |
- F |
- 28 |
- 2 |
- 1562224032 |
- B |
- 15 |
- 8 |
-
-
- | 116 |
- R1964H2 |
- LXS7 |
- 78 |
- M |
- 28 |
- 2 |
- 1562224032 |
- C |
- 15 |
- 8 |
-
-
- | 117 |
- R2166H2 |
- LXS70 |
- 72 |
- F |
- 27 |
- 2 |
- 1523516033 |
- F |
- 8 |
- 4 |
-
-
- | 118 |
- R2745H2 |
- LXS70 |
- 71 |
- M |
- 28 |
- 2 |
- 1562224054 |
- F |
- 21 |
- 10 |
-
-
- | 119 |
- R2848H2 |
- LXS72 |
- 72 |
- F |
- 27 |
- 2 |
- 1562224038 |
- A |
- 25 |
- 11 |
-
-
- | 120 |
- R1902H2 |
- LXS72 |
- 66 |
- M |
- 27 |
- 2 |
- 1523516024 |
- A |
- 13 |
- 7 |
-
-
- | 121 |
- R2750H2 |
- LXS73 |
- 81 |
- F |
- 25 |
- 2 |
- 1523516030 |
- D |
- 4 |
- 2 |
-
-
- | 122 |
- R1835H2 |
- LXS73 |
- 90 |
- M |
- 24 |
- 2 |
- 1523516009 |
- D |
- 12 |
- 6 |
-
-
- | 123 |
- R1979H2 |
- LXS75 |
- 59 |
- F |
- 27 |
- 2 |
- 1562224047 |
- D |
- 16 |
- 8 |
-
-
- | 124 |
- R2826H2 |
- LXS75 |
- 72 |
- M |
- 27 |
- 2 |
- 1523516003 |
- F |
- 1 |
- 1 |
-
-
- | 125 |
- R2142H2 |
- LXS76 |
- 77 |
- F |
- 26 |
- 2 |
- 1562224050 |
- E |
- 19 |
- 9 |
-
-
- | 126 |
- R1884H2 |
- LXS76 |
- 85 |
- M |
- 26 |
- 2 |
- 1562224041 |
- A |
- 26 |
- 12 |
-
-
- | 127 |
- R1959H2 |
- LXS78 |
- 69 |
- F |
- 26 |
- 2 |
- 1523516029 |
- E |
- 14 |
- 7 |
-
-
- | 128 |
- R1958H2 |
- LXS78 |
- 69 |
- M |
- 26 |
- 2 |
- 1523516029 |
- D |
- 14 |
- 7 |
-
-
- | 129 |
- R2845H1 |
- LXS8 |
- 70 |
- F |
- 28 |
- 2 |
- 1523516006 |
- C |
- 6 |
- 3 |
-
-
- | 130 |
- R2156H2 |
- LXS8 |
- 76 |
- M |
- 27 |
- 2 |
- 1562224053 |
- B |
- 20 |
- 10 |
-
-
- | 131 |
- R1955H2 |
- LXS80 |
- 71 |
- F |
- 25 |
- 2 |
- 1523516029 |
- A |
- 14 |
- 7 |
-
-
- | 132 |
- R1956H2 |
- LXS80 |
- 71 |
- M |
- 25 |
- 2 |
- 1523516029 |
- B |
- 14 |
- 7 |
-
-
- | 133 |
- R2830H1 |
- LXS84 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516011 |
- D |
- 2 |
- 1 |
-
-
- | 134 |
- R2829H2 |
- LXS84 |
- 66 |
- M |
- 26 |
- 2 |
- 1562224037 |
- A |
- 24 |
- 11 |
-
-
- | 135 |
- R2839H2 |
- LXS86 |
- 68 |
- F |
- 27 |
- 2 |
- 1562224037 |
- C |
- 24 |
- 11 |
-
-
- | 136 |
- R2838H1 |
- LXS86 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516006 |
- B |
- 6 |
- 3 |
-
-
- | 137 |
- R2882H1 |
- LXS87 |
- 66 |
- F |
- 27 |
- 2 |
- 1523516006 |
- F |
- 6 |
- 3 |
-
-
- | 138 |
- R2744H2 |
- LXS87 |
- 71 |
- M |
- 26 |
- 2 |
- 1562224054 |
- E |
- 21 |
- 10 |
-
-
- | 139 |
- R2831H2 |
- LXS88 |
- 69 |
- F |
- 27 |
- 2 |
- 1562224037 |
- B |
- 24 |
- 11 |
-
-
- | 140 |
- R2762H2 |
- LXS88 |
- 71 |
- M |
- 27 |
- 2 |
- 1523516005 |
- A |
- 5 |
- 3 |
-
-
- | 141 |
- R2828H1 |
- LXS89 |
- 75 |
- F |
- 26 |
- 2 |
- 1523516011 |
- C |
- 2 |
- 1 |
-
-
- | 142 |
- R1962H2 |
- LXS89 |
- 73 |
- M |
- 25 |
- 2 |
- 1562224032 |
- A |
- 15 |
- 8 |
-
-
- | 143 |
- R1746H2 |
- LXS9 |
- 66 |
- F |
- 26 |
- 2 |
- 1523516015 |
- F |
- 10 |
- 5 |
-
-
- | 144 |
- R2801H2 |
- LXS9 |
- 68 |
- M |
- 27 |
- 2 |
- 1523516003 |
- D |
- 1 |
- 1 |
-
-
- | 145 |
- R1812H2 |
- LXS90 |
- 61 |
- F |
- 25 |
- 2 |
- 1562224038 |
- F |
- 25 |
- 11 |
-
-
- | 146 |
- R1813H2 |
- LXS90 |
- 61 |
- M |
- 25 |
- 2 |
- 1523516009 |
- A |
- 12 |
- 6 |
-
-
- | 147 |
- R1736H2 |
- LXS92 |
- 66 |
- F |
- 23 |
- 2 |
- 1523516015 |
- E |
- 10 |
- 5 |
-
-
- | 148 |
- R1609H2 |
- LXS92 |
- 87 |
- M |
- 23 |
- 2 |
- 1523516032 |
- A |
- 7 |
- 4 |
-
-
- | 149 |
- R1624H2 |
- LXS93 |
- 74 |
- F |
- 26 |
- 2 |
- 1523516032 |
- B |
- 7 |
- 4 |
-
-
- | 150 |
- R1815H2 |
- LXS93 |
- 61 |
- M |
- 26 |
- 2 |
- 1523516009 |
- B |
- 12 |
- 6 |
-
-
- | 151 |
- R1991H2 |
- LXS94 |
- 70 |
- F |
- 25 |
- 2 |
- 1562224036 |
- C |
- 17 |
- 9 |
-
-
- | 152 |
- R2002H2 |
- LXS94 |
- 70 |
- M |
- 25 |
- 2 |
- 1562224049 |
- B |
- 18 |
- 9 |
-
-
- | 153 |
- R1996H2 |
- LXS96 |
- 75 |
- F |
- 23 |
- 2 |
- 1562224036 |
- F |
- 17 |
- 9 |
-
-
- | 154 |
- R1772H2 |
- LXS96 |
- 63 |
- M |
- 23 |
- 2 |
- 1523516007 |
- C |
- 11 |
- 6 |
-
-
- | 155 |
- R2759H2 |
- LXS97 |
- 73 |
- F |
- 26 |
- 2 |
- 1562224060 |
- B |
- 22 |
- 10 |
-
-
- | 156 |
- R2739H2 |
- LXS97 |
- 79 |
- M |
- 26 |
- 2 |
- 1523516028 |
- F |
- 3 |
- 2 |
-
-
- | 157 |
- R2149H2 |
- LXS98 |
- 78 |
- F |
- 26 |
- 2 |
- 1523516033 |
- C |
- 8 |
- 4 |
-
-
- | 158 |
- R1888H2 |
- LXS98 |
- 76 |
- M |
- 26 |
- 2 |
- 1562224041 |
- B |
- 26 |
- 12 |
-
-
- | 159 |
- R1644H2 |
- LXS99 |
- 79 |
- F |
- 26 |
- 2 |
- 1523516015 |
- B |
- 10 |
- 5 |
-
-
- | 160 |
- R2145H2 |
- LXS99 |
- 77 |
- M |
- 27 |
- 2 |
- 1562224050 |
- F |
- 19 |
- 9 |
-
-
-
- |
-
-
-
-
-
- |
-
-
- |
- Downloading all data:
-
- All data links (right-most column above) will be available as soon as the global analysis of these data has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of data. Please contact Dr. Lu Lu if you have any questions on the use of these open data.
- |
-
-
-
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/experiment-design.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/experiment-design.rtf
deleted file mode 100644
index f477cb7..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Experimental Design and Batch Structure: This data set consists arrays processed in 13 groups over a five month period (July 2006 to Dec 2006). Most groups consisted of 12 samples. All arrays in this data set were processed using a single protocol by a single operator, Feng Yiao. Processing was supervised directly by Dr. Lu Lu. All samples were scanned on a single Illumina Beadstation housed in the Hamilton Eye Institute between July 28 and Dec 21, 2006. Details on sample assignment to slides and batches is provide in the table below.
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/notes.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/notes.rtf
deleted file mode 100644
index 938409b..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ANNOTATION: In spring of 2007, Robert W. Williams and Hongqiang Li reannotated the Illumina Mouse-6 array content. This new annotation is now incorporated into GeneNetwork. For 46166 probes on the Mouse 6 array platform (including control probes) we have identified 35975 NCBI Entrez Gene IDs; 26481 matched human Gene IDs; 23899 matched rat Gene IDs; 26883 NCBI HomoloGene IDs; and 12791 OMIM IDs.
-
-Position data for the 50-mer Illumina Mouse-6 array were initially downloaded from Sanger at http://www.sanger.ac.uk/Users/avc/Illumina/Mouse-6_V1.gff.gz but we then updated all positions by BLAT analysis from mm6 positions to mm8 positions (Hongqiang Li).
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/platform.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/platform.rtf
deleted file mode 100644
index 2ac899d..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/platform.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-About the array platform:
-
-Illumina Sentrix Mouse-6 BeadArray Platform: The Mouse6 array consists of 46,116 unique probe sequences, each 50 nucleotides in length, that have been arrayed on glass slides using a novel bead technology.
-
-Dunning M, Smith M, Thorne N, Tavare S (2006) beadarray: An R package to analyse Illumina BeadArrays. R News (the Newsletter of the P Project) 6:17-23. (see pages 17-23 of http://CRAN.R-project.org/doc/Rnews/Rnews_2006-5.pdf).
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/processing.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/processing.rtf
deleted file mode 100644
index c3d0555..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-This data set uses the LOESS with Variance Stabilizing Transform (VST) and Background correction from the lumi package downloaded from Bioconductor (http://www.bioconductor.org/). For the more detailed information, please see the lumi package documentation.
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/summary.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/summary.rtf
deleted file mode 100644
index ebfc03f..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/summary.rtf
+++ /dev/null
@@ -1,33 +0,0 @@
-August 07 ILLUMINA Mouse-6 DATA SET RSN: The LXS Hippocampus Illumina Robust Spline Normalization with No Background correction data set provides estimates of mRNA expression in the hippocampus of 75 LXS recombinant inbred strains, the two parental strains, ILS/Ibg and ISS/Ibg (Inbred Long Sleep and Inbred Short Sleep strains from the Institute of Behavioral Genetics), and the two reciprocal F1 strains (ILSXISSF1, ISSXILSF1). All samples are from normal adult control animals raised in a standard laboratory environment. Subsequent data sets will provide estimates of mRNA expression following restraint stress, ethanol treatment, and stress followed by ethanol using many of the same strains (Lu Lu and colleagues).
-
-A total of 240 pooled hippocampal samples were processed using 40 Illumina Sentrix Mouse-6 v 1.0 oligomer microarray BeadArray slides. Twenty-seven Mouse-6 slides and a total of 160 samples passed stringent quality control and error checking. We should note that this is our first experience using the Illumina platform and the initial set of 13 slides were not included. This particular data set was processed using the Illumina "Robust Spline Normalization with No Background Correction" protocol. Values were log2 transformed and the current data range from 6.481 average (very low or no expression) to 24.852 (extremely high).
-
-As a measure of data quality we often count the number of probes that are associated with LOD scores of greater than 10 (LRS > 46). In this Hippocampus Illumina (Aug 07) RSN data set, ### probes have LRS values >46.
-
-In comparison, here are the yields of QTLs with LOD>10 for other closely related data sets:
-
-
- - 1050 for Hippocampus Illumina (Aug07) LOESS
- - 1162 for Hippocampus Illumina (Aug07) LOESS_NB
- - 1129 for Hippocampus Illumina (Aug07) QUANT
- - 1176 for Hippocampus Illumina (Aug07) QUANT_NB
- - NO DATA for Hippocampus Illumina (Aug07) RSN
- - NO DATA for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 1183 for Hippocampus Illumina (May 07) RankInv
- - 1167 for Hippocampus Illumina (Oct06) Rank
- - 1170 for Hippocampus Illumina (Oct06) RankInv
-
-
-The LRS achieved in the different version of the LXS Hippocampus data for probe ILM103520706 (Disabled 1; Dab1) are as follow
-
-
- - 338.4 for Hippocampus Illumina (Aug07) LOESS
- - 339.8 for Hippocampus Illumina (Aug07) LOESS_NB
- - 370.2 for Hippocampus Illumina (Aug07) QUANT
- - 363.5 for Hippocampus Illumina (Aug07) QUANT_NB
- - 374.8 for Hippocampus Illumina (Aug07) RSN
- - 363.0 for Hippocampus Illumina (Aug07) RSN_NB (THIS DATA SET)
- - 360.3 for Hippocampus Illumina (May 07) RankInv
- - 358.1 for Hippocampus Illumina (Oct06) Rank
- - 358.8 for Hippocampus Illumina (Oct06) RankInv
-
diff --git a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/tissue.rtf b/general/datasets/Illum_LXS_Hipp_rsn_nb0807/tissue.rtf
deleted file mode 100644
index febccce..0000000
--- a/general/datasets/Illum_LXS_Hipp_rsn_nb0807/tissue.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-About the animals and tissue used to generate this set of data:
-
-All animals were raised at the IBG by Bennett and colleagues in an SPF facility. No cases were MHV positive. Mice were killed by cervical dislocation. Whole brain dissections were performed at the IBG by Bennett and colleagues and shipped in RNAlater to Lu Lu and colleagues at UTHSC. Most hippocampal dissections (all were bilateral) were performed by Zhiping Jia. Cerebella, olfactory bulbs, and brain stems were also dissected and stored at -80 deg C using further use. Hippocampal samples are very close to complete (see Lu et al., 2001 but probably include variable amounts of fimbria and choroid plexus (see expression of transthyretin, Ttr, as a marker of choroid plexus).
-
-A pool of dissected tissue from four hippocampi taken from two naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia.
-
-All animals used in this study were between 53 and 90 days of age (average of 72 days; see Table 1 below).
-
-
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/acknowledgment.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/acknowledgment.rtf
deleted file mode 100644
index a41ff76..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/acknowledgment.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The HEI Retinal Database is supported by National Eye Institute Grants:
-
-
-
-
- - R01EY017841 (Dr. Eldon E. Geisert, PI)
-
-
- - P030EY13080 (NEI Vision Core Grant), and
-
-
- - A Unrestricted Grand from Research to Prevent Blindness (Dr. Barrett Haik, PI)
-
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/cases.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/cases.rtf
deleted file mode 100644
index b37d700..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/cases.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 48 and maximum age is 118 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J.
-
-BXD strains:
-
-
- - The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s.
- - In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset.
- - The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set.
-
-
-
-
-What Makes the G2 HEI Retina Database different from the HEI Retina Database Examination of Gfap expression across all of the strains in the HEI Retinal Dataset, reveals that some strains express very high levels of Gfap relative to others. For example, BXD24 expresses Gfap at a 9-fold higher level, than BXD22. It has been established that BXD24 acquired a mutation in Cep290 that results in early onset photoreceptor degeneration (Chang et al., 2006). This degeneration results in reactive gliosis throughout the retina. In addition to BXD24, other BXD strains expressed very high levels of Gfap including: BXD32, BXD49, BXD70, BXD83 and BXD89. For the G2 dataset all of these strains with potential reactive gliosis were removed from the dataset.
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/experiment-design.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/experiment-design.rtf
deleted file mode 100644
index 4fff707..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/experiment-design.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Expression profiling by array
-
-We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.
-
-All normalization was performed by William E. Orr in the HEI Vision Core Facility
-
-
- - Computed the log base 2 of each raw signal value
- - Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
- - Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/notes.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/notes.rtf
deleted file mode 100644
index 13ff99a..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/platform.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/platform.rtf
deleted file mode 100644
index 2c52707..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina MouseWG-6 v2.0 arrays: The Illumina Sentrix Mouse-6 BeadChip uses 50-nucleotide probes to interrogate approximately 46,000 sequences from the mouse transcriptome. For each array, the RNA was pooled from two retinas.
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/processing.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/processing.rtf
deleted file mode 100644
index 97cc2be..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/processing.rtf
+++ /dev/null
@@ -1,2654 +0,0 @@
-Values of all 45,281 probe sets in this data set range from a low of 6.25 (Rho GTPase activating protein 11A, Arhgap11a, probe ID ILMN_2747167) to a high of 18.08 (Ubiquitin B, Ubb, probe ID ILMN_2516699). This corresponds to 11.83 units or a 1 to 3641 dynamic range of expression (2^11.83). We normalized raw signal values using Beadstudio’s rank invariant normalization algorithm. BXD62 was the strain used as the control group
-
-
-
-Sample Processing: Drs. Natalie E. Freeman-Anderson and Justin P. Templeton extracted the retinas from the mice and Dr. Natalie Freeman-Anderson processed all samples in the HEI Vision Core Facility. The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX) listed above. The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system. The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA. The cRNA for each sample was then hybridized to an Illumina Sentrix® Mouse-6-V2 BeadChip (Illumina, San Diego, CA)
-
-
-
-
-
-Quality control analysis of the raw image data was performed using the Illumina BeadStudio software. MIAME standards were used for all microarray data. Rank invariant normalization with BeadStudio software was used to calculate the data. Once this data was collected, the data was globally normalized across all samples using the formula 2 (z-score of log2 [intensity]) + 8.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.
-
-Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice
-
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain |
- Age |
- Sex |
- Source of Animal |
-
-
- | 1 |
- 121608_11-C57BL/6JcFA |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 2 |
- 121608_12-C57BL/6JcFB |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 3 |
- KA7444-C57BL/6JcMC |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 4 |
- KA7444-C57BL/6JcMD |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 5 |
- 31209.05-DBA2JcFA |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 6 |
- 31209.05-DBA2JcFB |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 7 |
- 121608_13-DBA/2JcMA |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 8 |
- 121608_14-DBA/2JcMB |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 9 |
- KA7446-B6D2F1cFA |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 10 |
- KA7446-B6D2F1cFB |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 11 |
- KA7446-B6D2F1cMC |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 12 |
- KA7446-B6D2F1cMD |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 13 |
- KA7466-D2B6F1cFA |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 14 |
- KA7466-D2B6F1cFB |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 15 |
- KA7466-D2B6F1cMC |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 16 |
- KA7466-D2B6F1cMD |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 17 |
- 82609.13-1cFA |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 18 |
- 82609.14-1cFB |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 19 |
- KA7389-1cFA |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 20 |
- KA7389-1cFB |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 21 |
- KA7389-1cMC |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 22 |
- KA7389-1cMD |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 23 |
- KA7300-2cFA |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 24 |
- KA7300-2cFB |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 25 |
- 100909.01-2cMA |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 26 |
- 100909.02-2cMB |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 27 |
- KA6699-5cFA |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 28 |
- KA6699-5cFB |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 29 |
- KA6699-5cFC |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 30 |
- KA6699-5cFD |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 31 |
- 82609.09-5cMA |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 32 |
- 82609.1-5cMB |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 33 |
- KA6763-6cFA |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 34 |
- KA6763-6cFB |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 35 |
- 81209.06-6cMA |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 36 |
- 81209.07-6cMB |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 37 |
- 82609.07-8cFA |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 38 |
- 82609.08-8cFB |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 39 |
- JAX-8cMA |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 40 |
- JAX-8cMB |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 41 |
- KA7289-9cFA |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 42 |
- KA7289-9cFB |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 43 |
- KA7289-9cMC |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 44 |
- KA7289-9cMD |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 45 |
- JAX-11cFA |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 46 |
- JAX-11cFB |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 47 |
- JAX-11cMC |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 48 |
- JAX-11cMD |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 49 |
- 40209.07-12cFA |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 50 |
- 40209.08-12cFB |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 51 |
- 011309.01-12cMA |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 52 |
- 011309.02-12cMB |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 53 |
- KA7286-13cFA |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 54 |
- KA7286-13cFB |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 55 |
- KA7286-13cMC |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 56 |
- KA7286-13cMD |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 57 |
- KA7302-14cFA |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 58 |
- KA7302-14cFB |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 59 |
- 100909.05-14cMA |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 60 |
- 100909.06-14cMB |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 61 |
- KA7288-15cFA |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 62 |
- KA7288-15cFB |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 63 |
- KA7288-15cMC |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 64 |
- KA7288-15cMD |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 65 |
- 062509.01-16cFA |
- BXD16 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 66 |
- KA7267-16cMA |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 67 |
- KA7267-16cMB |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 68 |
- KA6686-18cFB |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 69 |
- KA6686-18cFC |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 70 |
- KA6686-18cME |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 71 |
- KA6686-18cMF |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 72 |
- KA6676-19cFB |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 73 |
- KA6676-19cFC |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 74 |
- KA6676-19cME |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 75 |
- KA6676-19cMF |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 76 |
- 060409.05-20cFA |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- 060409.06-20cFB |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 78 |
- 021909.03-20cMA |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 79 |
- 021909.04-20cMB |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 80 |
- 82609.02-21cFC |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 81 |
- 82609.03-21cFD |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 82 |
- 121709.01-21cMA |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 83 |
- 121709.02-21cMB |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 84 |
- 121709.03-22cFA |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 85 |
- 121709.04-22cFB |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 86 |
- 092308_03-22cMA |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 87 |
- 092308_04-22cMB |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 88 |
- 80409.01-24AcFA |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 89 |
- 080409_02_24AcFB |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 90 |
- 82609.26-24AcFC |
- BXD24A |
- 64 |
- F |
- UTHSC RW |
-
-
- | 91 |
- 81209.03-24AcMC |
- BXD24A |
- 62 |
- M |
- UTHSC RW |
-
-
- | 92 |
- KA6678-24cFA |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 93 |
- KA6678-24cFB |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 94 |
- KA6678-24cME |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 95 |
- KA6678-24cMF |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- 060409.07-27cFA |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 97 |
- 060409.08-27cFB |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 98 |
- 80409.03-27cMA |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 99 |
- 80409.04-27cMB |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 100 |
- JAX-28cFA |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 101 |
- JAX-28cFB |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 102 |
- JAX-28cMC |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 103 |
- JAX-28cMD |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 104 |
- 82609.11-29cFA |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 105 |
- 82609.12-29cFB |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 106 |
- 82609.04-29cMA |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 107 |
- 82609.05-29cMB |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 108 |
- JAX-31cMB |
- BXD 31 |
- 56 |
- M |
- JAX |
-
-
- | 109 |
- JAX-31cFC |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 110 |
- JAX-31cFD |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 111 |
- 011309.03-32cFA |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 112 |
- 011309.04-32cFB |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 113 |
- KA7318-32cFC |
- BXD32 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 114 |
- KA7319-32cMA |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 115 |
- KA7319-32cMB |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 116 |
- 100909.07-33cFA |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 117 |
- 100909.08-33cFB |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 118 |
- 022609.01-33cMA |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 119 |
- 022609.02-33cMB |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 120 |
- KA7416-34cFA |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 121 |
- KA7416-34cFB |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 122 |
- KA6321-34cMA |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 123 |
- KA6321-34cMB |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 124 |
- 060409.01-36cFA |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 125 |
- 060409.02-36cFB |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 126 |
- 060409.03-36cMC |
- BXD36 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 127 |
- KA6702-38cFA |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 128 |
- KA6702-38cFB |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 129 |
- 82609.24-38cFA |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 130 |
- 82609.25-38cFB |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 131 |
- 100909.03-38cMA |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 132 |
- 100909.04-38cMB |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 133 |
- 022609.05-39cFA |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 134 |
- 022609.06-39cFB |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 135 |
- 31209.01-39cMC |
- BXD39 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 136 |
- 92409.01-40cFA |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 137 |
- 92409.02-40cFB |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 138 |
- KA6173-40cMA |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 139 |
- KA6173-40cMB |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 140 |
- KA6173-40cMC |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 141 |
- 091809.01-42cFA |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 142 |
- 091809.02-42cFB |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 143 |
- 021909.01-42cFA |
- BXD42 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 144 |
- 011309.06-42cMA |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 145 |
- 011309.07-42cMB |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- 110408_02-43cFA |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 147 |
- 110408_03-43cFB |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 148 |
- KA6158-43cMA |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 149 |
- KA6158-43cMB |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 150 |
- 100308_01-44cFA |
- BXD44 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 151 |
- 102208_02-44cMD |
- BXD44 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 152 |
- 103009.03-45cFA |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 153 |
- 103009.04-45cFB |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 154 |
- 022609.03-45cFA |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 155 |
- 022609.04-45cFB |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 156 |
- 40309.05-45cMB |
- BXD45 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 157 |
- 40209.05-48cFB |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 158 |
- 40209.06-48cFC |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 159 |
- 81209.04-48cMA |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 160 |
- 81209.05-48cMB |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 161 |
- 81209.08-49cFA |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 162 |
- 81209.09-49cFB |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 163 |
- 40209.01-49cMA |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 164 |
- 40209.02-49cMB |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 165 |
- 40209.03-49cMC |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 166 |
- KA737850cFA |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 167 |
- KA737850cFB |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 168 |
- 121908_01-50cMA |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 169 |
- 121908_02-50cMB |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 170 |
- 111208_01-51cFA |
- BXD51 |
- 99 |
- F |
- UTHSC RW |
-
-
- | 171 |
- 102208_03-51cMA |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 172 |
- 102208_04-51cMB |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 173 |
- 090208_14-53BcFA |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 174 |
- 090208_15-53BcFB |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 175 |
- 090208_16-53BcMC |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 176 |
- 090208_17-53BcMD |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 177 |
- 111208_05-55cFB |
- BXD55 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 178 |
- KA6183-55cMA |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 179 |
- KA6183-55cMB |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 180 |
- KA7362-56cFB |
- BXD 56 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 181 |
- KA6088-56cMA |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 182 |
- KA6088-56cMB |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 183 |
- KA6088-56cMC |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 184 |
- 21810.01-60RFA |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 185 |
- 21810.02-60RFB |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 186 |
- 21810.02-60RFC |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 187 |
- SQ7325-60cMA |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 188 |
- SQ7325-60cMB |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 189 |
- 092308_10-61cFA |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 190 |
- 092308_11-61cFB |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 191 |
- 31909.01-61cMA |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 192 |
- 31909.02-61cMB |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 193 |
- KA7462-62cFA |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 194 |
- KA7462-62cFB |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 195 |
- KA5996-62cMA |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 196 |
- KA5996-62cMB |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 197 |
- KA5996-62cMC |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 198 |
- 090309.01-63cFA |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 199 |
- 090309.02-63cFB |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 200 |
- 110609.01-63cMA |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 201 |
- 110609.02-63cMB |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 202 |
- 091809.03-65cFA |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 203 |
- 091809.04-65cFB |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 204 |
- 103009.01-65cMA |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 205 |
- 103009.02-65cMB |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 206 |
- 110408_05-66cFB |
- BXD66 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 207 |
- KA7165-66cMA |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 208 |
- KA7165-66cMB |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 209 |
- 90809.01-67cMA |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 210 |
- 90809.02-67cMB |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 211 |
- 110609.03-67cFA |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 212 |
- 110609.04-67cFB |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 213 |
- 120408_01-68cFA |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 214 |
- 120408_02-68cFB |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 215 |
- SQ7205-68cMA |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 216 |
- SQ7205-68cMB |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 217 |
- KA6316-68cMA |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 218 |
- KA6316-68cMB |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 219 |
- KA6316-68cMC |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 220 |
- KA76-69cFA |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 221 |
- KA76-69cFB |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 222 |
- KA6074-69cMA |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 223 |
- KA6074-69cMB |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 224 |
- 121608_01-70cFA |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 225 |
- 121608_02-70cFB |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 226 |
- KA7394-70cMA |
- BXD70 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 227 |
- 81209.08-70cMA |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 228 |
- 81209.09-70cMB |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 229 |
- 052809.01-71cFA |
- BXD71 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 230 |
- 060409.09-71cMA |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 231 |
- 060409.10-71cMB |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 232 |
- 40809.01-73cFA |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 233 |
- 40809.02-73cFB |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 234 |
- 111708_01-73cFA |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 235 |
- 111708_01-73cFB |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 236 |
- KA6164-73cMB |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 237 |
- KA6164-73cMC |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 238 |
- 82609.22-74cFA |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 239 |
- 82609.23-74cFB |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 240 |
- 82609.20-74cMA |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 241 |
- 82609.21-74cMB |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 242 |
- KA733675cFA |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 243 |
- KA733675cFB |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 244 |
- KA38-75cMB |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 245 |
- KA38-75cMC |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 246 |
- 41509.01-77cFA |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 247 |
- 41509.02-77cFB |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 248 |
- 41509.03-77cMC |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 249 |
- 41509.04-77cMD |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 250 |
- 121608_03-80cFA |
- BXD80 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 251 |
- 121608_05-80cMC |
- BXD80 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 252 |
- KA23-80cMC |
- BXD80 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 253 |
- KA7305-81cFA |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 254 |
- KA7305-81cFB |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 255 |
- KA7305-81cMD |
- BXD81 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 256 |
- 060409.11-83cFA |
- BXD83 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 257 |
- KA24-83cFA |
- BXD83 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 258 |
- 121608_07-83cMA |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 259 |
- 121608_08-83cMB |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 260 |
- KA24-83cMD |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 261 |
- 090409.05-84cFA |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 262 |
- 090409.06-84cFB |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 263 |
- KA6203-84cMA |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 264 |
- KA6203-84cMB |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 265 |
- 40309.02-85cFD |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 266 |
- 40309.03-85cFE |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 267 |
- 32609.01-85cMA |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 268 |
- 32609.02-85cMB |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 269 |
- 41509.05-86cFA |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 270 |
- 41509.06-86cFB |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 271 |
- KA6101-86cMA |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 272 |
- KA6101-86cMC |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 273 |
- 070909.02-87cFA |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 274 |
- 070909.03-87cFB |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 275 |
- KA7407-87cMA |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 276 |
- KA7407-87cMB |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 277 |
- 102208_05-89cFA |
- BXD89 |
- 82 |
- F |
- UTHSC RW |
-
-
- | 278 |
- KA5974-89cMA |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 279 |
- KA5974-89cMB |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 280 |
- 102208_06-89cMC |
- BXD89 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 281 |
- 72309.01-90cFA |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 282 |
- 72309.02-90cFB |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 283 |
- 090409.03-90cMA |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 284 |
- 090409.04-90cMB |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 285 |
- KA6094-92cMA |
- BXD92 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 286 |
- 020609.01-95cFA |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 287 |
- 020609.02-95cFB |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 288 |
- KA6181-95cMA |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 289 |
- KA6181-95cMB |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 290 |
- 31209.03-96cFA |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 291 |
- 31209.04-96cFB |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 292 |
- KA7246-96cMA |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 293 |
- KA7246-96cMB |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 294 |
- 81209.10-97cFA |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 295 |
- 81209.11-97cFB |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 296 |
- 81209.1-97cMA |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 297 |
- 81209.11-97cMB |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 298 |
- SQ7520-98cFA |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 299 |
- SQ7520-98cFB |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 300 |
- SQ7520-98cMC |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 301 |
- SQ7520-98cMD |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 302 |
- 82609.17-99cFA |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 303 |
- 82609.18-99cFB |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 304 |
- 81409.01-99cMA |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 305 |
- 81409.02-99cMB |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 306 |
- 121608_09-100cFA |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 307 |
- 121608_10-100cFB |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 308 |
- KA6001-100cMA |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 309 |
- KA6001-100cMB |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 310 |
- 81209.12-101cFA |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 311 |
- 81209.13-101cFB |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 312 |
- KA7296-101cMA |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 313 |
- KA7296-101cMB |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 314 |
- 92409.03-102cFA |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 315 |
- 92409.04-102cFB |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 316 |
- KA7380-102cMA |
- BXD102 |
- 115 |
- M |
- UTHSC RW |
-
-
- | 317 |
- 43009.01-103cFA |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 318 |
- 43009.02-103cFB |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 319 |
- KA79-103cFA |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 320 |
- KA79-103cFB |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 321 |
- KA79-103cMC |
- BXD103 |
- 48 |
- M |
- UTHSC RW |
-
-
- | 322 |
- 82609.15-103cMA |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 323 |
- 82609.16-103cMB |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 324 |
- 102909.01-BALBCcFA |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 325 |
- 102909.02-BALBCcFB |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 326 |
- 102909.03-BALBCcMA |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
- | 327 |
- 102909.04-BALBCcMB |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/summary.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/summary.rtf
deleted file mode 100644
index 44e98a7..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/summary.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-
-This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork.
-
-HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified.
-
-COMMENT on FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set.
-
-The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as BXD24/TyJ-Cep290/J, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243).
-
-The data are now open and available for analysis.
-
-Please cite: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text PDF or HTML
-
-This is rank invariant expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.25 to 18.08 (11.83 units), a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.
-
-The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842.
-
-The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.
-
-
-
-
-Other Related Publications
-
-
-
-
-
- - Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (Link)
- - Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674
- - Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (Link)
- - Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90.(Link)
-
-
-
-
-
-
-
-Other Data Sets Users of these mouse retina data may also find the following complementary resources useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
-
diff --git a/general/datasets/Illum_Retina_BXD_RankInv0410/tissue.rtf b/general/datasets/Illum_Retina_BXD_RankInv0410/tissue.rtf
deleted file mode 100644
index 766ab59..0000000
--- a/general/datasets/Illum_Retina_BXD_RankInv0410/tissue.rtf
+++ /dev/null
@@ -1,32 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RNAlater at room temperature. Two retinas from one mouse were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.
-
-
-
-Dissecting and preparing eyes for RNA extraction
-
-
-
-Retinas for RNA extraction were placed in RNA STAT-60 (Tel-Test Inc.) and processed per manufacturer’s instructions (in brief form below). Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
-
-
- - Homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue via syringe)
- - Allow the homogenate to stand for 5-10 min at room temperature
- - Add 0.2 ml of chloroform per 1 ml RNA STAT-60
- - Mix the sample vigorously for 15 sec and let the sample incubate at room temperature for 5-10 min
- - Centrifuge at 12,000 g for 1 hr at 4°C
- - Transfer the aqueous phase to a clean centrifuge tube
- - Add 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - Vortex and incubate the sample at -20°C for 1 hr or overnight
- - Centrifuge at 12,000 g for 1 hr
- - Remove the supernatant and wash the RNA pellet with 75% ethanol
- - Remove ethanol, let air dry (5-10 min)
- - Dissolve the pellet in 50 μl of nuclease free water.
-
-
-
-
diff --git a/general/datasets/Inia_macfas_ac_rma_0110/experiment-type.rtf b/general/datasets/Inia_macfas_ac_rma_0110/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Inia_macfas_ac_rma_0110/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Inia_macfas_amg_rma_0110/experiment-type.rtf b/general/datasets/Inia_macfas_amg_rma_0110/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Inia_macfas_amg_rma_0110/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Inia_macfas_brain_rma_0110/experiment-type.rtf b/general/datasets/Inia_macfas_brain_rma_0110/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Inia_macfas_brain_rma_0110/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Inia_macfas_hc_rma_0110/experiment-type.rtf b/general/datasets/Inia_macfas_hc_rma_0110/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Inia_macfas_hc_rma_0110/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Inia_macfas_pf_rma_0110/experiment-type.rtf b/general/datasets/Inia_macfas_pf_rma_0110/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Inia_macfas_pf_rma_0110/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/IoP_SPL_RMA_0509/notes.rtf b/general/datasets/IoP_SPL_RMA_0509/notes.rtf
deleted file mode 100644
index b75c94f..0000000
--- a/general/datasets/IoP_SPL_RMA_0509/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Spleen mRNA expression levels are measured for 77 individual BXD RI mice from 24 different strains. The expressed gene set were characterised using the Affymetrix Mouse430_2.0 GeneChip which encompass over 34,000 known genes.
diff --git a/general/datasets/IoP_SPL_RMA_0509/summary.rtf b/general/datasets/IoP_SPL_RMA_0509/summary.rtf
deleted file mode 100644
index 53231ef..0000000
--- a/general/datasets/IoP_SPL_RMA_0509/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 74, Name: IoP Affy MOE 430v2 Spleen (May09)
diff --git a/general/datasets/JAX_CSB_L_0711/acknowledgment.rtf b/general/datasets/JAX_CSB_L_0711/acknowledgment.rtf
deleted file mode 100644
index 04d1867..0000000
--- a/general/datasets/JAX_CSB_L_0711/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Churchill GA, Paigen B, Shockley KR, Witmer D
diff --git a/general/datasets/JAX_CSB_L_0711/cases.rtf b/general/datasets/JAX_CSB_L_0711/cases.rtf
deleted file mode 100644
index 4c44710..0000000
--- a/general/datasets/JAX_CSB_L_0711/cases.rtf
+++ /dev/null
@@ -1,1030 +0,0 @@
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain ID |
- HF=high-fat (30% fat)
- 6C=low-fat (6% fat) |
- Replicate Animal |
-
-
- | 1 |
- GSM264767 |
- 129S1/SvImJ |
- 6C |
- Rep1 |
-
-
- | 2 |
- GSM264768 |
- 129S1/SvImJ |
- 6C |
- Rep2 |
-
-
- | 3 |
- GSM264769 |
- 129S1/SvImJ |
- 6C |
- Rep3 |
-
-
- | 4 |
- GSM264770 |
- 129S1/SvImJ |
- HF |
- Rep1 |
-
-
- | 5 |
- GSM264771 |
- 129S1/SvImJ |
- HF |
- Rep2 |
-
-
- | 6 |
- GSM264772 |
- 129S1/SvImJ |
- HF |
- Rep3 |
-
-
- | 7 |
- GSM264773 |
- 129S1/SvImJ |
- 6C |
- Rep1 |
-
-
- | 8 |
- GSM264774 |
- 129S1/SvImJ |
- 6C |
- Rep2 |
-
-
- | 9 |
- GSM264775 |
- 129S1/SvImJ |
- 6C |
- Rep3 |
-
-
- | 10 |
- GSM264776 |
- 129S1/SvImJ |
- HF |
- Rep1 |
-
-
- | 11 |
- GSM264777 |
- 129S1/SvImJ |
- HF |
- Rep2 |
-
-
- | 12 |
- GSM264778 |
- 129S1/SvImJ |
- HF |
- Rep3 |
-
-
- | 13 |
- GSM264779 |
- A/J |
- 6C |
- Rep1 |
-
-
- | 14 |
- GSM264780 |
- A/J |
- 6C |
- Rep2 |
-
-
- | 15 |
- GSM264781 |
- A/J |
- 6C |
- Rep3 |
-
-
- | 16 |
- GSM264782 |
- A/J |
- HF |
- Rep1 |
-
-
- | 17 |
- GSM264783 |
- A/J |
- HF |
- Rep2 |
-
-
- | 18 |
- GSM264784 |
- A/J |
- HF |
- Rep3 |
-
-
- | 19 |
- GSM264785 |
- A/J |
- 6C |
- Rep1 |
-
-
- | 20 |
- GSM264786 |
- A/J |
- 6C |
- Rep2 |
-
-
- | 21 |
- GSM264787 |
- A/J |
- 6C |
- Rep3 |
-
-
- | 22 |
- GSM264788 |
- A/J |
- HF |
- Rep1 |
-
-
- | 23 |
- GSM264789 |
- A/J |
- HF |
- Rep2 |
-
-
- | 24 |
- GSM264790 |
- A/J |
- HF |
- Rep3 |
-
-
- | 25 |
- GSM264791 |
- C57BL/6J |
- 6C |
- Rep1 |
-
-
- | 26 |
- GSM264792 |
- C57BL/6J |
- 6C |
- Rep2 |
-
-
- | 27 |
- GSM264793 |
- C57BL/6J |
- 6C |
- Rep3 |
-
-
- | 28 |
- GSM264794 |
- C57BL/6J |
- HF |
- Rep1 |
-
-
- | 29 |
- GSM264795 |
- C57BL/6J |
- HF |
- Rep2 |
-
-
- | 30 |
- GSM264796 |
- C57BL/6J |
- HF |
- Rep3 |
-
-
- | 31 |
- GSM264797 |
- C57BL/6J |
- 6C |
- Rep1 |
-
-
- | 32 |
- GSM264798 |
- C57BL/6J |
- 6C |
- Rep2 |
-
-
- | 33 |
- GSM264799 |
- C57BL/6J |
- 6C |
- Rep3 |
-
-
- | 34 |
- GSM264800 |
- C57BL/6J |
- HF |
- Rep1 |
-
-
- | 35 |
- GSM264801 |
- C57BL/6J |
- HF |
- Rep2 |
-
-
- | 36 |
- GSM264802 |
- C57BL/6J |
- HF |
- Rep3 |
-
-
- | 37 |
- GSM264803 |
- BALB/cJ |
- 6C |
- Rep1 |
-
-
- | 38 |
- GSM264804 |
- BALB/cJ |
- 6C |
- Rep2 |
-
-
- | 39 |
- GSM264805 |
- BALB/cJ |
- 6C |
- Rep3 |
-
-
- | 40 |
- GSM264806 |
- BALB/cJ |
- HF |
- Rep1 |
-
-
- | 41 |
- GSM264807 |
- BALB/cJ |
- HF |
- Rep2 |
-
-
- | 42 |
- GSM264808 |
- BALB/cJ |
- HF |
- Rep3 |
-
-
- | 43 |
- GSM264809 |
- BALB/cJ |
- 6C |
- Rep1 |
-
-
- | 44 |
- GSM264810 |
- BALB/cJ |
- 6C |
- Rep2 |
-
-
- | 45 |
- GSM264811 |
- BALB/cJ |
- 6C |
- Rep3 |
-
-
- | 46 |
- GSM264813 |
- BALB/cJ |
- HF |
- Rep1 |
-
-
- | 47 |
- GSM264814 |
- BALB/cJ |
- HF |
- Rep2 |
-
-
- | 48 |
- GSM264815 |
- BALB/cJ |
- HF |
- Rep3 |
-
-
- | 49 |
- GSM264845 |
- C3H/HeJ |
- 6C |
- Rep1 |
-
-
- | 50 |
- GSM264846 |
- C3H/HeJ |
- 6C |
- Rep2 |
-
-
- | 51 |
- GSM264847 |
- C3H/HeJ |
- 6C |
- Rep3 |
-
-
- | 52 |
- GSM264848 |
- C3H/HeJ |
- HF |
- Rep1 |
-
-
- | 53 |
- GSM264849 |
- C3H/HeJ |
- HF |
- Rep2 |
-
-
- | 54 |
- GSM264850 |
- C3H/HeJ |
- HF |
- Rep3 |
-
-
- | 55 |
- GSM264852 |
- C3H/HeJ |
- 6C |
- Rep1 |
-
-
- | 56 |
- GSM264853 |
- C3H/HeJ |
- 6C |
- Rep2 |
-
-
- | 57 |
- GSM264855 |
- C3H/HeJ |
- 6C |
- Rep3 |
-
-
- | 58 |
- GSM264856 |
- C3H/HeJ |
- HF |
- Rep1 |
-
-
- | 59 |
- GSM264857 |
- C3H/HeJ |
- HF |
- Rep2 |
-
-
- | 60 |
- GSM264858 |
- C3H/HeJ |
- HF |
- Rep3 |
-
-
- | 61 |
- GSM264859 |
- CAST/EiJ |
- 6C |
- Rep1 |
-
-
- | 62 |
- GSM264861 |
- CAST/EiJ |
- 6C |
- Rep2 |
-
-
- | 63 |
- GSM264862 |
- CAST/EiJ |
- 6C |
- Rep3 |
-
-
- | 64 |
- GSM264863 |
- CAST/EiJ |
- HF |
- Rep1 |
-
-
- | 65 |
- GSM264864 |
- CAST/EiJ |
- HF |
- Rep2 |
-
-
- | 66 |
- GSM264865 |
- CAST/EiJ |
- HF |
- Rep3 |
-
-
- | 67 |
- GSM264866 |
- CAST/EiJ |
- 6C |
- Rep1 |
-
-
- | 68 |
- GSM264867 |
- CAST/EiJ |
- 6C |
- Rep2 |
-
-
- | 69 |
- GSM264868 |
- CAST/EiJ |
- 6C |
- Rep3 |
-
-
- | 70 |
- GSM264869 |
- CAST/EiJ |
- HF |
- Rep1 |
-
-
- | 71 |
- GSM264870 |
- CAST/EiJ |
- HF |
- Rep2 |
-
-
- | 72 |
- GSM264871 |
- CAST/EiJ |
- HF |
- Rep3 |
-
-
- | 73 |
- GSM264872 |
- DBA/2J |
- 6C |
- Rep1 |
-
-
- | 74 |
- GSM264873 |
- DBA/2J |
- 6C |
- Rep2 |
-
-
- | 75 |
- GSM264874 |
- DBA/2J |
- 6C |
- Rep3 |
-
-
- | 76 |
- GSM264875 |
- DBA/2J |
- HF |
- Rep1 |
-
-
- | 77 |
- GSM264876 |
- DBA/2J |
- HF |
- Rep2 |
-
-
- | 78 |
- GSM264877 |
- DBA/2J |
- HF |
- Rep3 |
-
-
- | 79 |
- GSM264890 |
- DBA/2J |
- 6C |
- Rep1 |
-
-
- | 80 |
- GSM264891 |
- DBA/2J |
- 6C |
- Rep2 |
-
-
- | 81 |
- GSM264892 |
- DBA/2J |
- 6C |
- Rep3 |
-
-
- | 82 |
- GSM264893 |
- DBA/2J |
- HF |
- Rep1 |
-
-
- | 83 |
- GSM264894 |
- DBA/2J |
- HF |
- Rep2 |
-
-
- | 84 |
- GSM264895 |
- DBA/2J |
- HF |
- Rep3 |
-
-
- | 85 |
- GSM264896 |
- I/LnJ |
- 6C |
- Rep1 |
-
-
- | 86 |
- GSM264897 |
- I/LnJ |
- 6C |
- Rep2 |
-
-
- | 87 |
- GSM264898 |
- I/LnJ |
- 6C |
- Rep3 |
-
-
- | 88 |
- GSM264899 |
- I/LnJ |
- HF |
- Rep1 |
-
-
- | 89 |
- GSM264900 |
- I/LnJ |
- HF |
- Rep2 |
-
-
- | 90 |
- GSM264901 |
- I/LnJ |
- HF |
- Rep3 |
-
-
- | 91 |
- GSM264902 |
- I/LnJ |
- 6C |
- Rep1 |
-
-
- | 92 |
- GSM264903 |
- I/LnJ |
- 6C |
- Rep2 |
-
-
- | 93 |
- GSM264904 |
- I/LnJ |
- 6C |
- Rep3 |
-
-
- | 94 |
- GSM264905 |
- I/LnJ |
- HF |
- Rep1 |
-
-
- | 95 |
- GSM264906 |
- I/LnJ |
- HF |
- Rep2 |
-
-
- | 96 |
- GSM264907 |
- I/LnJ |
- HF |
- Rep3 |
-
-
- | 97 |
- GSM264908 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep1 |
-
-
- | 98 |
- GSM264909 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep2 |
-
-
- | 99 |
- GSM264910 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep3 |
-
-
- | 100 |
- GSM264912 |
- MRL/MpJ-Fas/J |
- HF |
- Rep1 |
-
-
- | 101 |
- GSM264913 |
- MRL/MpJ-Fas/J |
- HF |
- Rep2 |
-
-
- | 102 |
- GSM264914 |
- MRL/MpJ-Fas/J |
- HF |
- Rep3 |
-
-
- | 103 |
- GSM264915 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep1 |
-
-
- | 104 |
- GSM264916 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep2 |
-
-
- | 105 |
- GSM264917 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep3 |
-
-
- | 106 |
- GSM264918 |
- MRL/MpJ-Fas/J |
- HF |
- Rep1 |
-
-
- | 107 |
- GSM264920 |
- MRL/MpJ-Fas/J |
- HF |
- Rep2 |
-
-
- | 108 |
- GSM264921 |
- MRL/MpJ-Fas/J |
- HF |
- Rep3 |
-
-
- | 109 |
- GSM264922 |
- NZB/BlNJ |
- 6C |
- Rep1 |
-
-
- | 110 |
- GSM264924 |
- NZB/BlNJ |
- 6C |
- Rep2 |
-
-
- | 111 |
- GSM264925 |
- NZB/BlNJ |
- 6C |
- Rep3 |
-
-
- | 112 |
- GSM264926 |
- NZB/BlNJ |
- HF |
- Rep1 |
-
-
- | 113 |
- GSM264928 |
- NZB/BlNJ |
- HF |
- Rep2 |
-
-
- | 114 |
- GSM264929 |
- NZB/BlNJ |
- HF |
- Rep3 |
-
-
- | 115 |
- GSM264930 |
- NZB/BlNJ |
- 6C |
- Rep1 |
-
-
- | 116 |
- GSM264931 |
- NZB/BlNJ |
- 6C |
- Rep2 |
-
-
- | 117 |
- GSM264932 |
- NZB/BlNJ |
- 6C |
- Rep3 |
-
-
- | 118 |
- GSM264933 |
- NZB/BlNJ |
- HF |
- Rep1 |
-
-
- | 119 |
- GSM264935 |
- NZB/BlNJ |
- HF |
- Rep2 |
-
-
- | 120 |
- GSM264936 |
- NZB/BlNJ |
- HF |
- Rep3 |
-
-
- | 121 |
- GSM265061 |
- PERA/EiJ |
- 6C |
- Rep1 |
-
-
- | 122 |
- GSM265062 |
- PERA/EiJ |
- 6C |
- Rep2 |
-
-
- | 123 |
- GSM265063 |
- PERA/EiJ |
- 6C |
- Rep3 |
-
-
- | 124 |
- GSM265064 |
- PERA/EiJ |
- HF |
- Rep1 |
-
-
- | 125 |
- GSM265065 |
- PERA/EiJ |
- HF |
- Rep2 |
-
-
- | 126 |
- GSM265066 |
- PERA/EiJ |
- HF |
- Rep3 |
-
-
- | 127 |
- GSM265067 |
- PERA/EiJ |
- 6C |
- Rep1 |
-
-
- | 128 |
- GSM265068 |
- PERA/EiJ |
- 6C |
- Rep2 |
-
-
- | 129 |
- GSM265069 |
- PERA/EiJ |
- 6C |
- Rep3 |
-
-
- | 130 |
- GSM265070 |
- PERA/EiJ |
- HF |
- Rep1 |
-
-
- | 131 |
- GSM265071 |
- PERA/EiJ |
- HF |
- Rep2 |
-
-
- | 132 |
- GSM265072 |
- PERA/EiJ |
- HF |
- Rep3 |
-
-
- | 133 |
- GSM265074 |
- SM/J |
- 6C |
- Rep1 |
-
-
- | 134 |
- GSM265075 |
- SM/J |
- 6C |
- Rep2 |
-
-
- | 135 |
- GSM265105 |
- SM/J |
- 6C |
- Rep3 |
-
-
- | 136 |
- GSM265217 |
- SM/J |
- HF |
- Rep1 |
-
-
- | 137 |
- GSM265248 |
- SM/J |
- HF |
- Rep2 |
-
-
- | 138 |
- GSM265275 |
- SM/J |
- HF |
- Rep3 |
-
-
- | 139 |
- GSM265324 |
- SM/J |
- 6C |
- Rep1 |
-
-
- | 140 |
- GSM265331 |
- SM/J |
- 6C |
- Rep2 |
-
-
- | 141 |
- GSM265357 |
- SM/J |
- 6C |
- Rep3 |
-
-
- | 142 |
- GSM265358 |
- SM/J |
- HF |
- Rep1 |
-
-
- | 143 |
- GSM265359 |
- SM/J |
- HF |
- Rep2 |
-
-
- | 144 |
- GSM265360 |
- SM/J |
- HF |
- Rep3 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/JAX_CSB_L_0711/experiment-design.rtf b/general/datasets/JAX_CSB_L_0711/experiment-design.rtf
deleted file mode 100644
index dc5fef5..0000000
--- a/general/datasets/JAX_CSB_L_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Expression profiling by array.
-
-One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet. Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.
diff --git a/general/datasets/JAX_CSB_L_0711/platform.rtf b/general/datasets/JAX_CSB_L_0711/platform.rtf
deleted file mode 100644
index 459d486..0000000
--- a/general/datasets/JAX_CSB_L_0711/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array. Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html All probe sets represented on the GeneChip Mouse Expression Set 430 are included on the GeneChip Mouse Genome 430 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank«, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute for Genome Research (MGSC, April 2002).
diff --git a/general/datasets/JAX_CSB_L_0711/summary.rtf b/general/datasets/JAX_CSB_L_0711/summary.rtf
deleted file mode 100644
index a06430b..0000000
--- a/general/datasets/JAX_CSB_L_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-High-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis. Keywords: gene expression analysis, strain comparision, effect of dietary fat, sex-specific effects
diff --git a/general/datasets/JAX_CSB_L_0711/tissue.rtf b/general/datasets/JAX_CSB_L_0711/tissue.rtf
deleted file mode 100644
index 778c4a2..0000000
--- a/general/datasets/JAX_CSB_L_0711/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver
diff --git a/general/datasets/JAX_CSB_L_6C_0711/acknowledgment.rtf b/general/datasets/JAX_CSB_L_6C_0711/acknowledgment.rtf
deleted file mode 100644
index 04d1867..0000000
--- a/general/datasets/JAX_CSB_L_6C_0711/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Churchill GA, Paigen B, Shockley KR, Witmer D
diff --git a/general/datasets/JAX_CSB_L_6C_0711/cases.rtf b/general/datasets/JAX_CSB_L_6C_0711/cases.rtf
deleted file mode 100644
index 4c44710..0000000
--- a/general/datasets/JAX_CSB_L_6C_0711/cases.rtf
+++ /dev/null
@@ -1,1030 +0,0 @@
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain ID |
- HF=high-fat (30% fat)
- 6C=low-fat (6% fat) |
- Replicate Animal |
-
-
- | 1 |
- GSM264767 |
- 129S1/SvImJ |
- 6C |
- Rep1 |
-
-
- | 2 |
- GSM264768 |
- 129S1/SvImJ |
- 6C |
- Rep2 |
-
-
- | 3 |
- GSM264769 |
- 129S1/SvImJ |
- 6C |
- Rep3 |
-
-
- | 4 |
- GSM264770 |
- 129S1/SvImJ |
- HF |
- Rep1 |
-
-
- | 5 |
- GSM264771 |
- 129S1/SvImJ |
- HF |
- Rep2 |
-
-
- | 6 |
- GSM264772 |
- 129S1/SvImJ |
- HF |
- Rep3 |
-
-
- | 7 |
- GSM264773 |
- 129S1/SvImJ |
- 6C |
- Rep1 |
-
-
- | 8 |
- GSM264774 |
- 129S1/SvImJ |
- 6C |
- Rep2 |
-
-
- | 9 |
- GSM264775 |
- 129S1/SvImJ |
- 6C |
- Rep3 |
-
-
- | 10 |
- GSM264776 |
- 129S1/SvImJ |
- HF |
- Rep1 |
-
-
- | 11 |
- GSM264777 |
- 129S1/SvImJ |
- HF |
- Rep2 |
-
-
- | 12 |
- GSM264778 |
- 129S1/SvImJ |
- HF |
- Rep3 |
-
-
- | 13 |
- GSM264779 |
- A/J |
- 6C |
- Rep1 |
-
-
- | 14 |
- GSM264780 |
- A/J |
- 6C |
- Rep2 |
-
-
- | 15 |
- GSM264781 |
- A/J |
- 6C |
- Rep3 |
-
-
- | 16 |
- GSM264782 |
- A/J |
- HF |
- Rep1 |
-
-
- | 17 |
- GSM264783 |
- A/J |
- HF |
- Rep2 |
-
-
- | 18 |
- GSM264784 |
- A/J |
- HF |
- Rep3 |
-
-
- | 19 |
- GSM264785 |
- A/J |
- 6C |
- Rep1 |
-
-
- | 20 |
- GSM264786 |
- A/J |
- 6C |
- Rep2 |
-
-
- | 21 |
- GSM264787 |
- A/J |
- 6C |
- Rep3 |
-
-
- | 22 |
- GSM264788 |
- A/J |
- HF |
- Rep1 |
-
-
- | 23 |
- GSM264789 |
- A/J |
- HF |
- Rep2 |
-
-
- | 24 |
- GSM264790 |
- A/J |
- HF |
- Rep3 |
-
-
- | 25 |
- GSM264791 |
- C57BL/6J |
- 6C |
- Rep1 |
-
-
- | 26 |
- GSM264792 |
- C57BL/6J |
- 6C |
- Rep2 |
-
-
- | 27 |
- GSM264793 |
- C57BL/6J |
- 6C |
- Rep3 |
-
-
- | 28 |
- GSM264794 |
- C57BL/6J |
- HF |
- Rep1 |
-
-
- | 29 |
- GSM264795 |
- C57BL/6J |
- HF |
- Rep2 |
-
-
- | 30 |
- GSM264796 |
- C57BL/6J |
- HF |
- Rep3 |
-
-
- | 31 |
- GSM264797 |
- C57BL/6J |
- 6C |
- Rep1 |
-
-
- | 32 |
- GSM264798 |
- C57BL/6J |
- 6C |
- Rep2 |
-
-
- | 33 |
- GSM264799 |
- C57BL/6J |
- 6C |
- Rep3 |
-
-
- | 34 |
- GSM264800 |
- C57BL/6J |
- HF |
- Rep1 |
-
-
- | 35 |
- GSM264801 |
- C57BL/6J |
- HF |
- Rep2 |
-
-
- | 36 |
- GSM264802 |
- C57BL/6J |
- HF |
- Rep3 |
-
-
- | 37 |
- GSM264803 |
- BALB/cJ |
- 6C |
- Rep1 |
-
-
- | 38 |
- GSM264804 |
- BALB/cJ |
- 6C |
- Rep2 |
-
-
- | 39 |
- GSM264805 |
- BALB/cJ |
- 6C |
- Rep3 |
-
-
- | 40 |
- GSM264806 |
- BALB/cJ |
- HF |
- Rep1 |
-
-
- | 41 |
- GSM264807 |
- BALB/cJ |
- HF |
- Rep2 |
-
-
- | 42 |
- GSM264808 |
- BALB/cJ |
- HF |
- Rep3 |
-
-
- | 43 |
- GSM264809 |
- BALB/cJ |
- 6C |
- Rep1 |
-
-
- | 44 |
- GSM264810 |
- BALB/cJ |
- 6C |
- Rep2 |
-
-
- | 45 |
- GSM264811 |
- BALB/cJ |
- 6C |
- Rep3 |
-
-
- | 46 |
- GSM264813 |
- BALB/cJ |
- HF |
- Rep1 |
-
-
- | 47 |
- GSM264814 |
- BALB/cJ |
- HF |
- Rep2 |
-
-
- | 48 |
- GSM264815 |
- BALB/cJ |
- HF |
- Rep3 |
-
-
- | 49 |
- GSM264845 |
- C3H/HeJ |
- 6C |
- Rep1 |
-
-
- | 50 |
- GSM264846 |
- C3H/HeJ |
- 6C |
- Rep2 |
-
-
- | 51 |
- GSM264847 |
- C3H/HeJ |
- 6C |
- Rep3 |
-
-
- | 52 |
- GSM264848 |
- C3H/HeJ |
- HF |
- Rep1 |
-
-
- | 53 |
- GSM264849 |
- C3H/HeJ |
- HF |
- Rep2 |
-
-
- | 54 |
- GSM264850 |
- C3H/HeJ |
- HF |
- Rep3 |
-
-
- | 55 |
- GSM264852 |
- C3H/HeJ |
- 6C |
- Rep1 |
-
-
- | 56 |
- GSM264853 |
- C3H/HeJ |
- 6C |
- Rep2 |
-
-
- | 57 |
- GSM264855 |
- C3H/HeJ |
- 6C |
- Rep3 |
-
-
- | 58 |
- GSM264856 |
- C3H/HeJ |
- HF |
- Rep1 |
-
-
- | 59 |
- GSM264857 |
- C3H/HeJ |
- HF |
- Rep2 |
-
-
- | 60 |
- GSM264858 |
- C3H/HeJ |
- HF |
- Rep3 |
-
-
- | 61 |
- GSM264859 |
- CAST/EiJ |
- 6C |
- Rep1 |
-
-
- | 62 |
- GSM264861 |
- CAST/EiJ |
- 6C |
- Rep2 |
-
-
- | 63 |
- GSM264862 |
- CAST/EiJ |
- 6C |
- Rep3 |
-
-
- | 64 |
- GSM264863 |
- CAST/EiJ |
- HF |
- Rep1 |
-
-
- | 65 |
- GSM264864 |
- CAST/EiJ |
- HF |
- Rep2 |
-
-
- | 66 |
- GSM264865 |
- CAST/EiJ |
- HF |
- Rep3 |
-
-
- | 67 |
- GSM264866 |
- CAST/EiJ |
- 6C |
- Rep1 |
-
-
- | 68 |
- GSM264867 |
- CAST/EiJ |
- 6C |
- Rep2 |
-
-
- | 69 |
- GSM264868 |
- CAST/EiJ |
- 6C |
- Rep3 |
-
-
- | 70 |
- GSM264869 |
- CAST/EiJ |
- HF |
- Rep1 |
-
-
- | 71 |
- GSM264870 |
- CAST/EiJ |
- HF |
- Rep2 |
-
-
- | 72 |
- GSM264871 |
- CAST/EiJ |
- HF |
- Rep3 |
-
-
- | 73 |
- GSM264872 |
- DBA/2J |
- 6C |
- Rep1 |
-
-
- | 74 |
- GSM264873 |
- DBA/2J |
- 6C |
- Rep2 |
-
-
- | 75 |
- GSM264874 |
- DBA/2J |
- 6C |
- Rep3 |
-
-
- | 76 |
- GSM264875 |
- DBA/2J |
- HF |
- Rep1 |
-
-
- | 77 |
- GSM264876 |
- DBA/2J |
- HF |
- Rep2 |
-
-
- | 78 |
- GSM264877 |
- DBA/2J |
- HF |
- Rep3 |
-
-
- | 79 |
- GSM264890 |
- DBA/2J |
- 6C |
- Rep1 |
-
-
- | 80 |
- GSM264891 |
- DBA/2J |
- 6C |
- Rep2 |
-
-
- | 81 |
- GSM264892 |
- DBA/2J |
- 6C |
- Rep3 |
-
-
- | 82 |
- GSM264893 |
- DBA/2J |
- HF |
- Rep1 |
-
-
- | 83 |
- GSM264894 |
- DBA/2J |
- HF |
- Rep2 |
-
-
- | 84 |
- GSM264895 |
- DBA/2J |
- HF |
- Rep3 |
-
-
- | 85 |
- GSM264896 |
- I/LnJ |
- 6C |
- Rep1 |
-
-
- | 86 |
- GSM264897 |
- I/LnJ |
- 6C |
- Rep2 |
-
-
- | 87 |
- GSM264898 |
- I/LnJ |
- 6C |
- Rep3 |
-
-
- | 88 |
- GSM264899 |
- I/LnJ |
- HF |
- Rep1 |
-
-
- | 89 |
- GSM264900 |
- I/LnJ |
- HF |
- Rep2 |
-
-
- | 90 |
- GSM264901 |
- I/LnJ |
- HF |
- Rep3 |
-
-
- | 91 |
- GSM264902 |
- I/LnJ |
- 6C |
- Rep1 |
-
-
- | 92 |
- GSM264903 |
- I/LnJ |
- 6C |
- Rep2 |
-
-
- | 93 |
- GSM264904 |
- I/LnJ |
- 6C |
- Rep3 |
-
-
- | 94 |
- GSM264905 |
- I/LnJ |
- HF |
- Rep1 |
-
-
- | 95 |
- GSM264906 |
- I/LnJ |
- HF |
- Rep2 |
-
-
- | 96 |
- GSM264907 |
- I/LnJ |
- HF |
- Rep3 |
-
-
- | 97 |
- GSM264908 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep1 |
-
-
- | 98 |
- GSM264909 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep2 |
-
-
- | 99 |
- GSM264910 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep3 |
-
-
- | 100 |
- GSM264912 |
- MRL/MpJ-Fas/J |
- HF |
- Rep1 |
-
-
- | 101 |
- GSM264913 |
- MRL/MpJ-Fas/J |
- HF |
- Rep2 |
-
-
- | 102 |
- GSM264914 |
- MRL/MpJ-Fas/J |
- HF |
- Rep3 |
-
-
- | 103 |
- GSM264915 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep1 |
-
-
- | 104 |
- GSM264916 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep2 |
-
-
- | 105 |
- GSM264917 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep3 |
-
-
- | 106 |
- GSM264918 |
- MRL/MpJ-Fas/J |
- HF |
- Rep1 |
-
-
- | 107 |
- GSM264920 |
- MRL/MpJ-Fas/J |
- HF |
- Rep2 |
-
-
- | 108 |
- GSM264921 |
- MRL/MpJ-Fas/J |
- HF |
- Rep3 |
-
-
- | 109 |
- GSM264922 |
- NZB/BlNJ |
- 6C |
- Rep1 |
-
-
- | 110 |
- GSM264924 |
- NZB/BlNJ |
- 6C |
- Rep2 |
-
-
- | 111 |
- GSM264925 |
- NZB/BlNJ |
- 6C |
- Rep3 |
-
-
- | 112 |
- GSM264926 |
- NZB/BlNJ |
- HF |
- Rep1 |
-
-
- | 113 |
- GSM264928 |
- NZB/BlNJ |
- HF |
- Rep2 |
-
-
- | 114 |
- GSM264929 |
- NZB/BlNJ |
- HF |
- Rep3 |
-
-
- | 115 |
- GSM264930 |
- NZB/BlNJ |
- 6C |
- Rep1 |
-
-
- | 116 |
- GSM264931 |
- NZB/BlNJ |
- 6C |
- Rep2 |
-
-
- | 117 |
- GSM264932 |
- NZB/BlNJ |
- 6C |
- Rep3 |
-
-
- | 118 |
- GSM264933 |
- NZB/BlNJ |
- HF |
- Rep1 |
-
-
- | 119 |
- GSM264935 |
- NZB/BlNJ |
- HF |
- Rep2 |
-
-
- | 120 |
- GSM264936 |
- NZB/BlNJ |
- HF |
- Rep3 |
-
-
- | 121 |
- GSM265061 |
- PERA/EiJ |
- 6C |
- Rep1 |
-
-
- | 122 |
- GSM265062 |
- PERA/EiJ |
- 6C |
- Rep2 |
-
-
- | 123 |
- GSM265063 |
- PERA/EiJ |
- 6C |
- Rep3 |
-
-
- | 124 |
- GSM265064 |
- PERA/EiJ |
- HF |
- Rep1 |
-
-
- | 125 |
- GSM265065 |
- PERA/EiJ |
- HF |
- Rep2 |
-
-
- | 126 |
- GSM265066 |
- PERA/EiJ |
- HF |
- Rep3 |
-
-
- | 127 |
- GSM265067 |
- PERA/EiJ |
- 6C |
- Rep1 |
-
-
- | 128 |
- GSM265068 |
- PERA/EiJ |
- 6C |
- Rep2 |
-
-
- | 129 |
- GSM265069 |
- PERA/EiJ |
- 6C |
- Rep3 |
-
-
- | 130 |
- GSM265070 |
- PERA/EiJ |
- HF |
- Rep1 |
-
-
- | 131 |
- GSM265071 |
- PERA/EiJ |
- HF |
- Rep2 |
-
-
- | 132 |
- GSM265072 |
- PERA/EiJ |
- HF |
- Rep3 |
-
-
- | 133 |
- GSM265074 |
- SM/J |
- 6C |
- Rep1 |
-
-
- | 134 |
- GSM265075 |
- SM/J |
- 6C |
- Rep2 |
-
-
- | 135 |
- GSM265105 |
- SM/J |
- 6C |
- Rep3 |
-
-
- | 136 |
- GSM265217 |
- SM/J |
- HF |
- Rep1 |
-
-
- | 137 |
- GSM265248 |
- SM/J |
- HF |
- Rep2 |
-
-
- | 138 |
- GSM265275 |
- SM/J |
- HF |
- Rep3 |
-
-
- | 139 |
- GSM265324 |
- SM/J |
- 6C |
- Rep1 |
-
-
- | 140 |
- GSM265331 |
- SM/J |
- 6C |
- Rep2 |
-
-
- | 141 |
- GSM265357 |
- SM/J |
- 6C |
- Rep3 |
-
-
- | 142 |
- GSM265358 |
- SM/J |
- HF |
- Rep1 |
-
-
- | 143 |
- GSM265359 |
- SM/J |
- HF |
- Rep2 |
-
-
- | 144 |
- GSM265360 |
- SM/J |
- HF |
- Rep3 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/JAX_CSB_L_6C_0711/experiment-design.rtf b/general/datasets/JAX_CSB_L_6C_0711/experiment-design.rtf
deleted file mode 100644
index dc5fef5..0000000
--- a/general/datasets/JAX_CSB_L_6C_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Expression profiling by array.
-
-One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet. Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.
diff --git a/general/datasets/JAX_CSB_L_6C_0711/platform.rtf b/general/datasets/JAX_CSB_L_6C_0711/platform.rtf
deleted file mode 100644
index 459d486..0000000
--- a/general/datasets/JAX_CSB_L_6C_0711/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array. Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html All probe sets represented on the GeneChip Mouse Expression Set 430 are included on the GeneChip Mouse Genome 430 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank«, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute for Genome Research (MGSC, April 2002).
diff --git a/general/datasets/JAX_CSB_L_6C_0711/summary.rtf b/general/datasets/JAX_CSB_L_6C_0711/summary.rtf
deleted file mode 100644
index a06430b..0000000
--- a/general/datasets/JAX_CSB_L_6C_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-High-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis. Keywords: gene expression analysis, strain comparision, effect of dietary fat, sex-specific effects
diff --git a/general/datasets/JAX_CSB_L_6C_0711/tissue.rtf b/general/datasets/JAX_CSB_L_6C_0711/tissue.rtf
deleted file mode 100644
index 778c4a2..0000000
--- a/general/datasets/JAX_CSB_L_6C_0711/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver
diff --git a/general/datasets/JAX_CSB_L_HF_0711/acknowledgment.rtf b/general/datasets/JAX_CSB_L_HF_0711/acknowledgment.rtf
deleted file mode 100644
index 04d1867..0000000
--- a/general/datasets/JAX_CSB_L_HF_0711/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Churchill GA, Paigen B, Shockley KR, Witmer D
diff --git a/general/datasets/JAX_CSB_L_HF_0711/cases.rtf b/general/datasets/JAX_CSB_L_HF_0711/cases.rtf
deleted file mode 100644
index 4c44710..0000000
--- a/general/datasets/JAX_CSB_L_HF_0711/cases.rtf
+++ /dev/null
@@ -1,1030 +0,0 @@
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain ID |
- HF=high-fat (30% fat)
- 6C=low-fat (6% fat) |
- Replicate Animal |
-
-
- | 1 |
- GSM264767 |
- 129S1/SvImJ |
- 6C |
- Rep1 |
-
-
- | 2 |
- GSM264768 |
- 129S1/SvImJ |
- 6C |
- Rep2 |
-
-
- | 3 |
- GSM264769 |
- 129S1/SvImJ |
- 6C |
- Rep3 |
-
-
- | 4 |
- GSM264770 |
- 129S1/SvImJ |
- HF |
- Rep1 |
-
-
- | 5 |
- GSM264771 |
- 129S1/SvImJ |
- HF |
- Rep2 |
-
-
- | 6 |
- GSM264772 |
- 129S1/SvImJ |
- HF |
- Rep3 |
-
-
- | 7 |
- GSM264773 |
- 129S1/SvImJ |
- 6C |
- Rep1 |
-
-
- | 8 |
- GSM264774 |
- 129S1/SvImJ |
- 6C |
- Rep2 |
-
-
- | 9 |
- GSM264775 |
- 129S1/SvImJ |
- 6C |
- Rep3 |
-
-
- | 10 |
- GSM264776 |
- 129S1/SvImJ |
- HF |
- Rep1 |
-
-
- | 11 |
- GSM264777 |
- 129S1/SvImJ |
- HF |
- Rep2 |
-
-
- | 12 |
- GSM264778 |
- 129S1/SvImJ |
- HF |
- Rep3 |
-
-
- | 13 |
- GSM264779 |
- A/J |
- 6C |
- Rep1 |
-
-
- | 14 |
- GSM264780 |
- A/J |
- 6C |
- Rep2 |
-
-
- | 15 |
- GSM264781 |
- A/J |
- 6C |
- Rep3 |
-
-
- | 16 |
- GSM264782 |
- A/J |
- HF |
- Rep1 |
-
-
- | 17 |
- GSM264783 |
- A/J |
- HF |
- Rep2 |
-
-
- | 18 |
- GSM264784 |
- A/J |
- HF |
- Rep3 |
-
-
- | 19 |
- GSM264785 |
- A/J |
- 6C |
- Rep1 |
-
-
- | 20 |
- GSM264786 |
- A/J |
- 6C |
- Rep2 |
-
-
- | 21 |
- GSM264787 |
- A/J |
- 6C |
- Rep3 |
-
-
- | 22 |
- GSM264788 |
- A/J |
- HF |
- Rep1 |
-
-
- | 23 |
- GSM264789 |
- A/J |
- HF |
- Rep2 |
-
-
- | 24 |
- GSM264790 |
- A/J |
- HF |
- Rep3 |
-
-
- | 25 |
- GSM264791 |
- C57BL/6J |
- 6C |
- Rep1 |
-
-
- | 26 |
- GSM264792 |
- C57BL/6J |
- 6C |
- Rep2 |
-
-
- | 27 |
- GSM264793 |
- C57BL/6J |
- 6C |
- Rep3 |
-
-
- | 28 |
- GSM264794 |
- C57BL/6J |
- HF |
- Rep1 |
-
-
- | 29 |
- GSM264795 |
- C57BL/6J |
- HF |
- Rep2 |
-
-
- | 30 |
- GSM264796 |
- C57BL/6J |
- HF |
- Rep3 |
-
-
- | 31 |
- GSM264797 |
- C57BL/6J |
- 6C |
- Rep1 |
-
-
- | 32 |
- GSM264798 |
- C57BL/6J |
- 6C |
- Rep2 |
-
-
- | 33 |
- GSM264799 |
- C57BL/6J |
- 6C |
- Rep3 |
-
-
- | 34 |
- GSM264800 |
- C57BL/6J |
- HF |
- Rep1 |
-
-
- | 35 |
- GSM264801 |
- C57BL/6J |
- HF |
- Rep2 |
-
-
- | 36 |
- GSM264802 |
- C57BL/6J |
- HF |
- Rep3 |
-
-
- | 37 |
- GSM264803 |
- BALB/cJ |
- 6C |
- Rep1 |
-
-
- | 38 |
- GSM264804 |
- BALB/cJ |
- 6C |
- Rep2 |
-
-
- | 39 |
- GSM264805 |
- BALB/cJ |
- 6C |
- Rep3 |
-
-
- | 40 |
- GSM264806 |
- BALB/cJ |
- HF |
- Rep1 |
-
-
- | 41 |
- GSM264807 |
- BALB/cJ |
- HF |
- Rep2 |
-
-
- | 42 |
- GSM264808 |
- BALB/cJ |
- HF |
- Rep3 |
-
-
- | 43 |
- GSM264809 |
- BALB/cJ |
- 6C |
- Rep1 |
-
-
- | 44 |
- GSM264810 |
- BALB/cJ |
- 6C |
- Rep2 |
-
-
- | 45 |
- GSM264811 |
- BALB/cJ |
- 6C |
- Rep3 |
-
-
- | 46 |
- GSM264813 |
- BALB/cJ |
- HF |
- Rep1 |
-
-
- | 47 |
- GSM264814 |
- BALB/cJ |
- HF |
- Rep2 |
-
-
- | 48 |
- GSM264815 |
- BALB/cJ |
- HF |
- Rep3 |
-
-
- | 49 |
- GSM264845 |
- C3H/HeJ |
- 6C |
- Rep1 |
-
-
- | 50 |
- GSM264846 |
- C3H/HeJ |
- 6C |
- Rep2 |
-
-
- | 51 |
- GSM264847 |
- C3H/HeJ |
- 6C |
- Rep3 |
-
-
- | 52 |
- GSM264848 |
- C3H/HeJ |
- HF |
- Rep1 |
-
-
- | 53 |
- GSM264849 |
- C3H/HeJ |
- HF |
- Rep2 |
-
-
- | 54 |
- GSM264850 |
- C3H/HeJ |
- HF |
- Rep3 |
-
-
- | 55 |
- GSM264852 |
- C3H/HeJ |
- 6C |
- Rep1 |
-
-
- | 56 |
- GSM264853 |
- C3H/HeJ |
- 6C |
- Rep2 |
-
-
- | 57 |
- GSM264855 |
- C3H/HeJ |
- 6C |
- Rep3 |
-
-
- | 58 |
- GSM264856 |
- C3H/HeJ |
- HF |
- Rep1 |
-
-
- | 59 |
- GSM264857 |
- C3H/HeJ |
- HF |
- Rep2 |
-
-
- | 60 |
- GSM264858 |
- C3H/HeJ |
- HF |
- Rep3 |
-
-
- | 61 |
- GSM264859 |
- CAST/EiJ |
- 6C |
- Rep1 |
-
-
- | 62 |
- GSM264861 |
- CAST/EiJ |
- 6C |
- Rep2 |
-
-
- | 63 |
- GSM264862 |
- CAST/EiJ |
- 6C |
- Rep3 |
-
-
- | 64 |
- GSM264863 |
- CAST/EiJ |
- HF |
- Rep1 |
-
-
- | 65 |
- GSM264864 |
- CAST/EiJ |
- HF |
- Rep2 |
-
-
- | 66 |
- GSM264865 |
- CAST/EiJ |
- HF |
- Rep3 |
-
-
- | 67 |
- GSM264866 |
- CAST/EiJ |
- 6C |
- Rep1 |
-
-
- | 68 |
- GSM264867 |
- CAST/EiJ |
- 6C |
- Rep2 |
-
-
- | 69 |
- GSM264868 |
- CAST/EiJ |
- 6C |
- Rep3 |
-
-
- | 70 |
- GSM264869 |
- CAST/EiJ |
- HF |
- Rep1 |
-
-
- | 71 |
- GSM264870 |
- CAST/EiJ |
- HF |
- Rep2 |
-
-
- | 72 |
- GSM264871 |
- CAST/EiJ |
- HF |
- Rep3 |
-
-
- | 73 |
- GSM264872 |
- DBA/2J |
- 6C |
- Rep1 |
-
-
- | 74 |
- GSM264873 |
- DBA/2J |
- 6C |
- Rep2 |
-
-
- | 75 |
- GSM264874 |
- DBA/2J |
- 6C |
- Rep3 |
-
-
- | 76 |
- GSM264875 |
- DBA/2J |
- HF |
- Rep1 |
-
-
- | 77 |
- GSM264876 |
- DBA/2J |
- HF |
- Rep2 |
-
-
- | 78 |
- GSM264877 |
- DBA/2J |
- HF |
- Rep3 |
-
-
- | 79 |
- GSM264890 |
- DBA/2J |
- 6C |
- Rep1 |
-
-
- | 80 |
- GSM264891 |
- DBA/2J |
- 6C |
- Rep2 |
-
-
- | 81 |
- GSM264892 |
- DBA/2J |
- 6C |
- Rep3 |
-
-
- | 82 |
- GSM264893 |
- DBA/2J |
- HF |
- Rep1 |
-
-
- | 83 |
- GSM264894 |
- DBA/2J |
- HF |
- Rep2 |
-
-
- | 84 |
- GSM264895 |
- DBA/2J |
- HF |
- Rep3 |
-
-
- | 85 |
- GSM264896 |
- I/LnJ |
- 6C |
- Rep1 |
-
-
- | 86 |
- GSM264897 |
- I/LnJ |
- 6C |
- Rep2 |
-
-
- | 87 |
- GSM264898 |
- I/LnJ |
- 6C |
- Rep3 |
-
-
- | 88 |
- GSM264899 |
- I/LnJ |
- HF |
- Rep1 |
-
-
- | 89 |
- GSM264900 |
- I/LnJ |
- HF |
- Rep2 |
-
-
- | 90 |
- GSM264901 |
- I/LnJ |
- HF |
- Rep3 |
-
-
- | 91 |
- GSM264902 |
- I/LnJ |
- 6C |
- Rep1 |
-
-
- | 92 |
- GSM264903 |
- I/LnJ |
- 6C |
- Rep2 |
-
-
- | 93 |
- GSM264904 |
- I/LnJ |
- 6C |
- Rep3 |
-
-
- | 94 |
- GSM264905 |
- I/LnJ |
- HF |
- Rep1 |
-
-
- | 95 |
- GSM264906 |
- I/LnJ |
- HF |
- Rep2 |
-
-
- | 96 |
- GSM264907 |
- I/LnJ |
- HF |
- Rep3 |
-
-
- | 97 |
- GSM264908 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep1 |
-
-
- | 98 |
- GSM264909 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep2 |
-
-
- | 99 |
- GSM264910 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep3 |
-
-
- | 100 |
- GSM264912 |
- MRL/MpJ-Fas/J |
- HF |
- Rep1 |
-
-
- | 101 |
- GSM264913 |
- MRL/MpJ-Fas/J |
- HF |
- Rep2 |
-
-
- | 102 |
- GSM264914 |
- MRL/MpJ-Fas/J |
- HF |
- Rep3 |
-
-
- | 103 |
- GSM264915 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep1 |
-
-
- | 104 |
- GSM264916 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep2 |
-
-
- | 105 |
- GSM264917 |
- MRL/MpJ-Fas/J |
- 6C |
- Rep3 |
-
-
- | 106 |
- GSM264918 |
- MRL/MpJ-Fas/J |
- HF |
- Rep1 |
-
-
- | 107 |
- GSM264920 |
- MRL/MpJ-Fas/J |
- HF |
- Rep2 |
-
-
- | 108 |
- GSM264921 |
- MRL/MpJ-Fas/J |
- HF |
- Rep3 |
-
-
- | 109 |
- GSM264922 |
- NZB/BlNJ |
- 6C |
- Rep1 |
-
-
- | 110 |
- GSM264924 |
- NZB/BlNJ |
- 6C |
- Rep2 |
-
-
- | 111 |
- GSM264925 |
- NZB/BlNJ |
- 6C |
- Rep3 |
-
-
- | 112 |
- GSM264926 |
- NZB/BlNJ |
- HF |
- Rep1 |
-
-
- | 113 |
- GSM264928 |
- NZB/BlNJ |
- HF |
- Rep2 |
-
-
- | 114 |
- GSM264929 |
- NZB/BlNJ |
- HF |
- Rep3 |
-
-
- | 115 |
- GSM264930 |
- NZB/BlNJ |
- 6C |
- Rep1 |
-
-
- | 116 |
- GSM264931 |
- NZB/BlNJ |
- 6C |
- Rep2 |
-
-
- | 117 |
- GSM264932 |
- NZB/BlNJ |
- 6C |
- Rep3 |
-
-
- | 118 |
- GSM264933 |
- NZB/BlNJ |
- HF |
- Rep1 |
-
-
- | 119 |
- GSM264935 |
- NZB/BlNJ |
- HF |
- Rep2 |
-
-
- | 120 |
- GSM264936 |
- NZB/BlNJ |
- HF |
- Rep3 |
-
-
- | 121 |
- GSM265061 |
- PERA/EiJ |
- 6C |
- Rep1 |
-
-
- | 122 |
- GSM265062 |
- PERA/EiJ |
- 6C |
- Rep2 |
-
-
- | 123 |
- GSM265063 |
- PERA/EiJ |
- 6C |
- Rep3 |
-
-
- | 124 |
- GSM265064 |
- PERA/EiJ |
- HF |
- Rep1 |
-
-
- | 125 |
- GSM265065 |
- PERA/EiJ |
- HF |
- Rep2 |
-
-
- | 126 |
- GSM265066 |
- PERA/EiJ |
- HF |
- Rep3 |
-
-
- | 127 |
- GSM265067 |
- PERA/EiJ |
- 6C |
- Rep1 |
-
-
- | 128 |
- GSM265068 |
- PERA/EiJ |
- 6C |
- Rep2 |
-
-
- | 129 |
- GSM265069 |
- PERA/EiJ |
- 6C |
- Rep3 |
-
-
- | 130 |
- GSM265070 |
- PERA/EiJ |
- HF |
- Rep1 |
-
-
- | 131 |
- GSM265071 |
- PERA/EiJ |
- HF |
- Rep2 |
-
-
- | 132 |
- GSM265072 |
- PERA/EiJ |
- HF |
- Rep3 |
-
-
- | 133 |
- GSM265074 |
- SM/J |
- 6C |
- Rep1 |
-
-
- | 134 |
- GSM265075 |
- SM/J |
- 6C |
- Rep2 |
-
-
- | 135 |
- GSM265105 |
- SM/J |
- 6C |
- Rep3 |
-
-
- | 136 |
- GSM265217 |
- SM/J |
- HF |
- Rep1 |
-
-
- | 137 |
- GSM265248 |
- SM/J |
- HF |
- Rep2 |
-
-
- | 138 |
- GSM265275 |
- SM/J |
- HF |
- Rep3 |
-
-
- | 139 |
- GSM265324 |
- SM/J |
- 6C |
- Rep1 |
-
-
- | 140 |
- GSM265331 |
- SM/J |
- 6C |
- Rep2 |
-
-
- | 141 |
- GSM265357 |
- SM/J |
- 6C |
- Rep3 |
-
-
- | 142 |
- GSM265358 |
- SM/J |
- HF |
- Rep1 |
-
-
- | 143 |
- GSM265359 |
- SM/J |
- HF |
- Rep2 |
-
-
- | 144 |
- GSM265360 |
- SM/J |
- HF |
- Rep3 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/JAX_CSB_L_HF_0711/experiment-design.rtf b/general/datasets/JAX_CSB_L_HF_0711/experiment-design.rtf
deleted file mode 100644
index dc5fef5..0000000
--- a/general/datasets/JAX_CSB_L_HF_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Expression profiling by array.
-
-One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet. Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.
diff --git a/general/datasets/JAX_CSB_L_HF_0711/platform.rtf b/general/datasets/JAX_CSB_L_HF_0711/platform.rtf
deleted file mode 100644
index 459d486..0000000
--- a/general/datasets/JAX_CSB_L_HF_0711/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array. Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html All probe sets represented on the GeneChip Mouse Expression Set 430 are included on the GeneChip Mouse Genome 430 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank«, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute for Genome Research (MGSC, April 2002).
diff --git a/general/datasets/JAX_CSB_L_HF_0711/summary.rtf b/general/datasets/JAX_CSB_L_HF_0711/summary.rtf
deleted file mode 100644
index a06430b..0000000
--- a/general/datasets/JAX_CSB_L_HF_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-High-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis. Keywords: gene expression analysis, strain comparision, effect of dietary fat, sex-specific effects
diff --git a/general/datasets/JAX_CSB_L_HF_0711/tissue.rtf b/general/datasets/JAX_CSB_L_HF_0711/tissue.rtf
deleted file mode 100644
index 778c4a2..0000000
--- a/general/datasets/JAX_CSB_L_HF_0711/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver
diff --git a/general/datasets/JAX_liver_agil_MDP-0113/summary.rtf b/general/datasets/JAX_liver_agil_MDP-0113/summary.rtf
deleted file mode 100644
index f6be413..0000000
--- a/general/datasets/JAX_liver_agil_MDP-0113/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 160, Name: Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009)
\ No newline at end of file
diff --git a/general/datasets/KIN_YSM_A1C_0711/cases.rtf b/general/datasets/KIN_YSM_A1C_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_A1C_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_A1C_0711/experiment-design.rtf b/general/datasets/KIN_YSM_A1C_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_A1C_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_A1C_0711/notes.rtf b/general/datasets/KIN_YSM_A1C_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_A1C_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_A1C_0711/processing.rtf b/general/datasets/KIN_YSM_A1C_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_A1C_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_A1C_0711/summary.rtf b/general/datasets/KIN_YSM_A1C_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_A1C_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_A1C_0711/tissue.rtf b/general/datasets/KIN_YSM_A1C_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_A1C_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_AMY_0711/cases.rtf b/general/datasets/KIN_YSM_AMY_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_AMY_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_AMY_0711/experiment-design.rtf b/general/datasets/KIN_YSM_AMY_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_AMY_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_AMY_0711/notes.rtf b/general/datasets/KIN_YSM_AMY_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_AMY_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_AMY_0711/processing.rtf b/general/datasets/KIN_YSM_AMY_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_AMY_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_AMY_0711/summary.rtf b/general/datasets/KIN_YSM_AMY_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_AMY_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_AMY_0711/tissue.rtf b/general/datasets/KIN_YSM_AMY_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_AMY_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_CBC_0711/cases.rtf b/general/datasets/KIN_YSM_CBC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_CBC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_CBC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_CBC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_CBC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_CBC_0711/notes.rtf b/general/datasets/KIN_YSM_CBC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_CBC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_CBC_0711/processing.rtf b/general/datasets/KIN_YSM_CBC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_CBC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_CBC_0711/summary.rtf b/general/datasets/KIN_YSM_CBC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_CBC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_CBC_0711/tissue.rtf b/general/datasets/KIN_YSM_CBC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_CBC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_DFC_0711/cases.rtf b/general/datasets/KIN_YSM_DFC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_DFC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_DFC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_DFC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_DFC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_DFC_0711/notes.rtf b/general/datasets/KIN_YSM_DFC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_DFC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_DFC_0711/processing.rtf b/general/datasets/KIN_YSM_DFC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_DFC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_DFC_0711/summary.rtf b/general/datasets/KIN_YSM_DFC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_DFC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_DFC_0711/tissue.rtf b/general/datasets/KIN_YSM_DFC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_DFC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_HIP_0711/cases.rtf b/general/datasets/KIN_YSM_HIP_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_HIP_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_HIP_0711/experiment-design.rtf b/general/datasets/KIN_YSM_HIP_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_HIP_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_HIP_0711/notes.rtf b/general/datasets/KIN_YSM_HIP_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_HIP_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_HIP_0711/processing.rtf b/general/datasets/KIN_YSM_HIP_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_HIP_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_HIP_0711/summary.rtf b/general/datasets/KIN_YSM_HIP_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_HIP_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_HIP_0711/tissue.rtf b/general/datasets/KIN_YSM_HIP_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_HIP_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_IPC_0711/cases.rtf b/general/datasets/KIN_YSM_IPC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_IPC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_IPC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_IPC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_IPC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_IPC_0711/notes.rtf b/general/datasets/KIN_YSM_IPC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_IPC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_IPC_0711/processing.rtf b/general/datasets/KIN_YSM_IPC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_IPC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_IPC_0711/summary.rtf b/general/datasets/KIN_YSM_IPC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_IPC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_IPC_0711/tissue.rtf b/general/datasets/KIN_YSM_IPC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_IPC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_ITC_0711/cases.rtf b/general/datasets/KIN_YSM_ITC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_ITC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_ITC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_ITC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_ITC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_ITC_0711/notes.rtf b/general/datasets/KIN_YSM_ITC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_ITC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_ITC_0711/processing.rtf b/general/datasets/KIN_YSM_ITC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_ITC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_ITC_0711/summary.rtf b/general/datasets/KIN_YSM_ITC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_ITC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_ITC_0711/tissue.rtf b/general/datasets/KIN_YSM_ITC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_ITC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_M1C_0711/cases.rtf b/general/datasets/KIN_YSM_M1C_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_M1C_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_M1C_0711/experiment-design.rtf b/general/datasets/KIN_YSM_M1C_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_M1C_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_M1C_0711/notes.rtf b/general/datasets/KIN_YSM_M1C_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_M1C_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_M1C_0711/processing.rtf b/general/datasets/KIN_YSM_M1C_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_M1C_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_M1C_0711/summary.rtf b/general/datasets/KIN_YSM_M1C_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_M1C_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_M1C_0711/tissue.rtf b/general/datasets/KIN_YSM_M1C_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_M1C_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_MD_0711/cases.rtf b/general/datasets/KIN_YSM_MD_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_MD_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_MD_0711/experiment-design.rtf b/general/datasets/KIN_YSM_MD_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_MD_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_MD_0711/notes.rtf b/general/datasets/KIN_YSM_MD_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_MD_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_MD_0711/processing.rtf b/general/datasets/KIN_YSM_MD_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_MD_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_MD_0711/summary.rtf b/general/datasets/KIN_YSM_MD_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_MD_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_MD_0711/tissue.rtf b/general/datasets/KIN_YSM_MD_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_MD_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_MFC_0711/cases.rtf b/general/datasets/KIN_YSM_MFC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_MFC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_MFC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_MFC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_MFC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_MFC_0711/notes.rtf b/general/datasets/KIN_YSM_MFC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_MFC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_MFC_0711/processing.rtf b/general/datasets/KIN_YSM_MFC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_MFC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_MFC_0711/summary.rtf b/general/datasets/KIN_YSM_MFC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_MFC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_MFC_0711/tissue.rtf b/general/datasets/KIN_YSM_MFC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_MFC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_OFC_0711/cases.rtf b/general/datasets/KIN_YSM_OFC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_OFC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_OFC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_OFC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_OFC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_OFC_0711/notes.rtf b/general/datasets/KIN_YSM_OFC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_OFC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_OFC_0711/processing.rtf b/general/datasets/KIN_YSM_OFC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_OFC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_OFC_0711/summary.rtf b/general/datasets/KIN_YSM_OFC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_OFC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_OFC_0711/tissue.rtf b/general/datasets/KIN_YSM_OFC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_OFC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_S1C_0711/cases.rtf b/general/datasets/KIN_YSM_S1C_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_S1C_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_S1C_0711/experiment-design.rtf b/general/datasets/KIN_YSM_S1C_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_S1C_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_S1C_0711/notes.rtf b/general/datasets/KIN_YSM_S1C_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_S1C_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_S1C_0711/processing.rtf b/general/datasets/KIN_YSM_S1C_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_S1C_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_S1C_0711/summary.rtf b/general/datasets/KIN_YSM_S1C_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_S1C_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_S1C_0711/tissue.rtf b/general/datasets/KIN_YSM_S1C_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_S1C_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_STC_0711/cases.rtf b/general/datasets/KIN_YSM_STC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_STC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_STC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_STC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_STC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_STC_0711/notes.rtf b/general/datasets/KIN_YSM_STC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_STC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_STC_0711/processing.rtf b/general/datasets/KIN_YSM_STC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_STC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_STC_0711/summary.rtf b/general/datasets/KIN_YSM_STC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_STC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_STC_0711/tissue.rtf b/general/datasets/KIN_YSM_STC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_STC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_STR_0711/cases.rtf b/general/datasets/KIN_YSM_STR_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_STR_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_STR_0711/experiment-design.rtf b/general/datasets/KIN_YSM_STR_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_STR_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_STR_0711/notes.rtf b/general/datasets/KIN_YSM_STR_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_STR_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_STR_0711/processing.rtf b/general/datasets/KIN_YSM_STR_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_STR_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_STR_0711/summary.rtf b/general/datasets/KIN_YSM_STR_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_STR_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_STR_0711/tissue.rtf b/general/datasets/KIN_YSM_STR_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_STR_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_V1C_0711/cases.rtf b/general/datasets/KIN_YSM_V1C_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_V1C_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_V1C_0711/experiment-design.rtf b/general/datasets/KIN_YSM_V1C_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_V1C_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_V1C_0711/notes.rtf b/general/datasets/KIN_YSM_V1C_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_V1C_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_V1C_0711/processing.rtf b/general/datasets/KIN_YSM_V1C_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_V1C_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_V1C_0711/summary.rtf b/general/datasets/KIN_YSM_V1C_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_V1C_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_V1C_0711/tissue.rtf b/general/datasets/KIN_YSM_V1C_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_V1C_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KIN_YSM_VFC_0711/cases.rtf b/general/datasets/KIN_YSM_VFC_0711/cases.rtf
deleted file mode 100644
index 7b0ef71..0000000
--- a/general/datasets/KIN_YSM_VFC_0711/cases.rtf
+++ /dev/null
@@ -1,88 +0,0 @@
-RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).
-
-Table 1 | Periods of human development and adulthood as defined in this study.
-
-
-
-
- | Period |
- Description |
- Age |
-
-
- | 1 |
- Embryonic |
- 4≤ Age <8 Postconceptual weeks (PCW) |
-
-
- | 2 |
- Early fetal |
- 8≤ Age <10 PCW |
-
-
- | 3 |
- Early fetal |
- 10≤ Age <13 PCW |
-
-
- | 4 |
- Early midfetal |
- 13≤ Age <16 PCW |
-
-
- | 5 |
- Early midfetal |
- 16≤ Age <19 PCW |
-
-
- | 6 |
- Late midfetal |
- 19≤ Age <24 PCW |
-
-
- | 7 |
- Late fetal |
- 24≤ Age <38 PCW |
-
-
- | 8 |
- Neonatal and early infancy |
- Birth≤ Age <6 Postnatal months (M) |
-
-
- | 9 |
- Late infancy |
- 6 M≤ Age <12 M |
-
-
- | 10 |
- Early childhood |
- 1≤ Age <6 Postnatal years (Y) |
-
-
- | 11 |
- Middle and late childhood |
- 6≤ Age <12 Y |
-
-
- | 12 |
- Adolescence |
- 12≤ Age <20 Y |
-
-
- | 13 |
- Young adulthood |
- 20≤ Age <40 Y |
-
-
- | 14 |
- Middle adulthood |
- 40≤ Age <60 Y |
-
-
- | 15 |
- Late adulthood |
- 60 Y ≤ Age |
-
-
-
diff --git a/general/datasets/KIN_YSM_VFC_0711/experiment-design.rtf b/general/datasets/KIN_YSM_VFC_0711/experiment-design.rtf
deleted file mode 100644
index 963e517..0000000
--- a/general/datasets/KIN_YSM_VFC_0711/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Human Brain Specimens and Tissue Processing This study was carried out using post-mortem human brain specimens collected from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM). Dissected tissue was fresh-frozen in Trizol for RNA and DNA extraction, with a post-mortem interval of less than 1 hour. Remaining tissue was fixed and frozen, and sections were analyzed for neuropathological or developmental defects. Details of specimens, tissue processing, microdissection, and neuropathological assessment are given in the Supplemental Experimental Procedures and Table S1. These studies were approved by the Human Investigation Committees of AECOM and Yale University.
-
-For initial analysis, all neocortex samples were grouped together. In subsequent analyses, neocortex areas were compared with each other. In most analyses reported, left and right side samples were treated as additional biological replicates.
diff --git a/general/datasets/KIN_YSM_VFC_0711/notes.rtf b/general/datasets/KIN_YSM_VFC_0711/notes.rtf
deleted file mode 100644
index 8d266d3..0000000
--- a/general/datasets/KIN_YSM_VFC_0711/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The raw microarray data are available via the NCBI Gene Expression Omnibus. Data in GeneNetwork as of July 2015 are only gene-level data. We could also enter exon-level data on request.
diff --git a/general/datasets/KIN_YSM_VFC_0711/processing.rtf b/general/datasets/KIN_YSM_VFC_0711/processing.rtf
deleted file mode 100644
index 1920ca7..0000000
--- a/general/datasets/KIN_YSM_VFC_0711/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Normalized method: Quantile normalization. Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values.
diff --git a/general/datasets/KIN_YSM_VFC_0711/summary.rtf b/general/datasets/KIN_YSM_VFC_0711/summary.rtf
deleted file mode 100644
index 66a2289..0000000
--- a/general/datasets/KIN_YSM_VFC_0711/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.
diff --git a/general/datasets/KIN_YSM_VFC_0711/tissue.rtf b/general/datasets/KIN_YSM_VFC_0711/tissue.rtf
deleted file mode 100644
index f08a838..0000000
--- a/general/datasets/KIN_YSM_VFC_0711/tissue.rtf
+++ /dev/null
@@ -1,109 +0,0 @@
-Tissue was microdissected from 13 regions, including 9 distinct neocortical areas, from both left and right sides of four late second trimester human brain specimens. Gene- and exon-level differential expression analyses were performed by mixed model, nested analysis of variance using the XRAY software from Biotique Systems. Further details available in Johnson, Kawasawa, et al., "Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis" Neuron, Volume 62, Issue 4, 2009.
-
-Ethnicity codes are as follows: AA = African American, A = , A/E = X, As,= , H = , E = , CC = and n/a= unknown
-
-
-
-This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.
-
-Table 2 | Ontology and nomenclature of analyzed brain regions and neocortical areas.
-
-
-
-
- | Period 1 |
- Period 2 |
- Period 3 - 15 |
-
-
- | FC: Frontal cerebral wall |
- FC |
- OFC: Orbital prefrontal cortex |
-
-
- | |
- |
- DFC: Dorsolateral prefrontal cortex |
-
-
- | |
- |
- VFC: Ventrolateral prefrontal cortex |
-
-
- | |
- |
- MFC: Medial prefrontal cortex |
-
-
- | |
- |
- M1C: Primary motor (M1) cortex |
-
-
- | PC: Parietal cerebral wall |
- PC |
- S1C: Primary somatosensory (S1) cortex |
-
-
- | |
- |
- IPC: Posterior inferior parietal cortex |
-
-
- | TC: Temporal cerebral wall |
- TC |
-  A1C: Primary auditory (A1) cortex |
-
-
- | |
- |
- STC: Posterior superior temporal cortex |
-
-
- | |
- |
- ITC: Inferior temporal cortex |
-
-
- | OC: Occipital cerebral wall |
- OC |
- V1C: Primary visual (V1) cortex |
-
-
- | HIP: Hippocampal anlage |
- HIP |
- HIP: Hippocampus |
-
-
- | |
- |
- AMY: Amygdala |
-
-
- | VF: Ventral forebrain |
- CGE: Caudal ganglionic eminence |
- STR: Striatum |
-
-
- | |
- LGE: Lateral ganglionic eminence |
- |
-
-
- | |
- MGE: Medial ganglionic eminence |
- |
-
-
- | DIE: Diencephalon |
- DTH: Dorsal thalamus |
- MD: Mediodorsal nucleus of thalamus |
-
-
- | URL: Upper (rostral) rhombic lip |
- URL |
- CBC: Cerebellar cortex |
-
-
-
diff --git a/general/datasets/KI_2A_0405_M/acknowledgment.rtf b/general/datasets/KI_2A_0405_M/acknowledgment.rtf
deleted file mode 100644
index 956eaca..0000000
--- a/general/datasets/KI_2A_0405_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Intiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
diff --git a/general/datasets/KI_2A_0405_M/cases.rtf b/general/datasets/KI_2A_0405_M/cases.rtf
deleted file mode 100644
index 862deec..0000000
--- a/general/datasets/KI_2A_0405_M/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv or HSR = H) and Brown Norway (BN.Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth geenration of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of kidney and fat (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hubner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
-
diff --git a/general/datasets/KI_2A_0405_M/notes.rtf b/general/datasets/KI_2A_0405_M/notes.rtf
deleted file mode 100644
index 1af325d..0000000
--- a/general/datasets/KI_2A_0405_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman, April 19, 2005. Updated by RWW, May 13, 2005.
-
diff --git a/general/datasets/KI_2A_0405_M/platform.rtf b/general/datasets/KI_2A_0405_M/platform.rtf
deleted file mode 100644
index 78c5815..0000000
--- a/general/datasets/KI_2A_0405_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 230A GeneChip: Expression data were generated using the Affymetrix 230A array. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
-
diff --git a/general/datasets/KI_2A_0405_M/processing.rtf b/general/datasets/KI_2A_0405_M/processing.rtf
deleted file mode 100644
index d75d1db..0000000
--- a/general/datasets/KI_2A_0405_M/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of pixel measured in each cell.
-
-
-Probe set data: The original CEL values were log2 transformed and quantile normalized. We then took the antilog values of these quantile adjusted CEL values as input to the standard MAS5 algorithm. Probe set values listed in WebQTL pages are typically the averages of four biological replicates within strain.
-
-
-About Quality Control Procedures:
-
-
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. Fat samples were processed at this step using the Enzo Diagnostics Bioarray High Yield RNA Transcript labeling kit. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.
-
-Probe level QC: All 128 CEL files were collected into a single DataDesk 6.2 file. Probe data from pairs of arrays were plotted and compared. Eight arrays were considered potential outliers (despite having passed RNA quality control) and in the interest of minimizing technical variance, a decision was made to withhold them from the calculation of strain means used in WebQTL. The remaining 120 arrays were quantile normalized and reexamined in DataDesk to ensure reasonble colinearity of all array data sets.
-
-Probe set level QC: Probe set level QC involves counting the number of times that a single array data set from a single sample generates outliers at the level of the probe set consensus estimates of expression. With 120 arrays, any single array should generate a comparatively small fraction of the total number of outlier calls. This final step of array QC has NOT been implemented yet in this data set.
-
diff --git a/general/datasets/KI_2A_0405_M/summary.rtf b/general/datasets/KI_2A_0405_M/summary.rtf
deleted file mode 100644
index 44fd86e..0000000
--- a/general/datasets/KI_2A_0405_M/summary.rtf
+++ /dev/null
@@ -1,19 +0,0 @@
-This April 2005 data set provides estimates of mRNA expression in normal kidneys of 32 strains of rats. The set includes the hypertensive SHR strain, the normotensive BN strain, and 30 HXB/BXH recombinant inbred strains. Each strain was sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by Nobert Hübner and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of 128 Affymetrix RAE230A array. This particular data set includes 120 arrays processed using a quantile normalized variant of the Affymetrix MAS5 protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a stardard deviation of 2 (mean and variance stabilized). This data set complements the original MAS5 data set exploited by Hübner and colleagues 2005. Download the particular transform in an Excel work book with both strain means and SEMs.
-
-These data can also be viewed using the eQTL Explorer Java application by John Mangion, Tim Aitman, and colleagues (Mueller et al. 2006).
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/KI_2A_0405_M/tissue.rtf b/general/datasets/KI_2A_0405_M/tissue.rtf
deleted file mode 100644
index 8184532..0000000
--- a/general/datasets/KI_2A_0405_M/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All tissues were collected at the age of 6 weeks. Kidneys and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction.
-
-The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR3 |
-
-
- | HSR |
- HSR4 |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN4 |
-
-
- | BN |
- BN5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-3 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- *RI 02-4 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- *RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HXB10 |
- RI 10-1 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-3 |
-
-
- | HXB15 |
- RI 15-4 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- *RI 24-4 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-2 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- *RI 25-4 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-3 |
-
-
- | HXB29 |
- *RI 29-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-3 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- RI 05c-3 |
-
-
- | BXH5 |
- *RI 05c-4 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-2 |
-
-
- | BXH6 |
- RI 06c-3 |
-
-
- | BXH6 |
- *RI 06c-4 |
-
-
- | BXH8 |
- RI 08c-1 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-3 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- *RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
-
- |
-
-
-
-
-*: These eight arrays were excluded in the final strain summary data. See section of Quality Control for further explanation.
diff --git a/general/datasets/KI_2A_0405_R/acknowledgment.rtf b/general/datasets/KI_2A_0405_R/acknowledgment.rtf
deleted file mode 100644
index 956eaca..0000000
--- a/general/datasets/KI_2A_0405_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Intiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
diff --git a/general/datasets/KI_2A_0405_R/cases.rtf b/general/datasets/KI_2A_0405_R/cases.rtf
deleted file mode 100644
index 862deec..0000000
--- a/general/datasets/KI_2A_0405_R/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv or HSR = H) and Brown Norway (BN.Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth geenration of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of kidney and fat (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hubner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
-
diff --git a/general/datasets/KI_2A_0405_R/notes.rtf b/general/datasets/KI_2A_0405_R/notes.rtf
deleted file mode 100644
index 1af325d..0000000
--- a/general/datasets/KI_2A_0405_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman, April 19, 2005. Updated by RWW, May 13, 2005.
-
diff --git a/general/datasets/KI_2A_0405_R/platform.rtf b/general/datasets/KI_2A_0405_R/platform.rtf
deleted file mode 100644
index 78c5815..0000000
--- a/general/datasets/KI_2A_0405_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 230A GeneChip: Expression data were generated using the Affymetrix 230A array. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
-
diff --git a/general/datasets/KI_2A_0405_R/processing.rtf b/general/datasets/KI_2A_0405_R/processing.rtf
deleted file mode 100644
index d75d1db..0000000
--- a/general/datasets/KI_2A_0405_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of pixel measured in each cell.
-
-
-Probe set data: The original CEL values were log2 transformed and quantile normalized. We then took the antilog values of these quantile adjusted CEL values as input to the standard MAS5 algorithm. Probe set values listed in WebQTL pages are typically the averages of four biological replicates within strain.
-
-
-About Quality Control Procedures:
-
-
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. Fat samples were processed at this step using the Enzo Diagnostics Bioarray High Yield RNA Transcript labeling kit. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.
-
-Probe level QC: All 128 CEL files were collected into a single DataDesk 6.2 file. Probe data from pairs of arrays were plotted and compared. Eight arrays were considered potential outliers (despite having passed RNA quality control) and in the interest of minimizing technical variance, a decision was made to withhold them from the calculation of strain means used in WebQTL. The remaining 120 arrays were quantile normalized and reexamined in DataDesk to ensure reasonble colinearity of all array data sets.
-
-Probe set level QC: Probe set level QC involves counting the number of times that a single array data set from a single sample generates outliers at the level of the probe set consensus estimates of expression. With 120 arrays, any single array should generate a comparatively small fraction of the total number of outlier calls. This final step of array QC has NOT been implemented yet in this data set.
-
diff --git a/general/datasets/KI_2A_0405_R/summary.rtf b/general/datasets/KI_2A_0405_R/summary.rtf
deleted file mode 100644
index 44fd86e..0000000
--- a/general/datasets/KI_2A_0405_R/summary.rtf
+++ /dev/null
@@ -1,19 +0,0 @@
-This April 2005 data set provides estimates of mRNA expression in normal kidneys of 32 strains of rats. The set includes the hypertensive SHR strain, the normotensive BN strain, and 30 HXB/BXH recombinant inbred strains. Each strain was sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by Nobert Hübner and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of 128 Affymetrix RAE230A array. This particular data set includes 120 arrays processed using a quantile normalized variant of the Affymetrix MAS5 protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a stardard deviation of 2 (mean and variance stabilized). This data set complements the original MAS5 data set exploited by Hübner and colleagues 2005. Download the particular transform in an Excel work book with both strain means and SEMs.
-
-These data can also be viewed using the eQTL Explorer Java application by John Mangion, Tim Aitman, and colleagues (Mueller et al. 2006).
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/KI_2A_0405_R/tissue.rtf b/general/datasets/KI_2A_0405_R/tissue.rtf
deleted file mode 100644
index 8184532..0000000
--- a/general/datasets/KI_2A_0405_R/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All tissues were collected at the age of 6 weeks. Kidneys and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction.
-
-The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR3 |
-
-
- | HSR |
- HSR4 |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN4 |
-
-
- | BN |
- BN5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-3 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- *RI 02-4 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- *RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HXB10 |
- RI 10-1 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-3 |
-
-
- | HXB15 |
- RI 15-4 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- *RI 24-4 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-2 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- *RI 25-4 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-3 |
-
-
- | HXB29 |
- *RI 29-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-3 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- RI 05c-3 |
-
-
- | BXH5 |
- *RI 05c-4 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-2 |
-
-
- | BXH6 |
- RI 06c-3 |
-
-
- | BXH6 |
- *RI 06c-4 |
-
-
- | BXH8 |
- RI 08c-1 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-3 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- *RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
-
- |
-
-
-
-
-*: These eight arrays were excluded in the final strain summary data. See section of Quality Control for further explanation.
diff --git a/general/datasets/KI_2A_0405_Rz/acknowledgment.rtf b/general/datasets/KI_2A_0405_Rz/acknowledgment.rtf
deleted file mode 100644
index 956eaca..0000000
--- a/general/datasets/KI_2A_0405_Rz/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Intiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
diff --git a/general/datasets/KI_2A_0405_Rz/cases.rtf b/general/datasets/KI_2A_0405_Rz/cases.rtf
deleted file mode 100644
index 862deec..0000000
--- a/general/datasets/KI_2A_0405_Rz/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv or HSR = H) and Brown Norway (BN.Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.
-
-
-The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth geenration of continuous inbreeding (F60).
-
-Animals used in the transcriptome analyses of kidney and fat (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hubner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
-
diff --git a/general/datasets/KI_2A_0405_Rz/notes.rtf b/general/datasets/KI_2A_0405_Rz/notes.rtf
deleted file mode 100644
index 1af325d..0000000
--- a/general/datasets/KI_2A_0405_Rz/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman, April 19, 2005. Updated by RWW, May 13, 2005.
-
diff --git a/general/datasets/KI_2A_0405_Rz/platform.rtf b/general/datasets/KI_2A_0405_Rz/platform.rtf
deleted file mode 100644
index 78c5815..0000000
--- a/general/datasets/KI_2A_0405_Rz/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix 230A GeneChip: Expression data were generated using the Affymetrix 230A array. The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
-
diff --git a/general/datasets/KI_2A_0405_Rz/processing.rtf b/general/datasets/KI_2A_0405_Rz/processing.rtf
deleted file mode 100644
index d75d1db..0000000
--- a/general/datasets/KI_2A_0405_Rz/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of pixel measured in each cell.
-
-
-Probe set data: The original CEL values were log2 transformed and quantile normalized. We then took the antilog values of these quantile adjusted CEL values as input to the standard MAS5 algorithm. Probe set values listed in WebQTL pages are typically the averages of four biological replicates within strain.
-
-
-About Quality Control Procedures:
-
-
-RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. Fat samples were processed at this step using the Enzo Diagnostics Bioarray High Yield RNA Transcript labeling kit. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.
-
-Probe level QC: All 128 CEL files were collected into a single DataDesk 6.2 file. Probe data from pairs of arrays were plotted and compared. Eight arrays were considered potential outliers (despite having passed RNA quality control) and in the interest of minimizing technical variance, a decision was made to withhold them from the calculation of strain means used in WebQTL. The remaining 120 arrays were quantile normalized and reexamined in DataDesk to ensure reasonble colinearity of all array data sets.
-
-Probe set level QC: Probe set level QC involves counting the number of times that a single array data set from a single sample generates outliers at the level of the probe set consensus estimates of expression. With 120 arrays, any single array should generate a comparatively small fraction of the total number of outlier calls. This final step of array QC has NOT been implemented yet in this data set.
-
diff --git a/general/datasets/KI_2A_0405_Rz/summary.rtf b/general/datasets/KI_2A_0405_Rz/summary.rtf
deleted file mode 100644
index 44fd86e..0000000
--- a/general/datasets/KI_2A_0405_Rz/summary.rtf
+++ /dev/null
@@ -1,19 +0,0 @@
-This April 2005 data set provides estimates of mRNA expression in normal kidneys of 32 strains of rats. The set includes the hypertensive SHR strain, the normotensive BN strain, and 30 HXB/BXH recombinant inbred strains. Each strain was sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by Nobert Hübner and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of 128 Affymetrix RAE230A array. This particular data set includes 120 arrays processed using a quantile normalized variant of the Affymetrix MAS5 protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a stardard deviation of 2 (mean and variance stabilized). This data set complements the original MAS5 data set exploited by Hübner and colleagues 2005. Download the particular transform in an Excel work book with both strain means and SEMs.
-
-These data can also be viewed using the eQTL Explorer Java application by John Mangion, Tim Aitman, and colleagues (Mueller et al. 2006).
-
-Genome-wide co-expression analysis in multiple tissues.
-
-And see closely associate set of papers:
-
-
- - Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- - Heritability and tissue specificity of expression quantitative trait loci.
- - Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- - New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- - The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- - A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- - Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- - Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
-
diff --git a/general/datasets/KI_2A_0405_Rz/tissue.rtf b/general/datasets/KI_2A_0405_Rz/tissue.rtf
deleted file mode 100644
index 8184532..0000000
--- a/general/datasets/KI_2A_0405_Rz/tissue.rtf
+++ /dev/null
@@ -1,534 +0,0 @@
-All tissues were collected at the age of 6 weeks. Kidneys and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction.
-
-The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
-
-
-
-
-
-
-
-
- | Strain |
- SampleID |
-
-
- | HSR |
- HSR1 |
-
-
- | HSR |
- HSR2 |
-
-
- | HSR |
- HSR3 |
-
-
- | HSR |
- HSR4 |
-
-
- | BN |
- BN1 |
-
-
- | BN |
- BN2 |
-
-
- | BN |
- BN3 |
-
-
- | BN |
- BN4 |
-
-
- | BN |
- BN5 |
-
-
- | HXB1 |
- RI 01-1 |
-
-
- | HXB1 |
- RI 01-2 |
-
-
- | HXB1 |
- RI 01-3 |
-
-
- | HXB1 |
- RI 01-4 |
-
-
- | HXB2 |
- RI 02-1 |
-
-
- | HXB2 |
- RI 02-2 |
-
-
- | HXB2 |
- RI 02-3 |
-
-
- | HXB2 |
- *RI 02-4 |
-
-
- | HXB3 |
- RI 03-1 |
-
-
- | HXB3 |
- RI 03-2 |
-
-
- | HXB3 |
- RI 03-3 |
-
-
- | HXB3 |
- RI 03-4 |
-
-
- | HXB4 |
- RI 04-1 |
-
-
- | HXB4 |
- RI 04-2 |
-
-
- | HXB4 |
- RI 04-3 |
-
-
- | HXB4 |
- RI 04-4 |
-
-
- | HXB5 |
- RI 05-1 |
-
-
- | HXB5 |
- RI 05-2 |
-
-
- | HXB5 |
- RI 05-3 |
-
-
- | HXB5 |
- *RI 05-4 |
-
-
- | HXB7 |
- RI 07-1 |
-
-
- | HXB7 |
- RI 07-2 |
-
-
- | HXB7 |
- RI 07-3 |
-
-
- | HXB7 |
- RI 07-4 |
-
-
- | HXB10 |
- RI 10-1 |
-
-
- | HXB10 |
- RI 10-2 |
-
-
- | HXB10 |
- RI 10-3 |
-
-
- | HXB10 |
- RI 10-4 |
-
-
- | HXB15 |
- RI 15-1 |
-
-
- | HXB15 |
- RI 15-2 |
-
-
- | HXB15 |
- RI 15-3 |
-
-
- | HXB15 |
- RI 15-4 |
-
-
- | HXB17 |
- RI 17-1 |
-
-
- | HXB17 |
- RI 17-2 |
-
-
- | HXB17 |
- RI 17-3 |
-
-
- | HXB17 |
- RI 17-4 |
-
-
- | HXB18 |
- RI 18-1 |
-
-
- | HXB18 |
- RI 18-2 |
-
-
- | HXB18 |
- RI 18-3 |
-
-
- | HXB18 |
- RI 18-4 |
-
-
- | HXB20 |
- RI 20-1 |
-
-
- | HXB20 |
- RI 20-2 |
-
-
- | HXB20 |
- RI 20-3 |
-
-
- | HXB20 |
- RI 20-4 |
-
-
- | HXB21 |
- RI 21-1 |
-
-
- | HXB21 |
- RI 21-2 |
-
-
- | HXB21 |
- RI 21-3 |
-
-
- | HXB21 |
- RI 21-4 |
-
-
- | HXB22 |
- RI 22-1 |
-
-
- | HXB22 |
- RI 22-2 |
-
-
- | HXB22 |
- RI 22-3 |
-
-
- | HXB22 |
- RI 22-4 |
-
-
- | HXB23 |
- RI 23-1 |
-
-
- | HXB23 |
- RI 23-2 |
-
-
- | HXB23 |
- RI 23-3 |
-
-
- | HXB23 |
- RI 23-4 |
-
-
- | HXB24 |
- RI 24-1 |
-
-
- | HXB24 |
- RI 24-2 |
-
-
- | HXB24 |
- RI 24-3 |
-
-
- | HXB24 |
- *RI 24-4 |
-
-
- | HXB25 |
- RI 25-1 |
-
-
- | HXB25 |
- RI 25-2 |
-
-
- | HXB25 |
- RI 25-3 |
-
-
- | HXB25 |
- *RI 25-4 |
-
-
- | HXB26 |
- RI 26-1 |
-
-
- | HXB26 |
- RI 26-2 |
-
-
- | HXB26 |
- RI 26-3 |
-
-
- | HXB26 |
- RI 26-4 |
-
-
- | HXB27 |
- RI 27-1 |
-
-
- | HXB27 |
- RI 27-2 |
-
-
- | HXB27 |
- RI 27-3 |
-
-
- | HXB27 |
- RI 27-4 |
-
-
- | HXB29 |
- RI 29-1 |
-
-
- | HXB29 |
- RI 29-2 |
-
-
- | HXB29 |
- RI 29-3 |
-
-
- | HXB29 |
- *RI 29-4 |
-
-
- | HXB31 |
- RI 31-1 |
-
-
- | HXB31 |
- RI 31-2 |
-
-
- | HXB31 |
- RI 31-3 |
-
-
- | HXB31 |
- RI 31-4 |
-
-
- | BXH2 |
- RI 02c-1 |
-
-
- | BXH2 |
- RI 02c-2 |
-
-
- | BXH2 |
- RI 02c-3 |
-
-
- | BXH2 |
- RI 02c-4 |
-
-
- | BXH3 |
- RI 03c-1 |
-
-
- | BXH3 |
- RI 03c-2 |
-
-
- | BXH3 |
- RI 03c-3 |
-
-
- | BXH3 |
- RI 03c-4 |
-
-
- | BXH5 |
- RI 05c-1 |
-
-
- | BXH5 |
- RI 05c-2 |
-
-
- | BXH5 |
- RI 05c-3 |
-
-
- | BXH5 |
- *RI 05c-4 |
-
-
- | BXH6 |
- RI 06c-1 |
-
-
- | BXH6 |
- RI 06c-2 |
-
-
- | BXH6 |
- RI 06c-3 |
-
-
- | BXH6 |
- *RI 06c-4 |
-
-
- | BXH8 |
- RI 08c-1 |
-
-
- | BXH8 |
- RI 08c-2 |
-
-
- | BXH8 |
- RI 08c-3 |
-
-
- | BXH8 |
- RI 08c-4 |
-
-
- | BXH9 |
- RI 09c-1 |
-
-
- | BXH9 |
- RI 09c-2 |
-
-
- | BXH9 |
- RI 09c-3 |
-
-
- | BXH9 |
- RI 09c-4 |
-
-
- | BXH10 |
- RI 10c-1 |
-
-
- | BXH10 |
- RI 10c-2 |
-
-
- | BXH10 |
- RI 10c-3 |
-
-
- | BXH11 |
- RI 11c-1 |
-
-
- | BXH11 |
- RI 11c-2 |
-
-
- | BXH11 |
- RI 11c-3 |
-
-
- | BXH11 |
- *RI 11c-4 |
-
-
- | BXH12 |
- RI 12c-1 |
-
-
- | BXH12 |
- RI 12c-2 |
-
-
- | BXH12 |
- RI 12c-3 |
-
-
- | BXH12 |
- RI 12c-4 |
-
-
- | BXH13 |
- RI 13c-1 |
-
-
- | BXH13 |
- RI 13c-2 |
-
-
- | BXH13 |
- RI 13c-3 |
-
-
- | BXH13 |
- RI 13c-4 |
-
-
-
- |
-
-
-
-
-*: These eight arrays were excluded in the final strain summary data. See section of Quality Control for further explanation.
diff --git a/general/datasets/LVF2_M_0704_M/acknowledgment.rtf b/general/datasets/LVF2_M_0704_M/acknowledgment.rtf
deleted file mode 100644
index 42f7eec..0000000
--- a/general/datasets/LVF2_M_0704_M/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This project was supported in part by NIH/NIDDK 5803701, NIH/NIDDK 66369-01 and American Diabetes Association 7-03-IG-01 to Alan D. Attie, USDA CSREES grants to the University of Wisconsin-Madison to Brian S. Yandell, and HHMI grant A-53-1200-4 to Christina Kendziorski.
-
-B6BTBRF2 Liver Database. All of the original (B6 x BTBR)F2-ob/ob liver mRNA M430AB array data were generated by Hong Lan and Alan Attie at The University of Wisconsin-Madison. For contact and citations and other information on these data sets, please review the INFO pages and contact Drs. Alan Attie, Christina Kendziorski, and Brian Yandell regarding use of this data set in publications or projects.
diff --git a/general/datasets/LVF2_M_0704_M/cases.rtf b/general/datasets/LVF2_M_0704_M/cases.rtf
deleted file mode 100644
index ece7be7..0000000
--- a/general/datasets/LVF2_M_0704_M/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The F2-ob/ob mice were chosen from a mapping panel that we created to map diabetes related physiological phenotypes (Stoehr et al. 2000). About 110 of these F2-ob/ob mice were also used to map mRNA abundance traits derived by quantitative real-time RT-PCR (Lan et al. 2003). The sixty F2-ob/ob mice that were used to generate microarray-derived mRNA abundance traits were selected from the 110 mice based on a selective phenotyping algorithm (Jin et al. 2004). The F2-ob/ob mice were housed at weaning at the University of Wisconsin-Madison animal care facility on a 12-h light/dark cycle. Mice were provided Purina Formulab Chow 5008 (6.5% fat) and acidified water ad libitum. Mice were killed at 14 weeks of age by CO2 asphyxiation after a 4-hour fast. The livers, along with other tissues, were immediately foil wrapped and frozen in liquid nitrogen, and subsequently transferred to -80 °C freezers for storage.
diff --git a/general/datasets/LVF2_M_0704_M/notes.rtf b/general/datasets/LVF2_M_0704_M/notes.rtf
deleted file mode 100644
index 5e9c255..0000000
--- a/general/datasets/LVF2_M_0704_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and Alan Attie, July 2, 2004. Updated by RWW, Aug 20, 5, 2004; April 7, 2005; August 20, 2005.
-
diff --git a/general/datasets/LVF2_M_0704_M/platform.rtf b/general/datasets/LVF2_M_0704_M/platform.rtf
deleted file mode 100644
index 29c90d3..0000000
--- a/general/datasets/LVF2_M_0704_M/platform.rtf
+++ /dev/null
@@ -1,876 +0,0 @@
-
-Affymetrix Mouse Genome 430A and 430B array pairs: The 430A and B array pairs collectively consist of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (some are variant transcipts and many are duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequence as the 430 2.0 series. However, roughy 75000 probes differ between those on A and B arrays and those on the 430 2.0.
-
-
-Liver samples were assayed individually using 60 M430A and B Affymetrix oligonucleotide microarray pairs. Each array ID is denoted by a 10-letter code: the first three letters represent the F2-ob/ob mouse ID number, the fourth letter (either A or B) denotes M430A or M430B arrays, and the last six letters represent the date the array was scanned (MMDDYY).
-
-All 120 M430A and B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Animal ID, sex, and ArrayID.
-
-
-
-
-
-
-
-
-
- |
- Animal ID
- |
-
- sex
- |
-
- MOE430A ArrayID
- |
-
- MOE430B ArrayID
- |
-
-
- |
- 2
- |
-
- M
- |
-
- 002A100203
- |
-
- 002B100503
- |
-
-
- |
- 12
- |
-
- M
- |
-
- 012A100203
- |
-
- 012B100503
- |
-
-
- |
- 22
- |
-
- M
- |
-
- 022A100203
- |
-
- 022B100503
- |
-
-
- |
- 44
- |
-
- M
- |
-
- 044A100203
- |
-
- 044B100503
- |
-
-
- |
- 46
- |
-
- M
- |
-
- 046A100203
- |
-
- 046B100503
- |
-
-
- |
- 61
- |
-
- M
- |
-
- 061A100203
- |
-
- 061B100503
- |
-
-
- |
- 100
- |
-
- M
- |
-
- 100A100303
- |
-
- 100B100503
- |
-
-
- |
- 105
- |
-
- F
- |
-
- 105A100303
- |
-
- 105B100503
- |
-
-
- |
- 111
- |
-
- F
- |
-
- 111A100303
- |
-
- 111B100503
- |
-
-
- |
- 123
- |
-
- M
- |
-
- 123A100303
- |
-
- 123B100503
- |
-
-
- |
- 156
- |
-
- F
- |
-
- 156A100303
- |
-
- 156B100503
- |
-
-
- |
- 165
- |
-
- M
- |
-
- 165A100303
- |
-
- 165B100503
- |
-
-
- |
- 167
- |
-
- M
- |
-
- 167A100303
- |
-
- 167B100503
- |
-
-
- |
- 173
- |
-
- M
- |
-
- 173A100303
- |
-
- 173B100503
- |
-
-
- |
- 186
- |
-
- F
- |
-
- 186A100203
- |
-
- 186B100503
- |
-
-
- |
- 190
- |
-
- F
- |
-
- 190A100303
- |
-
- 190B100503
- |
-
-
- |
- 194
- |
-
- M
- |
-
- 194A100303
- |
-
- 194B100503
- |
-
-
- |
- 200
- |
-
- F
- |
-
- 200A100303
- |
-
- 200B100503
- |
-
-
- |
- 207
- |
-
- F
- |
-
- 207A100303
- |
-
- 207B100503
- |
-
-
- |
- 209
- |
-
- F
- |
-
- 209A100203
- |
-
- 209B100503
- |
-
-
- |
- 212
- |
-
- F
- |
-
- 212A100303
- |
-
- 212B100503
- |
-
-
- |
- 223
- |
-
- M
- |
-
- 223A100303
- |
-
- 223B100503
- |
-
-
- |
- 224
- |
-
- M
- |
-
- 224A100303
- |
-
- 224B100503
- |
-
-
- |
- 253
- |
-
- F
- |
-
- 253A100303
- |
-
- 253B100503
- |
-
-
- |
- 254
- |
-
- F
- |
-
- 254A100603
- |
-
- 254B100703
- |
-
-
- |
- 260
- |
-
- F
- |
-
- 260A100603
- |
-
- 260B100703
- |
-
-
- |
- 264
- |
-
- F
- |
-
- 264A100603
- |
-
- 264B100703
- |
-
-
- |
- 310
- |
-
- F
- |
-
- 310A100603
- |
-
- 310B100703
- |
-
-
- |
- 317
- |
-
- M
- |
-
- 317A100603
- |
-
- 317B100703
- |
-
-
- |
- 318
- |
-
- F
- |
-
- 318A100603
- |
-
- 318B100703
- |
-
-
- |
- 324
- |
-
- F
- |
-
- 324A100603
- |
-
- 324B100703
- |
-
-
- |
- 327
- |
-
- F
- |
-
- 327A100603
- |
-
- 327B100703
- |
-
-
- |
- 343
- |
-
- M
- |
-
- 343A100603
- |
-
- 343B100703
- |
-
-
- |
- 416
- |
-
- M
- |
-
- 416A100603
- |
-
- 416B100703
- |
-
-
- |
- 419
- |
-
- F
- |
-
- 419A100603
- |
-
- 419B100703
- |
-
-
- |
- 438
- |
-
- M
- |
-
- 438A100603
- |
-
- 438B100703
- |
-
-
- |
- 440
- |
-
- M
- |
-
- 440A100603
- |
-
- 440B100803
- |
-
-
- |
- 455
- |
-
- M
- |
-
- 455A100603
- |
-
- 455B100803
- |
-
-
- |
- 458
- |
-
- F
- |
-
- 458A100603
- |
-
- 458B100803
- |
-
-
- |
- 472
- |
-
- M
- |
-
- 472A100603
- |
-
- 472B100803
- |
-
-
- |
- 474
- |
-
- F
- |
-
- 474A100603
- |
-
- 474B100803
- |
-
-
- |
- 479
- |
-
- F
- |
-
- 479A100603
- |
-
- 479B100803
- |
-
-
- |
- 484
- |
-
- F
- |
-
- 484A100603
- |
-
- 484B100803
- |
-
-
- |
- 486
- |
-
- F
- |
-
- 486A100603
- |
-
- 486B100803
- |
-
-
- |
- 489
- |
-
- F
- |
-
- 489A100603
- |
-
- 489B100803
- |
-
-
- |
- 493
- |
-
- F
- |
-
- 493A100603
- |
-
- 493B100803
- |
-
-
- |
- 499
- |
-
- M
- |
-
- 499A100603
- |
-
- 499B100803
- |
-
-
- |
- 513
- |
-
- M
- |
-
- 513A100603
- |
-
- 513B100803
- |
-
-
- |
- 517
- |
-
- M
- |
-
- 517A100703
- |
-
- 517B100803
- |
-
-
- |
- 523
- |
-
- M
- |
-
- 523A100703
- |
-
- 523B100803
- |
-
-
- |
- 549
- |
-
- M
- |
-
- 549A100703
- |
-
- 549B100803
- |
-
-
- |
- 553
- |
-
- F
- |
-
- 553A100703
- |
-
- 553B100803
- |
-
-
- |
- 554
- |
-
- F
- |
-
- 554A100703
- |
-
- 554B100803
- |
-
-
- |
- 559
- |
-
- F
- |
-
- 559A100703
- |
-
- 559B100803
- |
-
-
- |
- 560
- |
-
- F
- |
-
- 560A100703
- |
-
- 560B100803
- |
-
-
- |
- 566
- |
-
- M
- |
-
- 566A100703
- |
-
- 566B100803
- |
-
-
- |
- 608
- |
-
- F
- |
-
- 608A100703
- |
-
- 608B100803
- |
-
-
- |
- 615
- |
-
- F
- |
-
- 615A100703
- |
-
- 615B100803
- |
-
-
- |
- 617
- |
-
- M
- |
-
- 617A100703
- |
-
- 617B100803
- |
-
-
- |
- 620
- |
-
- M
- |
-
- 620A100703
- |
-
- 620B100803
- |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/LVF2_M_0704_M/processing.rtf b/general/datasets/LVF2_M_0704_M/processing.rtf
deleted file mode 100644
index 3ed08db..0000000
--- a/general/datasets/LVF2_M_0704_M/processing.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z scores for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-Probe set data from the .CHP file: The expression data were generated using MAS5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-The 60 mice were each genotyped at 194 MIT microsatellite markers an average of approximately 10 cM (and always < 30 cM) apart across the entire genome (Y chromsome, excepted). The genotyping error-check routine implemented within R/qtl (Broman et al. 2003) showed no likely errors at p <0.01 probability.
diff --git a/general/datasets/LVF2_M_0704_M/summary.rtf b/general/datasets/LVF2_M_0704_M/summary.rtf
deleted file mode 100644
index 9492e80..0000000
--- a/general/datasets/LVF2_M_0704_M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This August 2005 data freeze provides estimates of mRNA expression in adult liver from a selected set of 60 F2 animals generated by crossing strain C57BL/6J-ob/+ with BTBR and then intercrossing the F1-ob/+ progeny. The F2 progeny included, in a total of 350 progeny, 110 ob/ob progeny homozygous for the obese (ob) allele of leptin (Lep) on Chr 6. Sixty of the ob/ob progeny were selected for expression assays. This selection means that the data set is not useful for defining QTLs on Chr 6. Array data were generated at the University of Wisconsin by Alan Attie and colleagues. This data release accompanies the paper of Lan and colleagues (in submission, 2005). A set of 24 complementary phenotypes such as body weight, blood chemistry, and rtPCR results, are also available for these animals and an additional set of 50 F2s (see Phenotypes database. Samples were hybridized to 60 pairs of Affymetrix M430A and B arrays. This particular data set was processed using the RMA normalization method. To simplify comparison among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of two units.
-
diff --git a/general/datasets/LVF2_M_0704_M/tissue.rtf b/general/datasets/LVF2_M_0704_M/tissue.rtf
deleted file mode 100644
index de3964c..0000000
--- a/general/datasets/LVF2_M_0704_M/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Liver samples were taken from 29 male and 31 females. Total RNA was isolated with RNAzol Reagent (Tel-Test, Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer's protocol. The extracted RNA was purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for concentration. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. RNA samples were converted to cDNA, and then biotin-labeled cRNA according to Affymetrix Expression Analysis Technical Manual. The labeled samples were hybridized to the M430A, and subsequently the M430B array. The hybridization, washing and scanning steps were carried out by Hong Lan using the Affymetrix core facility at the Gene Expression Center of University of Wisconsin-Madison.
-
diff --git a/general/datasets/LVF2_M_0704_R/acknowledgment.rtf b/general/datasets/LVF2_M_0704_R/acknowledgment.rtf
deleted file mode 100644
index 42f7eec..0000000
--- a/general/datasets/LVF2_M_0704_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This project was supported in part by NIH/NIDDK 5803701, NIH/NIDDK 66369-01 and American Diabetes Association 7-03-IG-01 to Alan D. Attie, USDA CSREES grants to the University of Wisconsin-Madison to Brian S. Yandell, and HHMI grant A-53-1200-4 to Christina Kendziorski.
-
-B6BTBRF2 Liver Database. All of the original (B6 x BTBR)F2-ob/ob liver mRNA M430AB array data were generated by Hong Lan and Alan Attie at The University of Wisconsin-Madison. For contact and citations and other information on these data sets, please review the INFO pages and contact Drs. Alan Attie, Christina Kendziorski, and Brian Yandell regarding use of this data set in publications or projects.
diff --git a/general/datasets/LVF2_M_0704_R/cases.rtf b/general/datasets/LVF2_M_0704_R/cases.rtf
deleted file mode 100644
index ece7be7..0000000
--- a/general/datasets/LVF2_M_0704_R/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The F2-ob/ob mice were chosen from a mapping panel that we created to map diabetes related physiological phenotypes (Stoehr et al. 2000). About 110 of these F2-ob/ob mice were also used to map mRNA abundance traits derived by quantitative real-time RT-PCR (Lan et al. 2003). The sixty F2-ob/ob mice that were used to generate microarray-derived mRNA abundance traits were selected from the 110 mice based on a selective phenotyping algorithm (Jin et al. 2004). The F2-ob/ob mice were housed at weaning at the University of Wisconsin-Madison animal care facility on a 12-h light/dark cycle. Mice were provided Purina Formulab Chow 5008 (6.5% fat) and acidified water ad libitum. Mice were killed at 14 weeks of age by CO2 asphyxiation after a 4-hour fast. The livers, along with other tissues, were immediately foil wrapped and frozen in liquid nitrogen, and subsequently transferred to -80 °C freezers for storage.
diff --git a/general/datasets/LVF2_M_0704_R/notes.rtf b/general/datasets/LVF2_M_0704_R/notes.rtf
deleted file mode 100644
index 5e9c255..0000000
--- a/general/datasets/LVF2_M_0704_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by RWW and Alan Attie, July 2, 2004. Updated by RWW, Aug 20, 5, 2004; April 7, 2005; August 20, 2005.
-
diff --git a/general/datasets/LVF2_M_0704_R/platform.rtf b/general/datasets/LVF2_M_0704_R/platform.rtf
deleted file mode 100644
index 29c90d3..0000000
--- a/general/datasets/LVF2_M_0704_R/platform.rtf
+++ /dev/null
@@ -1,876 +0,0 @@
-
-Affymetrix Mouse Genome 430A and 430B array pairs: The 430A and B array pairs collectively consist of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (some are variant transcipts and many are duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequence as the 430 2.0 series. However, roughy 75000 probes differ between those on A and B arrays and those on the 430 2.0.
-
-
-Liver samples were assayed individually using 60 M430A and B Affymetrix oligonucleotide microarray pairs. Each array ID is denoted by a 10-letter code: the first three letters represent the F2-ob/ob mouse ID number, the fourth letter (either A or B) denotes M430A or M430B arrays, and the last six letters represent the date the array was scanned (MMDDYY).
-
-All 120 M430A and B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Animal ID, sex, and ArrayID.
-
-
-
-
-
-
-
-
-
- |
- Animal ID
- |
-
- sex
- |
-
- MOE430A ArrayID
- |
-
- MOE430B ArrayID
- |
-
-
- |
- 2
- |
-
- M
- |
-
- 002A100203
- |
-
- 002B100503
- |
-
-
- |
- 12
- |
-
- M
- |
-
- 012A100203
- |
-
- 012B100503
- |
-
-
- |
- 22
- |
-
- M
- |
-
- 022A100203
- |
-
- 022B100503
- |
-
-
- |
- 44
- |
-
- M
- |
-
- 044A100203
- |
-
- 044B100503
- |
-
-
- |
- 46
- |
-
- M
- |
-
- 046A100203
- |
-
- 046B100503
- |
-
-
- |
- 61
- |
-
- M
- |
-
- 061A100203
- |
-
- 061B100503
- |
-
-
- |
- 100
- |
-
- M
- |
-
- 100A100303
- |
-
- 100B100503
- |
-
-
- |
- 105
- |
-
- F
- |
-
- 105A100303
- |
-
- 105B100503
- |
-
-
- |
- 111
- |
-
- F
- |
-
- 111A100303
- |
-
- 111B100503
- |
-
-
- |
- 123
- |
-
- M
- |
-
- 123A100303
- |
-
- 123B100503
- |
-
-
- |
- 156
- |
-
- F
- |
-
- 156A100303
- |
-
- 156B100503
- |
-
-
- |
- 165
- |
-
- M
- |
-
- 165A100303
- |
-
- 165B100503
- |
-
-
- |
- 167
- |
-
- M
- |
-
- 167A100303
- |
-
- 167B100503
- |
-
-
- |
- 173
- |
-
- M
- |
-
- 173A100303
- |
-
- 173B100503
- |
-
-
- |
- 186
- |
-
- F
- |
-
- 186A100203
- |
-
- 186B100503
- |
-
-
- |
- 190
- |
-
- F
- |
-
- 190A100303
- |
-
- 190B100503
- |
-
-
- |
- 194
- |
-
- M
- |
-
- 194A100303
- |
-
- 194B100503
- |
-
-
- |
- 200
- |
-
- F
- |
-
- 200A100303
- |
-
- 200B100503
- |
-
-
- |
- 207
- |
-
- F
- |
-
- 207A100303
- |
-
- 207B100503
- |
-
-
- |
- 209
- |
-
- F
- |
-
- 209A100203
- |
-
- 209B100503
- |
-
-
- |
- 212
- |
-
- F
- |
-
- 212A100303
- |
-
- 212B100503
- |
-
-
- |
- 223
- |
-
- M
- |
-
- 223A100303
- |
-
- 223B100503
- |
-
-
- |
- 224
- |
-
- M
- |
-
- 224A100303
- |
-
- 224B100503
- |
-
-
- |
- 253
- |
-
- F
- |
-
- 253A100303
- |
-
- 253B100503
- |
-
-
- |
- 254
- |
-
- F
- |
-
- 254A100603
- |
-
- 254B100703
- |
-
-
- |
- 260
- |
-
- F
- |
-
- 260A100603
- |
-
- 260B100703
- |
-
-
- |
- 264
- |
-
- F
- |
-
- 264A100603
- |
-
- 264B100703
- |
-
-
- |
- 310
- |
-
- F
- |
-
- 310A100603
- |
-
- 310B100703
- |
-
-
- |
- 317
- |
-
- M
- |
-
- 317A100603
- |
-
- 317B100703
- |
-
-
- |
- 318
- |
-
- F
- |
-
- 318A100603
- |
-
- 318B100703
- |
-
-
- |
- 324
- |
-
- F
- |
-
- 324A100603
- |
-
- 324B100703
- |
-
-
- |
- 327
- |
-
- F
- |
-
- 327A100603
- |
-
- 327B100703
- |
-
-
- |
- 343
- |
-
- M
- |
-
- 343A100603
- |
-
- 343B100703
- |
-
-
- |
- 416
- |
-
- M
- |
-
- 416A100603
- |
-
- 416B100703
- |
-
-
- |
- 419
- |
-
- F
- |
-
- 419A100603
- |
-
- 419B100703
- |
-
-
- |
- 438
- |
-
- M
- |
-
- 438A100603
- |
-
- 438B100703
- |
-
-
- |
- 440
- |
-
- M
- |
-
- 440A100603
- |
-
- 440B100803
- |
-
-
- |
- 455
- |
-
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- 455A100603
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- 458
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- F
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- 474
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- 484A100603
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- 486A100603
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- 489
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- F
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- 489A100603
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- 489B100803
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- 493
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- F
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- 493A100603
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- 499
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- M
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- 499A100603
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- 499B100803
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- 513A100603
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- 513B100803
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- 517A100703
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- 517B100803
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-
-
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- 523
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-
- M
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- 523A100703
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- 523B100803
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diff --git a/general/datasets/LVF2_M_0704_R/processing.rtf b/general/datasets/LVF2_M_0704_R/processing.rtf
deleted file mode 100644
index 3ed08db..0000000
--- a/general/datasets/LVF2_M_0704_R/processing.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z scores for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-Probe set data from the .CHP file: The expression data were generated using MAS5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-The 60 mice were each genotyped at 194 MIT microsatellite markers an average of approximately 10 cM (and always < 30 cM) apart across the entire genome (Y chromsome, excepted). The genotyping error-check routine implemented within R/qtl (Broman et al. 2003) showed no likely errors at p <0.01 probability.
diff --git a/general/datasets/LVF2_M_0704_R/summary.rtf b/general/datasets/LVF2_M_0704_R/summary.rtf
deleted file mode 100644
index 9492e80..0000000
--- a/general/datasets/LVF2_M_0704_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This August 2005 data freeze provides estimates of mRNA expression in adult liver from a selected set of 60 F2 animals generated by crossing strain C57BL/6J-ob/+ with BTBR and then intercrossing the F1-ob/+ progeny. The F2 progeny included, in a total of 350 progeny, 110 ob/ob progeny homozygous for the obese (ob) allele of leptin (Lep) on Chr 6. Sixty of the ob/ob progeny were selected for expression assays. This selection means that the data set is not useful for defining QTLs on Chr 6. Array data were generated at the University of Wisconsin by Alan Attie and colleagues. This data release accompanies the paper of Lan and colleagues (in submission, 2005). A set of 24 complementary phenotypes such as body weight, blood chemistry, and rtPCR results, are also available for these animals and an additional set of 50 F2s (see Phenotypes database. Samples were hybridized to 60 pairs of Affymetrix M430A and B arrays. This particular data set was processed using the RMA normalization method. To simplify comparison among transforms, RMA values of each array were adjusted to an average of 8 units and a standard deviation of two units.
-
diff --git a/general/datasets/LVF2_M_0704_R/tissue.rtf b/general/datasets/LVF2_M_0704_R/tissue.rtf
deleted file mode 100644
index de3964c..0000000
--- a/general/datasets/LVF2_M_0704_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Liver samples were taken from 29 male and 31 females. Total RNA was isolated with RNAzol Reagent (Tel-Test, Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer's protocol. The extracted RNA was purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for concentration. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. RNA samples were converted to cDNA, and then biotin-labeled cRNA according to Affymetrix Expression Analysis Technical Manual. The labeled samples were hybridized to the M430A, and subsequently the M430B array. The hybridization, washing and scanning steps were carried out by Hong Lan using the Affymetrix core facility at the Gene Expression Center of University of Wisconsin-Madison.
-
diff --git a/general/datasets/LV_G_0106_B/platform.rtf b/general/datasets/LV_G_0106_B/platform.rtf
deleted file mode 100644
index dd35c6a..0000000
--- a/general/datasets/LV_G_0106_B/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The arrays were Agilent two color arrays.
diff --git a/general/datasets/LV_G_0106_B/processing.rtf b/general/datasets/LV_G_0106_B/processing.rtf
deleted file mode 100644
index ae2363c..0000000
--- a/general/datasets/LV_G_0106_B/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-We used a mix of C57BL/6J RNA as the reference (liver, kidney, lung, brain and spleen). Each measurement is the ratio of sample intensity over the reference intensity. The data was normalized using a robust LOWESS smoothing method that adjusts for non-linearity between the two color channels (see Yang Yee Hwa et. al., Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucl. Acid Res., 2002). We then took the log2 of these ratios. A value of 1 indicates that the expression of that gene in the sample is twice that of the reference. Since the reference, includes liver, the range of values is more modest than some other scales of gene expression. (From Dan Gatti, Sept 2012).
diff --git a/general/datasets/LV_G_0106_B/summary.rtf b/general/datasets/LV_G_0106_B/summary.rtf
deleted file mode 100644
index fe91a13..0000000
--- a/general/datasets/LV_G_0106_B/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Genome-level analysis of genetic regulation of liver gene expression networks
-
-Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I
-
-Hepatology. 2007 Aug;46(2):548-57
-
-Source: Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
-
-The liver is the primary site for the metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variations in gene expression levels, introduces complexity into research on liver disease. This study dissected genetic networks that control liver gene expression through the combination of large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive single-nucleotide polymorphism, haplotype, and phenotypic data are publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 37 BXD strains using Agilent oligonucleotide microarrays. These data were used to map quantitative trait loci (QTLs) responsible for variations in the expression of about 19,000 transcripts. We identified polymorphic local and distant QTLs, including several loci that control the expression of large numbers of genes in liver, by comparing the physical transcript position with the location of the controlling QTL. CONCLUSION: The data are available through a public web-based resource (www.genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses.
diff --git a/general/datasets/LV_G_0106_F/platform.rtf b/general/datasets/LV_G_0106_F/platform.rtf
deleted file mode 100644
index dd35c6a..0000000
--- a/general/datasets/LV_G_0106_F/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The arrays were Agilent two color arrays.
diff --git a/general/datasets/LV_G_0106_F/processing.rtf b/general/datasets/LV_G_0106_F/processing.rtf
deleted file mode 100644
index ae2363c..0000000
--- a/general/datasets/LV_G_0106_F/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-We used a mix of C57BL/6J RNA as the reference (liver, kidney, lung, brain and spleen). Each measurement is the ratio of sample intensity over the reference intensity. The data was normalized using a robust LOWESS smoothing method that adjusts for non-linearity between the two color channels (see Yang Yee Hwa et. al., Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucl. Acid Res., 2002). We then took the log2 of these ratios. A value of 1 indicates that the expression of that gene in the sample is twice that of the reference. Since the reference, includes liver, the range of values is more modest than some other scales of gene expression. (From Dan Gatti, Sept 2012).
diff --git a/general/datasets/LV_G_0106_F/summary.rtf b/general/datasets/LV_G_0106_F/summary.rtf
deleted file mode 100644
index fe91a13..0000000
--- a/general/datasets/LV_G_0106_F/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Genome-level analysis of genetic regulation of liver gene expression networks
-
-Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I
-
-Hepatology. 2007 Aug;46(2):548-57
-
-Source: Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
-
-The liver is the primary site for the metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variations in gene expression levels, introduces complexity into research on liver disease. This study dissected genetic networks that control liver gene expression through the combination of large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive single-nucleotide polymorphism, haplotype, and phenotypic data are publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 37 BXD strains using Agilent oligonucleotide microarrays. These data were used to map quantitative trait loci (QTLs) responsible for variations in the expression of about 19,000 transcripts. We identified polymorphic local and distant QTLs, including several loci that control the expression of large numbers of genes in liver, by comparing the physical transcript position with the location of the controlling QTL. CONCLUSION: The data are available through a public web-based resource (www.genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses.
diff --git a/general/datasets/LV_G_0106_M/platform.rtf b/general/datasets/LV_G_0106_M/platform.rtf
deleted file mode 100644
index dd35c6a..0000000
--- a/general/datasets/LV_G_0106_M/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The arrays were Agilent two color arrays.
diff --git a/general/datasets/LV_G_0106_M/processing.rtf b/general/datasets/LV_G_0106_M/processing.rtf
deleted file mode 100644
index ae2363c..0000000
--- a/general/datasets/LV_G_0106_M/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-We used a mix of C57BL/6J RNA as the reference (liver, kidney, lung, brain and spleen). Each measurement is the ratio of sample intensity over the reference intensity. The data was normalized using a robust LOWESS smoothing method that adjusts for non-linearity between the two color channels (see Yang Yee Hwa et. al., Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucl. Acid Res., 2002). We then took the log2 of these ratios. A value of 1 indicates that the expression of that gene in the sample is twice that of the reference. Since the reference, includes liver, the range of values is more modest than some other scales of gene expression. (From Dan Gatti, Sept 2012).
diff --git a/general/datasets/LV_G_0106_M/summary.rtf b/general/datasets/LV_G_0106_M/summary.rtf
deleted file mode 100644
index fe91a13..0000000
--- a/general/datasets/LV_G_0106_M/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Genome-level analysis of genetic regulation of liver gene expression networks
-
-Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I
-
-Hepatology. 2007 Aug;46(2):548-57
-
-Source: Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
-
-The liver is the primary site for the metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variations in gene expression levels, introduces complexity into research on liver disease. This study dissected genetic networks that control liver gene expression through the combination of large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive single-nucleotide polymorphism, haplotype, and phenotypic data are publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 37 BXD strains using Agilent oligonucleotide microarrays. These data were used to map quantitative trait loci (QTLs) responsible for variations in the expression of about 19,000 transcripts. We identified polymorphic local and distant QTLs, including several loci that control the expression of large numbers of genes in liver, by comparing the physical transcript position with the location of the controlling QTL. CONCLUSION: The data are available through a public web-based resource (www.genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses.
diff --git a/general/datasets/LV_G_0704_A/platform.rtf b/general/datasets/LV_G_0704_A/platform.rtf
deleted file mode 100644
index dd35c6a..0000000
--- a/general/datasets/LV_G_0704_A/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The arrays were Agilent two color arrays.
diff --git a/general/datasets/LV_G_0704_A/processing.rtf b/general/datasets/LV_G_0704_A/processing.rtf
deleted file mode 100644
index ae2363c..0000000
--- a/general/datasets/LV_G_0704_A/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-We used a mix of C57BL/6J RNA as the reference (liver, kidney, lung, brain and spleen). Each measurement is the ratio of sample intensity over the reference intensity. The data was normalized using a robust LOWESS smoothing method that adjusts for non-linearity between the two color channels (see Yang Yee Hwa et. al., Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucl. Acid Res., 2002). We then took the log2 of these ratios. A value of 1 indicates that the expression of that gene in the sample is twice that of the reference. Since the reference, includes liver, the range of values is more modest than some other scales of gene expression. (From Dan Gatti, Sept 2012).
diff --git a/general/datasets/LV_G_0704_A/summary.rtf b/general/datasets/LV_G_0704_A/summary.rtf
deleted file mode 100644
index fe91a13..0000000
--- a/general/datasets/LV_G_0704_A/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Genome-level analysis of genetic regulation of liver gene expression networks
-
-Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I
-
-Hepatology. 2007 Aug;46(2):548-57
-
-Source: Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
-
-The liver is the primary site for the metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variations in gene expression levels, introduces complexity into research on liver disease. This study dissected genetic networks that control liver gene expression through the combination of large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive single-nucleotide polymorphism, haplotype, and phenotypic data are publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 37 BXD strains using Agilent oligonucleotide microarrays. These data were used to map quantitative trait loci (QTLs) responsible for variations in the expression of about 19,000 transcripts. We identified polymorphic local and distant QTLs, including several loci that control the expression of large numbers of genes in liver, by comparing the physical transcript position with the location of the controlling QTL. CONCLUSION: The data are available through a public web-based resource (www.genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses.
diff --git a/general/datasets/LV_G_0704_R/platform.rtf b/general/datasets/LV_G_0704_R/platform.rtf
deleted file mode 100644
index dd35c6a..0000000
--- a/general/datasets/LV_G_0704_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The arrays were Agilent two color arrays.
diff --git a/general/datasets/LV_G_0704_R/processing.rtf b/general/datasets/LV_G_0704_R/processing.rtf
deleted file mode 100644
index ae2363c..0000000
--- a/general/datasets/LV_G_0704_R/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-We used a mix of C57BL/6J RNA as the reference (liver, kidney, lung, brain and spleen). Each measurement is the ratio of sample intensity over the reference intensity. The data was normalized using a robust LOWESS smoothing method that adjusts for non-linearity between the two color channels (see Yang Yee Hwa et. al., Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucl. Acid Res., 2002). We then took the log2 of these ratios. A value of 1 indicates that the expression of that gene in the sample is twice that of the reference. Since the reference, includes liver, the range of values is more modest than some other scales of gene expression. (From Dan Gatti, Sept 2012).
diff --git a/general/datasets/LV_G_0704_R/summary.rtf b/general/datasets/LV_G_0704_R/summary.rtf
deleted file mode 100644
index fe91a13..0000000
--- a/general/datasets/LV_G_0704_R/summary.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-Genome-level analysis of genetic regulation of liver gene expression networks
-
-Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I
-
-Hepatology. 2007 Aug;46(2):548-57
-
-Source: Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
-
-The liver is the primary site for the metabolism of nutrients, drugs, and chemical agents. Although metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variations in gene expression levels, introduces complexity into research on liver disease. This study dissected genetic networks that control liver gene expression through the combination of large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive single-nucleotide polymorphism, haplotype, and phenotypic data are publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 37 BXD strains using Agilent oligonucleotide microarrays. These data were used to map quantitative trait loci (QTLs) responsible for variations in the expression of about 19,000 transcripts. We identified polymorphic local and distant QTLs, including several loci that control the expression of large numbers of genes in liver, by comparing the physical transcript position with the location of the controlling QTL. CONCLUSION: The data are available through a public web-based resource (www.genenetwork.org) that allows custom data mining, identification of coregulated transcripts and correlated phenotypes, cross-tissue, and cross-species comparisons, as well as testing of a broad array of hypotheses.
diff --git a/general/datasets/LXSGeno/summary.rtf b/general/datasets/LXSGeno/summary.rtf
deleted file mode 100644
index dc176b3..0000000
--- a/general/datasets/LXSGeno/summary.rtf
+++ /dev/null
@@ -1,21 +0,0 @@
-
-The LXS genotype file used by WebQTL consists of a set of 2659 carefully error-checked SNPs and microsatellites typed across all 77 strains. Download all LXS genotypes as a 478 Kb text file.
-
-LXS strains were derived from a cross between the following 8 strains: A, AKR, BALB/c, C3H/2, C57BL, DBA/2, IS/Bi, and RIII. All of these strains were maintained at the Institute for Behavior Genetics, Bolder Colorado by Dr. Gerald McClearn and colleagues. C3H/2 is presumably the same as C3H/Crgl/2 (see paper by Green V (1981) Behavioral and Neural Biology 31:56). C57BL is presumably the same as C57BL/Crgl. IS/Bi is extinct.
-
-See Williams, Bennett, Johnson and colleagues (2004) for more details on the LXS panel.
-
-
- About the genotypes used in these studies:
-
-WebQTL mapping algorithms rely on an initial set of 330 microsatellites genotyped in 2002 and 2003 at UTHSC (labeled Mit). The current expanded marker set (n = 2659) have been selected from a total of 13377 SNPs genotyped in collaboration with Jonathan Flint, Richard Mott, Beth Bennett, Lu Lu, and Jing Gu. Closely linked genetic markers often have the same strain distribution pattern (SDP) across the LXS strains. For computational efficiency, we only use a single marker associated with each SDP.
-
-All LXS strains are from the Institute of Behavioral Genetics, Boulder Colorado. They were generated by Beth Bennett, Tom Johnson, and colleagues over a ten-year period. All of these strains are beyond the 22 generation of serial sibling mating and are formally fully inbred.
-
- Reference:
-
-
-Williams RW, Bennett B, Lu L, Gu J, DeFries JC, Carosone-Link P, Rikke B, Belknap JK, Johnson TE (2004) Genetic structure of the LXS panel of recombinant inbred mouse strains. Mammalian Genome 15:637-647
-
-
-This text file was originally written by RW Williams, July 26, 2005.
diff --git a/general/datasets/LXSPublish/acknowledgment.rtf b/general/datasets/LXSPublish/acknowledgment.rtf
deleted file mode 100644
index 3d302d7..0000000
--- a/general/datasets/LXSPublish/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The initial construction of this database was performed by Beth Bennett and colleagues at the University of Colorado, Boulder, and by Lu Lu and colleagues at the University of Tennessee Health Sciences Center.
diff --git a/general/datasets/LXSPublish/cases.rtf b/general/datasets/LXSPublish/cases.rtf
deleted file mode 100644
index 6bd4be6..0000000
--- a/general/datasets/LXSPublish/cases.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-The parental strains of the LXS set are Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) strains. These parental strains have been phenotyped intensively by behavioral geneticists and neuropharmacologists for a decade (e.g., Markel PD et al. 1995, Hanania and Zahniser 2004. The LXS strains have an intriguing history and trace back to an 8-way cross initiated in the 1950s by Gerald McClearn, the dean of mouse behavior genetics.
-
-The LXS panel has recently been genotyped at 330 microsatellite markers, and this panel can already be used to map Mendelian and quantitative trait loci. As an example, the current prototype LXS phenotype database contains information on coat color treated as an ordinal trait (1 = albino, 5 = black). This simple trait produces a QTL with an LRS score of 73 (LOD score of ~16) on Chr 7 with a peak within a few megabases of the tyrosinase gene.
-
-Submitting data and reporting errors:
-
-The utility of this resource increases greatly as new phenotypes are added to the database. To submit new data or report errors, please contact Beth Bennett at bennettb@colorado.edu or Lu Lu at lulu@uthsc.edu
diff --git a/general/datasets/LXSPublish/summary.rtf b/general/datasets/LXSPublish/summary.rtf
deleted file mode 100644
index af9cf31..0000000
--- a/general/datasets/LXSPublish/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The set of 77 LXS recombinant inbred strains were generated at the Institute for Behavioral Genetics (University of Colorado, Boulder) by Beth Bennett, John DeFries, Tom Johnson, and colleages. Strains first became available for phenotyping in 2003. The large size of this panel ensures good power in genetic studies of a wide variety of complex traits.
diff --git a/general/datasets/MA_M2F_0706_R/acknowledgment.rtf b/general/datasets/MA_M2F_0706_R/acknowledgment.rtf
deleted file mode 100644
index fea38e8..0000000
--- a/general/datasets/MA_M2F_0706_R/acknowledgment.rtf
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:
-
-
- - Erwin Bottinger, M.D.
- Grant Support: R01 DK60043-04
- - Russell Chesney, M.D.
- Grant Support: Le Bonheur Chair of Excellence in Pediatrics II
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Peter Mundel
- Grant Support: NIH R01DK57683, NIH R01 DK 62472
- - Paul Klotman
- Grant Support: PO1 DK56492, PO1 DK56492.
- - Matthew Breyer
- Grant Support: DK-38226
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/MA_M2F_0706_R/cases.rtf b/general/datasets/MA_M2F_0706_R/cases.rtf
deleted file mode 100644
index 465b87c..0000000
--- a/general/datasets/MA_M2F_0706_R/cases.rtf
+++ /dev/null
@@ -1,44 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-
- - BTBR T+tf/J
- Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - D2B6F1
- F1 hybrid generated by crossing C57BL/6J with DBA/2J
-
-
-These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>
-
-
diff --git a/general/datasets/MA_M2F_0706_R/experiment-design.rtf b/general/datasets/MA_M2F_0706_R/experiment-design.rtf
deleted file mode 100644
index 464e50d..0000000
--- a/general/datasets/MA_M2F_0706_R/experiment-design.rtf
+++ /dev/null
@@ -1,1864 +0,0 @@
-
-Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
-
-Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
-
-
-This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
-
-
-
-
-
- | Microarray_ID |
- # mice |
- Microarray Date |
- GAPDH (3`/5`) |
- % present |
- strains |
- generation |
- sex |
- age |
- Mice Source |
-
-
- | GKHI-KS-050603.07-051706 |
- 3 |
- 05/14/02 |
- 0.73 |
- 37.6 |
- C57BL/6J |
- |
- M |
- 56 |
- UTM RW |
-
-
- | GKHI-KS-070803.01-051706 |
- 3 |
- 05/14/02 |
- 0.75 |
- 41.6 |
- C57BL/6J |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-DBA-Male-070706 |
- 2 |
- 07/06/02 |
- 0.71 |
- 37.3 |
- DBA/2J |
- |
- M |
- 56 |
- JAX |
-
-
- | GKHI_KS_121404.75-042106 |
- 4 |
- 04/18/02 |
- |
- |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.75-033006 |
- 4 |
- 03/19/02 |
- 0.73 |
- 48.5 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.78-042006 |
- 4 |
- 04/17/02 |
- 0.83 |
- 40.6 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_070804.39-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 39.0 |
- D2B6F1 |
- |
- M |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_030904.01-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 35.9 |
- D2B6F1 |
- |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-121404.73-070706 |
- 2 |
- 07/06/02 |
- 0.76 |
- 36.3 |
- D2B6F1 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-010705.38-051206 |
- 5 |
- 05/09/02 |
- 0.81 |
- 39.9 |
- BXD1 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060905.19 |
- 5 |
- 06/05/02 |
- 0.75 |
- 42.3 |
- BXD1 |
- |
- M |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-051206.13-070706 |
- 3 |
- 07/06/02 |
- 0.71 |
- 36.3 |
- BXD1 |
- |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-021304.10-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 39.1 |
- BXD2 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-04-050406 |
- 3 |
- 05/01/02 |
- 0.80 |
- 37.6 |
- BXD5 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-010705-53-050306 |
- 5 |
- 05/01/02 |
- 0.76 |
- 37.1 |
- BXD5 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031103.01-062206 |
- 3 |
- 06/21/02 |
- 0.75 |
- 37.1 |
- BXD5 |
- |
- M |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-040505-51-050306 |
- 5 |
- 05/01/02 |
- 0.71 |
- 35.5 |
- BXD6 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-092705-29--050406 |
- 5 |
- 05/02/02 |
- 0.75 |
- 36.1 |
- BXD6 |
- 160 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_092404.01-042106 |
- 4 |
- 04/18/02 |
- 0.71 |
- 36.3 |
- BXD8 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051205-25-042706 |
- 5 |
- 04/23/02 |
- 0.92 |
- 37.9 |
- BXD8 |
- |
- F |
- 77 |
- UTM RW |
-
-
- | KS-021605-17-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 40.8 |
- BXD9 |
- |
- F |
- 67 |
- UTM RW |
-
-
- | KS-032905-32-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 36.8 |
- BXD9 |
- |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-062006.08-070706 |
- 3 |
- 07/06/02 |
- 0.74 |
- 36.3 |
- BXD9 |
- |
- M |
- 78 |
- UTM RW |
-
-
- | GKHI-KS-031505.22-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 39.5 |
- BXD11 |
- |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031605.01 |
- 5 |
- 06/05/02 |
- 0.74 |
- 43.4 |
- BXD11 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI_KS_102104.40-042106 |
- 4 |
- 04/18/02 |
- 0.72 |
- 38.5 |
- BXD12 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-112002.07-051106 |
- 2 |
- 05/08/02 |
- 0.77 |
- 42.0 |
- BXD12 |
- |
- F |
- 64 |
- UMemphis |
-
-
- | GKHI-KS-120904.33-051206 |
- 4 |
- 05/09/02 |
- 0.71 |
- 38.4 |
- BXD13 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-042304.01 |
- 4 |
- 06/05/02 |
- 0.71 |
- 44.1 |
- BXD13 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020905.34-051106 |
- 5 |
- 05/08/02 |
- 0.75 |
- 40.7 |
- BXD14 |
- |
- F |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-022405.46-051106 |
- 5 |
- 05/08/02 |
- 0.71 |
- 40.2 |
- BXD14 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-091704.09-062206 |
- 4 |
- 06/21/02 |
- 0.73 |
- 39.0 |
- BXD14 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-013004.45-062206 |
- 4 |
- 06/21/02 |
- 0.76 |
- 38.5 |
- BXD15 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022405.43-051106 |
- 5 |
- 05/08/02 |
- 0.73 |
- 40.5 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-041604.10-051106 |
- 4 |
- 05/08/02 |
- 0.73 |
- 42.6 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.01-051106 |
- 5 |
- 05/08/02 |
- 0.79 |
- 42.4 |
- BXD16 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.04-051106 |
- 5 |
- 05/08/02 |
- 0.77 |
- 39.9 |
- BXD16 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.10-051006 |
- 5 |
- 05/05/02 |
- 0.93 |
- 38.7 |
- BXD18 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052804.09-051106 |
- 4 |
- 05/05/02 |
- 0.67 |
- 37.6 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.47-051106 |
- 5 |
- 05/05/02 |
- 0.73 |
- 42.3 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.44-070706 |
- 3 |
- 07/06/02 |
- 0.73 |
- 36.1 |
- BXD19 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-062905.07-051106 |
- 5 |
- 05/05/02 |
- 0.72 |
- 37.9 |
- BXD20 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-072104.58-051106 |
- 4 |
- 05/05/02 |
- 0.73 |
- 37.0 |
- BXD20 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-050405.21-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 35.1 |
- BXD21 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040705.24 |
- 5 |
- 06/05/02 |
- 0.80 |
- 40.2 |
- BXD21 |
- |
- F |
- 99 |
- UAB |
-
-
- | GKHI-KS-110405.01-051006 |
- 5 |
- 05/05/02 |
- 0.71 |
- 42.1 |
- BXD22 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-110405.04-051006 |
- 5 |
- 05/05/02 |
- 0.76 |
- 40.6 |
- BXD22 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.01-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 36.4 |
- BXD23 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.04-051006 |
- 5 |
- 05/05/02 |
- 0.73 |
- 39.3 |
- BXD23 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI_KS_091704.13-042106 |
- 4 |
- 04/18/02 |
- 0.73 |
- 37.7 |
- BXD24 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-20-050206 |
- 3 |
- 04/30/02 |
- 0.77 |
- 36.3 |
- BXD24 |
- |
- F |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-021805.20-051006 |
- 5 |
- 05/05/02 |
- 0.83 |
- 40.5 |
- BXD25 |
- |
- F |
- 67 |
- UAB |
-
-
- | GKHI-KS-090705.05-062206 |
- 5 |
- 06/21/02 |
- 0.76 |
- 38.4 |
- BXD25 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-090705.03-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 40.1 |
- BXD25 |
- |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-022105.42-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 41.8 |
- BXD27 |
- |
- M |
- 70 |
- UAB |
-
-
- | GKHI-KS-032205.31-051006 |
- 5 |
- 05/05/02 |
- 0.74 |
- 39.0 |
- BXD27 |
- |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-060706.10-070706 |
- 3 |
- 07/06/02 |
- 0.69 |
- 37.8 |
- BXD27 |
- |
- F |
- 85 |
- UTM RW |
-
-
- | GKHI-KS-012805-41-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 34.2 |
- BXD28 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-44-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 35.8 |
- BXD28 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-38-050506 |
- 5 |
- 05/04/02 |
- 0.77 |
- 42.7 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-35-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 35.8 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-32-050506 |
- 5 |
- 05/04/02 |
- 0.74 |
- 39.9 |
- BXD31 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-100604-07-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 40.2 |
- BXD31 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-021605.26-051706 |
- 5 |
- 05/14/02 |
- 1.11 |
- 39.0 |
- BXD32 |
- |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-112002.01-051206 |
- 2 |
- 05/09/02 |
- 0.76 |
- 38.1 |
- BXD32 |
- |
- F |
- 60 |
- UMemphis |
-
-
- | GKHI-KS-072605-01-050506 |
- 5 |
- 05/04/02 |
- 0.79 |
- 41.3 |
- BXD33 |
- 50 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-091405-23-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 38.4 |
- BXD33 |
- 50 |
- M |
- 76 |
- UTM RW |
-
-
- | GKHI-KS-111104-18-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 42.2 |
- BXD36 |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031804-07-050506 |
- 4 |
- 05/04/02 |
- 0.85 |
- 42.5 |
- BXD36 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-092005.16-051206 |
- 5 |
- 05/09/02 |
- 0.72 |
- 37.2 |
- BXD38 |
- 46 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031403.01-060806 |
- 1 |
- 06/07/02 |
- 0.69 |
- 39.6 |
- BXD38 |
- |
- M |
- 69 |
- UMemphis |
-
-
- | GKHI-KS-090104.21-051106 |
- 4 |
- 05/08/02 |
- 0.72 |
- 36.3 |
- BXD39 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040204.30 |
- 4 |
- 06/05/02 |
- 0.77 |
- 43.9 |
- BXD39 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051805-16-050506 |
- 5 |
- 05/04/02 |
- 2.16 |
- 43.8 |
- BXD40 |
- |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-111902-04-050506 |
- 2 |
- 05/04/02 |
- 0.84 |
- 41.0 |
- BXD40 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-050604-01-050406 |
- 4 |
- 05/01/02 |
- 0.85 |
- 35.6 |
- BXD43 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-080905-43-050406 |
- 5 |
- 05/01/02 |
- 0.78 |
- 33.7 |
- BXD43 |
- 28 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-031004-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 36.2 |
- BXD44 |
- 21 |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-020504-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 30.8 |
- BXD44 |
- 20 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-071504-01-050406 |
- 4 |
- 05/01/02 |
- 0.74 |
- 37.7 |
- BXD45 |
- 20 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-081104-05-050406 |
- 4 |
- 05/01/02 |
- 0.78 |
- 34.2 |
- BXD45 |
- 20 |
- M |
- 93 |
- UTM RW |
-
-
- | GKHI-KS-031204-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 35.6 |
- BXD48 |
- 22 |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-021104.06-051706 |
- 4 |
- 05/14/02 |
- 0.75 |
- 41.1 |
- BXD48 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-033005-21-050306 |
- 5 |
- 05/01/02 |
- 0.78 |
- 34.9 |
- BXD51 |
- 27 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-090204-01-050306 |
- 4 |
- 05/01/02 |
- 0.72 |
- 38.3 |
- BXD51 |
- 24 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI_KS-010704.01-040606 |
- 4 |
- 04/03/02 |
- 0.75 |
- 37.5 |
- BXD60 |
- 21 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_013004.38-042006 |
- 4 |
- 04/17/02 |
- 0.78 |
- 40.1 |
- BXD60 |
- 21 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-030905-28-050206 |
- 5 |
- 04/30/02 |
- 0.73 |
- 36.6 |
- BXD61 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-050305-18-050206 |
- 5 |
- 04/30/02 |
- 0.83 |
- 35.8 |
- BXD61 |
- 21 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-121803.01-040706 |
- 3 |
- 04/03/02 |
- 0.80 |
- 40.0 |
- BXD62 |
- 20 |
- M |
- 54 |
- UTM RW |
-
-
- | GKHI_KS_021204.01-042006 |
- 4 |
- 04/17/02 |
- 0.85 |
- 39.8 |
- BXD62 |
- 21 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-020905-25-050206 |
- 5 |
- 04/30/02 |
- 0.84 |
- 35.2 |
- BXD63 |
- 21 |
- M |
- 70 |
- UTM RW |
-
-
- | GKHI-KS-040705.49-060806 |
- 2 |
- 06/07/02 |
- 0.85 |
- 39.4 |
- BXD65 |
- 20 |
- F |
- 55 |
- UTM RW |
-
-
- | GKHI-KS-040406.12-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 40.4 |
- BXD65 |
- 23 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-052405-36-050406 |
- 5 |
- 05/02/02 |
- 0.84 |
- 36.8 |
- BXD67 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-041205-01-050206 |
- 5 |
- 04/30/02 |
- 0.77 |
- 39.7 |
- BXD67 |
- 20 |
- F |
- 54 |
- UTM RW |
-
-
- | GKHI-KS-062305-01-050206 |
- 5 |
- 04/30/02 |
- 0.76 |
- 36.0 |
- BXD68 |
- 20 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-062305-09-050206 |
- 5 |
- 04/30/02 |
- 0.93 |
- 37.4 |
- BXD68 |
- 20 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_110105.30-042006 |
- 5 |
- 04/17/02 |
- 0.80 |
- 39.0 |
- BXD69 |
- 26 |
- F |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-061504.64-062206 |
- 4 |
- 06/21/02 |
- 0.72 |
- 39.3 |
- BXD69 |
- 20 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS-050404.04-040606 |
- 4 |
- 04/03/02 |
- 0.77 |
- 38.3 |
- BXD69 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-042705-01-042706 |
- 5 |
- 04/23/02 |
- 0.83 |
- 38.6 |
- BXD70 |
- 21 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-051705-59-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 38.5 |
- BXD70 |
- 22 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-030805-40-042706 |
- 5 |
- 04/23/02 |
- 0.86 |
- 38.5 |
- BXD73 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-041905.172-062206 |
- 5 |
- 06/21/02 |
- 0.79 |
- 37.6 |
- BXD73 |
- 24 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-072605-03-042706 |
- 5 |
- 04/23/02 |
- 0.87 |
- 38.2 |
- BXD73 |
- 25 |
- F |
- 72 |
- UTM RW |
-
-
- | GKHI-KS-041205-04-050406 |
- 5 |
- 05/02/02 |
- 0.83 |
- 41.4 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-041205.07 |
- 5 |
- 06/05/02 |
- 0.79 |
- 45.8 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-101805-35-050406 |
- 5 |
- 05/02/02 |
- 0.79 |
- 38.4 |
- BXD77 |
- 24 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-070605.43 |
- 5 |
- 06/05/02 |
- 0.77 |
- 42.8 |
- BXD77 |
- 23 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-071205-31-042706 |
- 5 |
- 04/23/02 |
- 0.91 |
- 37.7 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-071205-2-042706 |
- 5 |
- 04/23/02 |
- 0.90 |
- 38.1 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | KS-011305-11-042606 |
- 5 |
- 04/22/02 |
- 0.82 |
- 39.0 |
- BXD85 |
- 22 |
- M |
- 91 |
- UTM RW |
-
-
- | KS-110805-27-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 35.2 |
- BXD85 |
- 25 |
- F |
- 63 |
- UTM RW |
-
-
- | KS-080404-28-042606 |
- 4 |
- 04/22/02 |
- 0.84 |
- 36.8 |
- BXD86 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | KS-080504-04-042606 |
- 4 |
- 04/22/02 |
- 0.81 |
- 33.4 |
- BXD86 |
- 20 |
- M |
- 77 |
- UTM RW |
-
-
- | KS-051705-57-042606 |
- 5 |
- 04/22/02 |
- 1.11 |
- 35.6 |
- BXD87 |
- 20 |
- M |
- 63 |
- UTM RW |
-
-
- | KS-032905-46-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 36.1 |
- BXD87 |
- 20 |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-080905-49-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 37.6 |
- BXD90 |
- 23 |
- F |
- 71 |
- UTM RW |
-
-
- | GKHI-KS-101105.26 |
- 5 |
- 06/05/02 |
- 0.84 |
- 43.6 |
- BXD90 |
- 25 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-062304.02-040606 |
- 4 |
- 04/03/02 |
- 0.85 |
- 40.9 |
- BXD92 |
- 21 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS_071404.01-042006 |
- 4 |
- 04/17/02 |
- 0.77 |
- 39.5 |
- BXD92 |
- 21 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI_KS_031005.17-042006 |
- 5 |
- 04/17/02 |
- 0.77 |
- 38.1 |
- BXD96 |
- 20 |
- M |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-111505.12 |
- 5 |
- 06/05/02 |
- 0.77 |
- 44.1 |
- BXD96 |
- 23 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-012406.21-060806 |
- 3 |
- 06/07/02 |
- 0.73 |
- 36.6 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.24-060806 |
- 3 |
- 06/07/02 |
- 1.28 |
- 39.2 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.13-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 41.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.16-060806 |
- 3 |
- 06/07/02 |
- 0.66 |
- 37.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.31-060806 |
- 3 |
- 06/07/02 |
- 0.80 |
- 37.2 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.34-060806 |
- 3 |
- 06/07/02 |
- 0.76 |
- 38.5 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060806.04-070706 |
- 3 |
- 07/06/02 |
- 0.68 |
- 37.3 |
- C3H/HeJ |
- |
- F |
- 76 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-071505.08-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-071505.11-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 39.2 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-030305.15-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- CAST/Ei |
- |
- F |
- 64 |
- JAX |
-
-
- | GKHI-KS-031005.35-060906 |
- 3 |
- 06/08/02 |
- 0.70 |
- 35.7 |
- CAST/Ei |
- |
- M |
- 64 |
- JAX |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 37.9 |
- KK/HlJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.07-060906 |
- 3 |
- 06/08/02 |
- 0.72 |
- 35.5 |
- KK/HlJ |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031606.01-060906 |
- 3 |
- 06/08/02 |
- 0.86 |
- 35.9 |
- MOLF/Ei |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.87 |
- 37.4 |
- MOLF/Ei |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.25-060906 |
- 3 |
- 06/08/02 |
- 0.75 |
- 38.3 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.28-061306 |
- 3 |
- 06/11/02 |
- 0.82 |
- 37.1 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.04.060906 |
- 3 |
- 06/08/02 |
- 0.73 |
- 40.2 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.07-060906 |
- 3 |
- 06/08/02 |
- 0.74 |
- 39.4 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020706.04-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 41.6 |
- NZW/LacJ |
- |
- F |
- 65 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.19-060906 |
- 3 |
- 06/08/02 |
- 0.77 |
- 36.7 |
- NZW/LacJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.33-061306 |
- 3 |
- 06/11/02 |
- 0.95 |
- 35.3 |
- PWD/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.30-062006 |
- 3 |
- 06/18/02 |
- 0.88 |
- 36.3 |
- PWD/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.01-062206 |
- 3 |
- 06/21/02 |
- 1.02 |
- 35.9 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.04-062206 |
- 3 |
- 06/21/02 |
- 0.96 |
- 38.7 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.07-062206 |
- 3 |
- 06/21/02 |
- 0.98 |
- 36.6 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.10-062206 |
- 3 |
- 06/21/02 |
- 0.87 |
- 35.2 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052705.01-061306 |
- 2 |
- 06/11/02 |
- 0.72 |
- 38.3 |
- WSB/EiJ |
- |
- F |
- 52 |
- UTM RW |
-
-
- | GKHI-KS-051005.07-061306 |
- 3 |
- 06/11/02 |
- 0.77 |
- 38.0 |
- WSB/EiJ |
- |
- M |
- 58 |
- JAX |
-
-
-
-
diff --git a/general/datasets/MA_M2F_0706_R/notes.rtf b/general/datasets/MA_M2F_0706_R/notes.rtf
deleted file mode 100644
index d41fda1..0000000
--- a/general/datasets/MA_M2F_0706_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.
-
diff --git a/general/datasets/MA_M2F_0706_R/platform.rtf b/general/datasets/MA_M2F_0706_R/platform.rtf
deleted file mode 100644
index cb0e8d5..0000000
--- a/general/datasets/MA_M2F_0706_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
-
diff --git a/general/datasets/MA_M2F_0706_R/processing.rtf b/general/datasets/MA_M2F_0706_R/processing.rtf
deleted file mode 100644
index b313d60..0000000
--- a/general/datasets/MA_M2F_0706_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/MA_M2F_0706_R/summary.rtf b/general/datasets/MA_M2F_0706_R/summary.rtf
deleted file mode 100644
index 9055ba0..0000000
--- a/general/datasets/MA_M2F_0706_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/MA_M2F_0706_R/tissue.rtf b/general/datasets/MA_M2F_0706_R/tissue.rtf
deleted file mode 100644
index 5bc52e9..0000000
--- a/general/datasets/MA_M2F_0706_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).
-
diff --git a/general/datasets/MA_M2M_0706_R/acknowledgment.rtf b/general/datasets/MA_M2M_0706_R/acknowledgment.rtf
deleted file mode 100644
index fea38e8..0000000
--- a/general/datasets/MA_M2M_0706_R/acknowledgment.rtf
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:
-
-
- - Erwin Bottinger, M.D.
- Grant Support: R01 DK60043-04
- - Russell Chesney, M.D.
- Grant Support: Le Bonheur Chair of Excellence in Pediatrics II
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Peter Mundel
- Grant Support: NIH R01DK57683, NIH R01 DK 62472
- - Paul Klotman
- Grant Support: PO1 DK56492, PO1 DK56492.
- - Matthew Breyer
- Grant Support: DK-38226
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/MA_M2M_0706_R/cases.rtf b/general/datasets/MA_M2M_0706_R/cases.rtf
deleted file mode 100644
index 465b87c..0000000
--- a/general/datasets/MA_M2M_0706_R/cases.rtf
+++ /dev/null
@@ -1,44 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-
- - BTBR T+tf/J
- Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - D2B6F1
- F1 hybrid generated by crossing C57BL/6J with DBA/2J
-
-
-These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>
-
-
diff --git a/general/datasets/MA_M2M_0706_R/experiment-design.rtf b/general/datasets/MA_M2M_0706_R/experiment-design.rtf
deleted file mode 100644
index 464e50d..0000000
--- a/general/datasets/MA_M2M_0706_R/experiment-design.rtf
+++ /dev/null
@@ -1,1864 +0,0 @@
-
-Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
-
-Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
-
-
-This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
-
-
-
-
-
- | Microarray_ID |
- # mice |
- Microarray Date |
- GAPDH (3`/5`) |
- % present |
- strains |
- generation |
- sex |
- age |
- Mice Source |
-
-
- | GKHI-KS-050603.07-051706 |
- 3 |
- 05/14/02 |
- 0.73 |
- 37.6 |
- C57BL/6J |
- |
- M |
- 56 |
- UTM RW |
-
-
- | GKHI-KS-070803.01-051706 |
- 3 |
- 05/14/02 |
- 0.75 |
- 41.6 |
- C57BL/6J |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-DBA-Male-070706 |
- 2 |
- 07/06/02 |
- 0.71 |
- 37.3 |
- DBA/2J |
- |
- M |
- 56 |
- JAX |
-
-
- | GKHI_KS_121404.75-042106 |
- 4 |
- 04/18/02 |
- |
- |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.75-033006 |
- 4 |
- 03/19/02 |
- 0.73 |
- 48.5 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.78-042006 |
- 4 |
- 04/17/02 |
- 0.83 |
- 40.6 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_070804.39-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 39.0 |
- D2B6F1 |
- |
- M |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_030904.01-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 35.9 |
- D2B6F1 |
- |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-121404.73-070706 |
- 2 |
- 07/06/02 |
- 0.76 |
- 36.3 |
- D2B6F1 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-010705.38-051206 |
- 5 |
- 05/09/02 |
- 0.81 |
- 39.9 |
- BXD1 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060905.19 |
- 5 |
- 06/05/02 |
- 0.75 |
- 42.3 |
- BXD1 |
- |
- M |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-051206.13-070706 |
- 3 |
- 07/06/02 |
- 0.71 |
- 36.3 |
- BXD1 |
- |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-021304.10-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 39.1 |
- BXD2 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-04-050406 |
- 3 |
- 05/01/02 |
- 0.80 |
- 37.6 |
- BXD5 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-010705-53-050306 |
- 5 |
- 05/01/02 |
- 0.76 |
- 37.1 |
- BXD5 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031103.01-062206 |
- 3 |
- 06/21/02 |
- 0.75 |
- 37.1 |
- BXD5 |
- |
- M |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-040505-51-050306 |
- 5 |
- 05/01/02 |
- 0.71 |
- 35.5 |
- BXD6 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-092705-29--050406 |
- 5 |
- 05/02/02 |
- 0.75 |
- 36.1 |
- BXD6 |
- 160 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_092404.01-042106 |
- 4 |
- 04/18/02 |
- 0.71 |
- 36.3 |
- BXD8 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051205-25-042706 |
- 5 |
- 04/23/02 |
- 0.92 |
- 37.9 |
- BXD8 |
- |
- F |
- 77 |
- UTM RW |
-
-
- | KS-021605-17-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 40.8 |
- BXD9 |
- |
- F |
- 67 |
- UTM RW |
-
-
- | KS-032905-32-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 36.8 |
- BXD9 |
- |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-062006.08-070706 |
- 3 |
- 07/06/02 |
- 0.74 |
- 36.3 |
- BXD9 |
- |
- M |
- 78 |
- UTM RW |
-
-
- | GKHI-KS-031505.22-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 39.5 |
- BXD11 |
- |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031605.01 |
- 5 |
- 06/05/02 |
- 0.74 |
- 43.4 |
- BXD11 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI_KS_102104.40-042106 |
- 4 |
- 04/18/02 |
- 0.72 |
- 38.5 |
- BXD12 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-112002.07-051106 |
- 2 |
- 05/08/02 |
- 0.77 |
- 42.0 |
- BXD12 |
- |
- F |
- 64 |
- UMemphis |
-
-
- | GKHI-KS-120904.33-051206 |
- 4 |
- 05/09/02 |
- 0.71 |
- 38.4 |
- BXD13 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-042304.01 |
- 4 |
- 06/05/02 |
- 0.71 |
- 44.1 |
- BXD13 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020905.34-051106 |
- 5 |
- 05/08/02 |
- 0.75 |
- 40.7 |
- BXD14 |
- |
- F |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-022405.46-051106 |
- 5 |
- 05/08/02 |
- 0.71 |
- 40.2 |
- BXD14 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-091704.09-062206 |
- 4 |
- 06/21/02 |
- 0.73 |
- 39.0 |
- BXD14 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-013004.45-062206 |
- 4 |
- 06/21/02 |
- 0.76 |
- 38.5 |
- BXD15 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022405.43-051106 |
- 5 |
- 05/08/02 |
- 0.73 |
- 40.5 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-041604.10-051106 |
- 4 |
- 05/08/02 |
- 0.73 |
- 42.6 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.01-051106 |
- 5 |
- 05/08/02 |
- 0.79 |
- 42.4 |
- BXD16 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.04-051106 |
- 5 |
- 05/08/02 |
- 0.77 |
- 39.9 |
- BXD16 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.10-051006 |
- 5 |
- 05/05/02 |
- 0.93 |
- 38.7 |
- BXD18 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052804.09-051106 |
- 4 |
- 05/05/02 |
- 0.67 |
- 37.6 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.47-051106 |
- 5 |
- 05/05/02 |
- 0.73 |
- 42.3 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.44-070706 |
- 3 |
- 07/06/02 |
- 0.73 |
- 36.1 |
- BXD19 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-062905.07-051106 |
- 5 |
- 05/05/02 |
- 0.72 |
- 37.9 |
- BXD20 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-072104.58-051106 |
- 4 |
- 05/05/02 |
- 0.73 |
- 37.0 |
- BXD20 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-050405.21-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 35.1 |
- BXD21 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040705.24 |
- 5 |
- 06/05/02 |
- 0.80 |
- 40.2 |
- BXD21 |
- |
- F |
- 99 |
- UAB |
-
-
- | GKHI-KS-110405.01-051006 |
- 5 |
- 05/05/02 |
- 0.71 |
- 42.1 |
- BXD22 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-110405.04-051006 |
- 5 |
- 05/05/02 |
- 0.76 |
- 40.6 |
- BXD22 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.01-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 36.4 |
- BXD23 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.04-051006 |
- 5 |
- 05/05/02 |
- 0.73 |
- 39.3 |
- BXD23 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI_KS_091704.13-042106 |
- 4 |
- 04/18/02 |
- 0.73 |
- 37.7 |
- BXD24 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-20-050206 |
- 3 |
- 04/30/02 |
- 0.77 |
- 36.3 |
- BXD24 |
- |
- F |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-021805.20-051006 |
- 5 |
- 05/05/02 |
- 0.83 |
- 40.5 |
- BXD25 |
- |
- F |
- 67 |
- UAB |
-
-
- | GKHI-KS-090705.05-062206 |
- 5 |
- 06/21/02 |
- 0.76 |
- 38.4 |
- BXD25 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-090705.03-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 40.1 |
- BXD25 |
- |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-022105.42-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 41.8 |
- BXD27 |
- |
- M |
- 70 |
- UAB |
-
-
- | GKHI-KS-032205.31-051006 |
- 5 |
- 05/05/02 |
- 0.74 |
- 39.0 |
- BXD27 |
- |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-060706.10-070706 |
- 3 |
- 07/06/02 |
- 0.69 |
- 37.8 |
- BXD27 |
- |
- F |
- 85 |
- UTM RW |
-
-
- | GKHI-KS-012805-41-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 34.2 |
- BXD28 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-44-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 35.8 |
- BXD28 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-38-050506 |
- 5 |
- 05/04/02 |
- 0.77 |
- 42.7 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-35-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 35.8 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-32-050506 |
- 5 |
- 05/04/02 |
- 0.74 |
- 39.9 |
- BXD31 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-100604-07-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 40.2 |
- BXD31 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-021605.26-051706 |
- 5 |
- 05/14/02 |
- 1.11 |
- 39.0 |
- BXD32 |
- |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-112002.01-051206 |
- 2 |
- 05/09/02 |
- 0.76 |
- 38.1 |
- BXD32 |
- |
- F |
- 60 |
- UMemphis |
-
-
- | GKHI-KS-072605-01-050506 |
- 5 |
- 05/04/02 |
- 0.79 |
- 41.3 |
- BXD33 |
- 50 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-091405-23-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 38.4 |
- BXD33 |
- 50 |
- M |
- 76 |
- UTM RW |
-
-
- | GKHI-KS-111104-18-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 42.2 |
- BXD36 |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031804-07-050506 |
- 4 |
- 05/04/02 |
- 0.85 |
- 42.5 |
- BXD36 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-092005.16-051206 |
- 5 |
- 05/09/02 |
- 0.72 |
- 37.2 |
- BXD38 |
- 46 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031403.01-060806 |
- 1 |
- 06/07/02 |
- 0.69 |
- 39.6 |
- BXD38 |
- |
- M |
- 69 |
- UMemphis |
-
-
- | GKHI-KS-090104.21-051106 |
- 4 |
- 05/08/02 |
- 0.72 |
- 36.3 |
- BXD39 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040204.30 |
- 4 |
- 06/05/02 |
- 0.77 |
- 43.9 |
- BXD39 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051805-16-050506 |
- 5 |
- 05/04/02 |
- 2.16 |
- 43.8 |
- BXD40 |
- |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-111902-04-050506 |
- 2 |
- 05/04/02 |
- 0.84 |
- 41.0 |
- BXD40 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-050604-01-050406 |
- 4 |
- 05/01/02 |
- 0.85 |
- 35.6 |
- BXD43 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-080905-43-050406 |
- 5 |
- 05/01/02 |
- 0.78 |
- 33.7 |
- BXD43 |
- 28 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-031004-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 36.2 |
- BXD44 |
- 21 |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-020504-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 30.8 |
- BXD44 |
- 20 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-071504-01-050406 |
- 4 |
- 05/01/02 |
- 0.74 |
- 37.7 |
- BXD45 |
- 20 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-081104-05-050406 |
- 4 |
- 05/01/02 |
- 0.78 |
- 34.2 |
- BXD45 |
- 20 |
- M |
- 93 |
- UTM RW |
-
-
- | GKHI-KS-031204-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 35.6 |
- BXD48 |
- 22 |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-021104.06-051706 |
- 4 |
- 05/14/02 |
- 0.75 |
- 41.1 |
- BXD48 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-033005-21-050306 |
- 5 |
- 05/01/02 |
- 0.78 |
- 34.9 |
- BXD51 |
- 27 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-090204-01-050306 |
- 4 |
- 05/01/02 |
- 0.72 |
- 38.3 |
- BXD51 |
- 24 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI_KS-010704.01-040606 |
- 4 |
- 04/03/02 |
- 0.75 |
- 37.5 |
- BXD60 |
- 21 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_013004.38-042006 |
- 4 |
- 04/17/02 |
- 0.78 |
- 40.1 |
- BXD60 |
- 21 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-030905-28-050206 |
- 5 |
- 04/30/02 |
- 0.73 |
- 36.6 |
- BXD61 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-050305-18-050206 |
- 5 |
- 04/30/02 |
- 0.83 |
- 35.8 |
- BXD61 |
- 21 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-121803.01-040706 |
- 3 |
- 04/03/02 |
- 0.80 |
- 40.0 |
- BXD62 |
- 20 |
- M |
- 54 |
- UTM RW |
-
-
- | GKHI_KS_021204.01-042006 |
- 4 |
- 04/17/02 |
- 0.85 |
- 39.8 |
- BXD62 |
- 21 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-020905-25-050206 |
- 5 |
- 04/30/02 |
- 0.84 |
- 35.2 |
- BXD63 |
- 21 |
- M |
- 70 |
- UTM RW |
-
-
- | GKHI-KS-040705.49-060806 |
- 2 |
- 06/07/02 |
- 0.85 |
- 39.4 |
- BXD65 |
- 20 |
- F |
- 55 |
- UTM RW |
-
-
- | GKHI-KS-040406.12-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 40.4 |
- BXD65 |
- 23 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-052405-36-050406 |
- 5 |
- 05/02/02 |
- 0.84 |
- 36.8 |
- BXD67 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-041205-01-050206 |
- 5 |
- 04/30/02 |
- 0.77 |
- 39.7 |
- BXD67 |
- 20 |
- F |
- 54 |
- UTM RW |
-
-
- | GKHI-KS-062305-01-050206 |
- 5 |
- 04/30/02 |
- 0.76 |
- 36.0 |
- BXD68 |
- 20 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-062305-09-050206 |
- 5 |
- 04/30/02 |
- 0.93 |
- 37.4 |
- BXD68 |
- 20 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_110105.30-042006 |
- 5 |
- 04/17/02 |
- 0.80 |
- 39.0 |
- BXD69 |
- 26 |
- F |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-061504.64-062206 |
- 4 |
- 06/21/02 |
- 0.72 |
- 39.3 |
- BXD69 |
- 20 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS-050404.04-040606 |
- 4 |
- 04/03/02 |
- 0.77 |
- 38.3 |
- BXD69 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-042705-01-042706 |
- 5 |
- 04/23/02 |
- 0.83 |
- 38.6 |
- BXD70 |
- 21 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-051705-59-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 38.5 |
- BXD70 |
- 22 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-030805-40-042706 |
- 5 |
- 04/23/02 |
- 0.86 |
- 38.5 |
- BXD73 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-041905.172-062206 |
- 5 |
- 06/21/02 |
- 0.79 |
- 37.6 |
- BXD73 |
- 24 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-072605-03-042706 |
- 5 |
- 04/23/02 |
- 0.87 |
- 38.2 |
- BXD73 |
- 25 |
- F |
- 72 |
- UTM RW |
-
-
- | GKHI-KS-041205-04-050406 |
- 5 |
- 05/02/02 |
- 0.83 |
- 41.4 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-041205.07 |
- 5 |
- 06/05/02 |
- 0.79 |
- 45.8 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-101805-35-050406 |
- 5 |
- 05/02/02 |
- 0.79 |
- 38.4 |
- BXD77 |
- 24 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-070605.43 |
- 5 |
- 06/05/02 |
- 0.77 |
- 42.8 |
- BXD77 |
- 23 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-071205-31-042706 |
- 5 |
- 04/23/02 |
- 0.91 |
- 37.7 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-071205-2-042706 |
- 5 |
- 04/23/02 |
- 0.90 |
- 38.1 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | KS-011305-11-042606 |
- 5 |
- 04/22/02 |
- 0.82 |
- 39.0 |
- BXD85 |
- 22 |
- M |
- 91 |
- UTM RW |
-
-
- | KS-110805-27-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 35.2 |
- BXD85 |
- 25 |
- F |
- 63 |
- UTM RW |
-
-
- | KS-080404-28-042606 |
- 4 |
- 04/22/02 |
- 0.84 |
- 36.8 |
- BXD86 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | KS-080504-04-042606 |
- 4 |
- 04/22/02 |
- 0.81 |
- 33.4 |
- BXD86 |
- 20 |
- M |
- 77 |
- UTM RW |
-
-
- | KS-051705-57-042606 |
- 5 |
- 04/22/02 |
- 1.11 |
- 35.6 |
- BXD87 |
- 20 |
- M |
- 63 |
- UTM RW |
-
-
- | KS-032905-46-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 36.1 |
- BXD87 |
- 20 |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-080905-49-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 37.6 |
- BXD90 |
- 23 |
- F |
- 71 |
- UTM RW |
-
-
- | GKHI-KS-101105.26 |
- 5 |
- 06/05/02 |
- 0.84 |
- 43.6 |
- BXD90 |
- 25 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-062304.02-040606 |
- 4 |
- 04/03/02 |
- 0.85 |
- 40.9 |
- BXD92 |
- 21 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS_071404.01-042006 |
- 4 |
- 04/17/02 |
- 0.77 |
- 39.5 |
- BXD92 |
- 21 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI_KS_031005.17-042006 |
- 5 |
- 04/17/02 |
- 0.77 |
- 38.1 |
- BXD96 |
- 20 |
- M |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-111505.12 |
- 5 |
- 06/05/02 |
- 0.77 |
- 44.1 |
- BXD96 |
- 23 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-012406.21-060806 |
- 3 |
- 06/07/02 |
- 0.73 |
- 36.6 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.24-060806 |
- 3 |
- 06/07/02 |
- 1.28 |
- 39.2 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.13-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 41.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.16-060806 |
- 3 |
- 06/07/02 |
- 0.66 |
- 37.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.31-060806 |
- 3 |
- 06/07/02 |
- 0.80 |
- 37.2 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.34-060806 |
- 3 |
- 06/07/02 |
- 0.76 |
- 38.5 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060806.04-070706 |
- 3 |
- 07/06/02 |
- 0.68 |
- 37.3 |
- C3H/HeJ |
- |
- F |
- 76 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-071505.08-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-071505.11-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 39.2 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-030305.15-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- CAST/Ei |
- |
- F |
- 64 |
- JAX |
-
-
- | GKHI-KS-031005.35-060906 |
- 3 |
- 06/08/02 |
- 0.70 |
- 35.7 |
- CAST/Ei |
- |
- M |
- 64 |
- JAX |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 37.9 |
- KK/HlJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.07-060906 |
- 3 |
- 06/08/02 |
- 0.72 |
- 35.5 |
- KK/HlJ |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031606.01-060906 |
- 3 |
- 06/08/02 |
- 0.86 |
- 35.9 |
- MOLF/Ei |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.87 |
- 37.4 |
- MOLF/Ei |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.25-060906 |
- 3 |
- 06/08/02 |
- 0.75 |
- 38.3 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.28-061306 |
- 3 |
- 06/11/02 |
- 0.82 |
- 37.1 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.04.060906 |
- 3 |
- 06/08/02 |
- 0.73 |
- 40.2 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.07-060906 |
- 3 |
- 06/08/02 |
- 0.74 |
- 39.4 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020706.04-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 41.6 |
- NZW/LacJ |
- |
- F |
- 65 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.19-060906 |
- 3 |
- 06/08/02 |
- 0.77 |
- 36.7 |
- NZW/LacJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.33-061306 |
- 3 |
- 06/11/02 |
- 0.95 |
- 35.3 |
- PWD/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.30-062006 |
- 3 |
- 06/18/02 |
- 0.88 |
- 36.3 |
- PWD/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.01-062206 |
- 3 |
- 06/21/02 |
- 1.02 |
- 35.9 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.04-062206 |
- 3 |
- 06/21/02 |
- 0.96 |
- 38.7 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.07-062206 |
- 3 |
- 06/21/02 |
- 0.98 |
- 36.6 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.10-062206 |
- 3 |
- 06/21/02 |
- 0.87 |
- 35.2 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052705.01-061306 |
- 2 |
- 06/11/02 |
- 0.72 |
- 38.3 |
- WSB/EiJ |
- |
- F |
- 52 |
- UTM RW |
-
-
- | GKHI-KS-051005.07-061306 |
- 3 |
- 06/11/02 |
- 0.77 |
- 38.0 |
- WSB/EiJ |
- |
- M |
- 58 |
- JAX |
-
-
-
-
diff --git a/general/datasets/MA_M2M_0706_R/notes.rtf b/general/datasets/MA_M2M_0706_R/notes.rtf
deleted file mode 100644
index d41fda1..0000000
--- a/general/datasets/MA_M2M_0706_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.
-
diff --git a/general/datasets/MA_M2M_0706_R/platform.rtf b/general/datasets/MA_M2M_0706_R/platform.rtf
deleted file mode 100644
index cb0e8d5..0000000
--- a/general/datasets/MA_M2M_0706_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
-
diff --git a/general/datasets/MA_M2M_0706_R/processing.rtf b/general/datasets/MA_M2M_0706_R/processing.rtf
deleted file mode 100644
index b313d60..0000000
--- a/general/datasets/MA_M2M_0706_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/MA_M2M_0706_R/summary.rtf b/general/datasets/MA_M2M_0706_R/summary.rtf
deleted file mode 100644
index 9055ba0..0000000
--- a/general/datasets/MA_M2M_0706_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/MA_M2M_0706_R/tissue.rtf b/general/datasets/MA_M2M_0706_R/tissue.rtf
deleted file mode 100644
index 5bc52e9..0000000
--- a/general/datasets/MA_M2M_0706_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).
-
diff --git a/general/datasets/MA_M2_0706_P/acknowledgment.rtf b/general/datasets/MA_M2_0706_P/acknowledgment.rtf
deleted file mode 100644
index fea38e8..0000000
--- a/general/datasets/MA_M2_0706_P/acknowledgment.rtf
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:
-
-
- - Erwin Bottinger, M.D.
- Grant Support: R01 DK60043-04
- - Russell Chesney, M.D.
- Grant Support: Le Bonheur Chair of Excellence in Pediatrics II
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Peter Mundel
- Grant Support: NIH R01DK57683, NIH R01 DK 62472
- - Paul Klotman
- Grant Support: PO1 DK56492, PO1 DK56492.
- - Matthew Breyer
- Grant Support: DK-38226
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/MA_M2_0706_P/cases.rtf b/general/datasets/MA_M2_0706_P/cases.rtf
deleted file mode 100644
index 465b87c..0000000
--- a/general/datasets/MA_M2_0706_P/cases.rtf
+++ /dev/null
@@ -1,44 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-
- - BTBR T+tf/J
- Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - D2B6F1
- F1 hybrid generated by crossing C57BL/6J with DBA/2J
-
-
-These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>
-
-
diff --git a/general/datasets/MA_M2_0706_P/experiment-design.rtf b/general/datasets/MA_M2_0706_P/experiment-design.rtf
deleted file mode 100644
index 464e50d..0000000
--- a/general/datasets/MA_M2_0706_P/experiment-design.rtf
+++ /dev/null
@@ -1,1864 +0,0 @@
-
-Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
-
-Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
-
-
-This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
-
-
-
-
-
- | Microarray_ID |
- # mice |
- Microarray Date |
- GAPDH (3`/5`) |
- % present |
- strains |
- generation |
- sex |
- age |
- Mice Source |
-
-
- | GKHI-KS-050603.07-051706 |
- 3 |
- 05/14/02 |
- 0.73 |
- 37.6 |
- C57BL/6J |
- |
- M |
- 56 |
- UTM RW |
-
-
- | GKHI-KS-070803.01-051706 |
- 3 |
- 05/14/02 |
- 0.75 |
- 41.6 |
- C57BL/6J |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-DBA-Male-070706 |
- 2 |
- 07/06/02 |
- 0.71 |
- 37.3 |
- DBA/2J |
- |
- M |
- 56 |
- JAX |
-
-
- | GKHI_KS_121404.75-042106 |
- 4 |
- 04/18/02 |
- |
- |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.75-033006 |
- 4 |
- 03/19/02 |
- 0.73 |
- 48.5 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.78-042006 |
- 4 |
- 04/17/02 |
- 0.83 |
- 40.6 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_070804.39-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 39.0 |
- D2B6F1 |
- |
- M |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_030904.01-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 35.9 |
- D2B6F1 |
- |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-121404.73-070706 |
- 2 |
- 07/06/02 |
- 0.76 |
- 36.3 |
- D2B6F1 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-010705.38-051206 |
- 5 |
- 05/09/02 |
- 0.81 |
- 39.9 |
- BXD1 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060905.19 |
- 5 |
- 06/05/02 |
- 0.75 |
- 42.3 |
- BXD1 |
- |
- M |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-051206.13-070706 |
- 3 |
- 07/06/02 |
- 0.71 |
- 36.3 |
- BXD1 |
- |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-021304.10-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 39.1 |
- BXD2 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-04-050406 |
- 3 |
- 05/01/02 |
- 0.80 |
- 37.6 |
- BXD5 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-010705-53-050306 |
- 5 |
- 05/01/02 |
- 0.76 |
- 37.1 |
- BXD5 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031103.01-062206 |
- 3 |
- 06/21/02 |
- 0.75 |
- 37.1 |
- BXD5 |
- |
- M |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-040505-51-050306 |
- 5 |
- 05/01/02 |
- 0.71 |
- 35.5 |
- BXD6 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-092705-29--050406 |
- 5 |
- 05/02/02 |
- 0.75 |
- 36.1 |
- BXD6 |
- 160 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_092404.01-042106 |
- 4 |
- 04/18/02 |
- 0.71 |
- 36.3 |
- BXD8 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051205-25-042706 |
- 5 |
- 04/23/02 |
- 0.92 |
- 37.9 |
- BXD8 |
- |
- F |
- 77 |
- UTM RW |
-
-
- | KS-021605-17-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 40.8 |
- BXD9 |
- |
- F |
- 67 |
- UTM RW |
-
-
- | KS-032905-32-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 36.8 |
- BXD9 |
- |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-062006.08-070706 |
- 3 |
- 07/06/02 |
- 0.74 |
- 36.3 |
- BXD9 |
- |
- M |
- 78 |
- UTM RW |
-
-
- | GKHI-KS-031505.22-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 39.5 |
- BXD11 |
- |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031605.01 |
- 5 |
- 06/05/02 |
- 0.74 |
- 43.4 |
- BXD11 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI_KS_102104.40-042106 |
- 4 |
- 04/18/02 |
- 0.72 |
- 38.5 |
- BXD12 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-112002.07-051106 |
- 2 |
- 05/08/02 |
- 0.77 |
- 42.0 |
- BXD12 |
- |
- F |
- 64 |
- UMemphis |
-
-
- | GKHI-KS-120904.33-051206 |
- 4 |
- 05/09/02 |
- 0.71 |
- 38.4 |
- BXD13 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-042304.01 |
- 4 |
- 06/05/02 |
- 0.71 |
- 44.1 |
- BXD13 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020905.34-051106 |
- 5 |
- 05/08/02 |
- 0.75 |
- 40.7 |
- BXD14 |
- |
- F |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-022405.46-051106 |
- 5 |
- 05/08/02 |
- 0.71 |
- 40.2 |
- BXD14 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-091704.09-062206 |
- 4 |
- 06/21/02 |
- 0.73 |
- 39.0 |
- BXD14 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-013004.45-062206 |
- 4 |
- 06/21/02 |
- 0.76 |
- 38.5 |
- BXD15 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022405.43-051106 |
- 5 |
- 05/08/02 |
- 0.73 |
- 40.5 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-041604.10-051106 |
- 4 |
- 05/08/02 |
- 0.73 |
- 42.6 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.01-051106 |
- 5 |
- 05/08/02 |
- 0.79 |
- 42.4 |
- BXD16 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.04-051106 |
- 5 |
- 05/08/02 |
- 0.77 |
- 39.9 |
- BXD16 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.10-051006 |
- 5 |
- 05/05/02 |
- 0.93 |
- 38.7 |
- BXD18 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052804.09-051106 |
- 4 |
- 05/05/02 |
- 0.67 |
- 37.6 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.47-051106 |
- 5 |
- 05/05/02 |
- 0.73 |
- 42.3 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.44-070706 |
- 3 |
- 07/06/02 |
- 0.73 |
- 36.1 |
- BXD19 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-062905.07-051106 |
- 5 |
- 05/05/02 |
- 0.72 |
- 37.9 |
- BXD20 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-072104.58-051106 |
- 4 |
- 05/05/02 |
- 0.73 |
- 37.0 |
- BXD20 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-050405.21-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 35.1 |
- BXD21 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040705.24 |
- 5 |
- 06/05/02 |
- 0.80 |
- 40.2 |
- BXD21 |
- |
- F |
- 99 |
- UAB |
-
-
- | GKHI-KS-110405.01-051006 |
- 5 |
- 05/05/02 |
- 0.71 |
- 42.1 |
- BXD22 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-110405.04-051006 |
- 5 |
- 05/05/02 |
- 0.76 |
- 40.6 |
- BXD22 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.01-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 36.4 |
- BXD23 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.04-051006 |
- 5 |
- 05/05/02 |
- 0.73 |
- 39.3 |
- BXD23 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI_KS_091704.13-042106 |
- 4 |
- 04/18/02 |
- 0.73 |
- 37.7 |
- BXD24 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-20-050206 |
- 3 |
- 04/30/02 |
- 0.77 |
- 36.3 |
- BXD24 |
- |
- F |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-021805.20-051006 |
- 5 |
- 05/05/02 |
- 0.83 |
- 40.5 |
- BXD25 |
- |
- F |
- 67 |
- UAB |
-
-
- | GKHI-KS-090705.05-062206 |
- 5 |
- 06/21/02 |
- 0.76 |
- 38.4 |
- BXD25 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-090705.03-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 40.1 |
- BXD25 |
- |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-022105.42-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 41.8 |
- BXD27 |
- |
- M |
- 70 |
- UAB |
-
-
- | GKHI-KS-032205.31-051006 |
- 5 |
- 05/05/02 |
- 0.74 |
- 39.0 |
- BXD27 |
- |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-060706.10-070706 |
- 3 |
- 07/06/02 |
- 0.69 |
- 37.8 |
- BXD27 |
- |
- F |
- 85 |
- UTM RW |
-
-
- | GKHI-KS-012805-41-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 34.2 |
- BXD28 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-44-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 35.8 |
- BXD28 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-38-050506 |
- 5 |
- 05/04/02 |
- 0.77 |
- 42.7 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-35-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 35.8 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-32-050506 |
- 5 |
- 05/04/02 |
- 0.74 |
- 39.9 |
- BXD31 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-100604-07-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 40.2 |
- BXD31 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-021605.26-051706 |
- 5 |
- 05/14/02 |
- 1.11 |
- 39.0 |
- BXD32 |
- |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-112002.01-051206 |
- 2 |
- 05/09/02 |
- 0.76 |
- 38.1 |
- BXD32 |
- |
- F |
- 60 |
- UMemphis |
-
-
- | GKHI-KS-072605-01-050506 |
- 5 |
- 05/04/02 |
- 0.79 |
- 41.3 |
- BXD33 |
- 50 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-091405-23-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 38.4 |
- BXD33 |
- 50 |
- M |
- 76 |
- UTM RW |
-
-
- | GKHI-KS-111104-18-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 42.2 |
- BXD36 |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031804-07-050506 |
- 4 |
- 05/04/02 |
- 0.85 |
- 42.5 |
- BXD36 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-092005.16-051206 |
- 5 |
- 05/09/02 |
- 0.72 |
- 37.2 |
- BXD38 |
- 46 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031403.01-060806 |
- 1 |
- 06/07/02 |
- 0.69 |
- 39.6 |
- BXD38 |
- |
- M |
- 69 |
- UMemphis |
-
-
- | GKHI-KS-090104.21-051106 |
- 4 |
- 05/08/02 |
- 0.72 |
- 36.3 |
- BXD39 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040204.30 |
- 4 |
- 06/05/02 |
- 0.77 |
- 43.9 |
- BXD39 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051805-16-050506 |
- 5 |
- 05/04/02 |
- 2.16 |
- 43.8 |
- BXD40 |
- |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-111902-04-050506 |
- 2 |
- 05/04/02 |
- 0.84 |
- 41.0 |
- BXD40 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-050604-01-050406 |
- 4 |
- 05/01/02 |
- 0.85 |
- 35.6 |
- BXD43 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-080905-43-050406 |
- 5 |
- 05/01/02 |
- 0.78 |
- 33.7 |
- BXD43 |
- 28 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-031004-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 36.2 |
- BXD44 |
- 21 |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-020504-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 30.8 |
- BXD44 |
- 20 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-071504-01-050406 |
- 4 |
- 05/01/02 |
- 0.74 |
- 37.7 |
- BXD45 |
- 20 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-081104-05-050406 |
- 4 |
- 05/01/02 |
- 0.78 |
- 34.2 |
- BXD45 |
- 20 |
- M |
- 93 |
- UTM RW |
-
-
- | GKHI-KS-031204-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 35.6 |
- BXD48 |
- 22 |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-021104.06-051706 |
- 4 |
- 05/14/02 |
- 0.75 |
- 41.1 |
- BXD48 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-033005-21-050306 |
- 5 |
- 05/01/02 |
- 0.78 |
- 34.9 |
- BXD51 |
- 27 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-090204-01-050306 |
- 4 |
- 05/01/02 |
- 0.72 |
- 38.3 |
- BXD51 |
- 24 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI_KS-010704.01-040606 |
- 4 |
- 04/03/02 |
- 0.75 |
- 37.5 |
- BXD60 |
- 21 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_013004.38-042006 |
- 4 |
- 04/17/02 |
- 0.78 |
- 40.1 |
- BXD60 |
- 21 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-030905-28-050206 |
- 5 |
- 04/30/02 |
- 0.73 |
- 36.6 |
- BXD61 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-050305-18-050206 |
- 5 |
- 04/30/02 |
- 0.83 |
- 35.8 |
- BXD61 |
- 21 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-121803.01-040706 |
- 3 |
- 04/03/02 |
- 0.80 |
- 40.0 |
- BXD62 |
- 20 |
- M |
- 54 |
- UTM RW |
-
-
- | GKHI_KS_021204.01-042006 |
- 4 |
- 04/17/02 |
- 0.85 |
- 39.8 |
- BXD62 |
- 21 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-020905-25-050206 |
- 5 |
- 04/30/02 |
- 0.84 |
- 35.2 |
- BXD63 |
- 21 |
- M |
- 70 |
- UTM RW |
-
-
- | GKHI-KS-040705.49-060806 |
- 2 |
- 06/07/02 |
- 0.85 |
- 39.4 |
- BXD65 |
- 20 |
- F |
- 55 |
- UTM RW |
-
-
- | GKHI-KS-040406.12-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 40.4 |
- BXD65 |
- 23 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-052405-36-050406 |
- 5 |
- 05/02/02 |
- 0.84 |
- 36.8 |
- BXD67 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-041205-01-050206 |
- 5 |
- 04/30/02 |
- 0.77 |
- 39.7 |
- BXD67 |
- 20 |
- F |
- 54 |
- UTM RW |
-
-
- | GKHI-KS-062305-01-050206 |
- 5 |
- 04/30/02 |
- 0.76 |
- 36.0 |
- BXD68 |
- 20 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-062305-09-050206 |
- 5 |
- 04/30/02 |
- 0.93 |
- 37.4 |
- BXD68 |
- 20 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_110105.30-042006 |
- 5 |
- 04/17/02 |
- 0.80 |
- 39.0 |
- BXD69 |
- 26 |
- F |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-061504.64-062206 |
- 4 |
- 06/21/02 |
- 0.72 |
- 39.3 |
- BXD69 |
- 20 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS-050404.04-040606 |
- 4 |
- 04/03/02 |
- 0.77 |
- 38.3 |
- BXD69 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-042705-01-042706 |
- 5 |
- 04/23/02 |
- 0.83 |
- 38.6 |
- BXD70 |
- 21 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-051705-59-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 38.5 |
- BXD70 |
- 22 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-030805-40-042706 |
- 5 |
- 04/23/02 |
- 0.86 |
- 38.5 |
- BXD73 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-041905.172-062206 |
- 5 |
- 06/21/02 |
- 0.79 |
- 37.6 |
- BXD73 |
- 24 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-072605-03-042706 |
- 5 |
- 04/23/02 |
- 0.87 |
- 38.2 |
- BXD73 |
- 25 |
- F |
- 72 |
- UTM RW |
-
-
- | GKHI-KS-041205-04-050406 |
- 5 |
- 05/02/02 |
- 0.83 |
- 41.4 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-041205.07 |
- 5 |
- 06/05/02 |
- 0.79 |
- 45.8 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-101805-35-050406 |
- 5 |
- 05/02/02 |
- 0.79 |
- 38.4 |
- BXD77 |
- 24 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-070605.43 |
- 5 |
- 06/05/02 |
- 0.77 |
- 42.8 |
- BXD77 |
- 23 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-071205-31-042706 |
- 5 |
- 04/23/02 |
- 0.91 |
- 37.7 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-071205-2-042706 |
- 5 |
- 04/23/02 |
- 0.90 |
- 38.1 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | KS-011305-11-042606 |
- 5 |
- 04/22/02 |
- 0.82 |
- 39.0 |
- BXD85 |
- 22 |
- M |
- 91 |
- UTM RW |
-
-
- | KS-110805-27-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 35.2 |
- BXD85 |
- 25 |
- F |
- 63 |
- UTM RW |
-
-
- | KS-080404-28-042606 |
- 4 |
- 04/22/02 |
- 0.84 |
- 36.8 |
- BXD86 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | KS-080504-04-042606 |
- 4 |
- 04/22/02 |
- 0.81 |
- 33.4 |
- BXD86 |
- 20 |
- M |
- 77 |
- UTM RW |
-
-
- | KS-051705-57-042606 |
- 5 |
- 04/22/02 |
- 1.11 |
- 35.6 |
- BXD87 |
- 20 |
- M |
- 63 |
- UTM RW |
-
-
- | KS-032905-46-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 36.1 |
- BXD87 |
- 20 |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-080905-49-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 37.6 |
- BXD90 |
- 23 |
- F |
- 71 |
- UTM RW |
-
-
- | GKHI-KS-101105.26 |
- 5 |
- 06/05/02 |
- 0.84 |
- 43.6 |
- BXD90 |
- 25 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-062304.02-040606 |
- 4 |
- 04/03/02 |
- 0.85 |
- 40.9 |
- BXD92 |
- 21 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS_071404.01-042006 |
- 4 |
- 04/17/02 |
- 0.77 |
- 39.5 |
- BXD92 |
- 21 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI_KS_031005.17-042006 |
- 5 |
- 04/17/02 |
- 0.77 |
- 38.1 |
- BXD96 |
- 20 |
- M |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-111505.12 |
- 5 |
- 06/05/02 |
- 0.77 |
- 44.1 |
- BXD96 |
- 23 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-012406.21-060806 |
- 3 |
- 06/07/02 |
- 0.73 |
- 36.6 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.24-060806 |
- 3 |
- 06/07/02 |
- 1.28 |
- 39.2 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.13-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 41.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.16-060806 |
- 3 |
- 06/07/02 |
- 0.66 |
- 37.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.31-060806 |
- 3 |
- 06/07/02 |
- 0.80 |
- 37.2 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.34-060806 |
- 3 |
- 06/07/02 |
- 0.76 |
- 38.5 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060806.04-070706 |
- 3 |
- 07/06/02 |
- 0.68 |
- 37.3 |
- C3H/HeJ |
- |
- F |
- 76 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-071505.08-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-071505.11-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 39.2 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-030305.15-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- CAST/Ei |
- |
- F |
- 64 |
- JAX |
-
-
- | GKHI-KS-031005.35-060906 |
- 3 |
- 06/08/02 |
- 0.70 |
- 35.7 |
- CAST/Ei |
- |
- M |
- 64 |
- JAX |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 37.9 |
- KK/HlJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.07-060906 |
- 3 |
- 06/08/02 |
- 0.72 |
- 35.5 |
- KK/HlJ |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031606.01-060906 |
- 3 |
- 06/08/02 |
- 0.86 |
- 35.9 |
- MOLF/Ei |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.87 |
- 37.4 |
- MOLF/Ei |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.25-060906 |
- 3 |
- 06/08/02 |
- 0.75 |
- 38.3 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.28-061306 |
- 3 |
- 06/11/02 |
- 0.82 |
- 37.1 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.04.060906 |
- 3 |
- 06/08/02 |
- 0.73 |
- 40.2 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.07-060906 |
- 3 |
- 06/08/02 |
- 0.74 |
- 39.4 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020706.04-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 41.6 |
- NZW/LacJ |
- |
- F |
- 65 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.19-060906 |
- 3 |
- 06/08/02 |
- 0.77 |
- 36.7 |
- NZW/LacJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.33-061306 |
- 3 |
- 06/11/02 |
- 0.95 |
- 35.3 |
- PWD/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.30-062006 |
- 3 |
- 06/18/02 |
- 0.88 |
- 36.3 |
- PWD/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.01-062206 |
- 3 |
- 06/21/02 |
- 1.02 |
- 35.9 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.04-062206 |
- 3 |
- 06/21/02 |
- 0.96 |
- 38.7 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.07-062206 |
- 3 |
- 06/21/02 |
- 0.98 |
- 36.6 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.10-062206 |
- 3 |
- 06/21/02 |
- 0.87 |
- 35.2 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052705.01-061306 |
- 2 |
- 06/11/02 |
- 0.72 |
- 38.3 |
- WSB/EiJ |
- |
- F |
- 52 |
- UTM RW |
-
-
- | GKHI-KS-051005.07-061306 |
- 3 |
- 06/11/02 |
- 0.77 |
- 38.0 |
- WSB/EiJ |
- |
- M |
- 58 |
- JAX |
-
-
-
-
diff --git a/general/datasets/MA_M2_0706_P/notes.rtf b/general/datasets/MA_M2_0706_P/notes.rtf
deleted file mode 100644
index d41fda1..0000000
--- a/general/datasets/MA_M2_0706_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.
-
diff --git a/general/datasets/MA_M2_0706_P/platform.rtf b/general/datasets/MA_M2_0706_P/platform.rtf
deleted file mode 100644
index cb0e8d5..0000000
--- a/general/datasets/MA_M2_0706_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
-
diff --git a/general/datasets/MA_M2_0706_P/processing.rtf b/general/datasets/MA_M2_0706_P/processing.rtf
deleted file mode 100644
index b313d60..0000000
--- a/general/datasets/MA_M2_0706_P/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/MA_M2_0706_P/summary.rtf b/general/datasets/MA_M2_0706_P/summary.rtf
deleted file mode 100644
index 9055ba0..0000000
--- a/general/datasets/MA_M2_0706_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/MA_M2_0706_P/tissue.rtf b/general/datasets/MA_M2_0706_P/tissue.rtf
deleted file mode 100644
index 5bc52e9..0000000
--- a/general/datasets/MA_M2_0706_P/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).
-
diff --git a/general/datasets/MA_M2_0706_R/acknowledgment.rtf b/general/datasets/MA_M2_0706_R/acknowledgment.rtf
deleted file mode 100644
index fea38e8..0000000
--- a/general/datasets/MA_M2_0706_R/acknowledgment.rtf
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:
-
-
- - Erwin Bottinger, M.D.
- Grant Support: R01 DK60043-04
- - Russell Chesney, M.D.
- Grant Support: Le Bonheur Chair of Excellence in Pediatrics II
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Peter Mundel
- Grant Support: NIH R01DK57683, NIH R01 DK 62472
- - Paul Klotman
- Grant Support: PO1 DK56492, PO1 DK56492.
- - Matthew Breyer
- Grant Support: DK-38226
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/MA_M2_0706_R/cases.rtf b/general/datasets/MA_M2_0706_R/cases.rtf
deleted file mode 100644
index 465b87c..0000000
--- a/general/datasets/MA_M2_0706_R/cases.rtf
+++ /dev/null
@@ -1,44 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-
- - BTBR T+tf/J
- Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - D2B6F1
- F1 hybrid generated by crossing C57BL/6J with DBA/2J
-
-
-These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>
-
-
diff --git a/general/datasets/MA_M2_0706_R/experiment-design.rtf b/general/datasets/MA_M2_0706_R/experiment-design.rtf
deleted file mode 100644
index 464e50d..0000000
--- a/general/datasets/MA_M2_0706_R/experiment-design.rtf
+++ /dev/null
@@ -1,1864 +0,0 @@
-
-Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
-
-Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
-
-
-This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
-
-
-
-
-
- | Microarray_ID |
- # mice |
- Microarray Date |
- GAPDH (3`/5`) |
- % present |
- strains |
- generation |
- sex |
- age |
- Mice Source |
-
-
- | GKHI-KS-050603.07-051706 |
- 3 |
- 05/14/02 |
- 0.73 |
- 37.6 |
- C57BL/6J |
- |
- M |
- 56 |
- UTM RW |
-
-
- | GKHI-KS-070803.01-051706 |
- 3 |
- 05/14/02 |
- 0.75 |
- 41.6 |
- C57BL/6J |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-DBA-Male-070706 |
- 2 |
- 07/06/02 |
- 0.71 |
- 37.3 |
- DBA/2J |
- |
- M |
- 56 |
- JAX |
-
-
- | GKHI_KS_121404.75-042106 |
- 4 |
- 04/18/02 |
- |
- |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.75-033006 |
- 4 |
- 03/19/02 |
- 0.73 |
- 48.5 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.78-042006 |
- 4 |
- 04/17/02 |
- 0.83 |
- 40.6 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_070804.39-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 39.0 |
- D2B6F1 |
- |
- M |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_030904.01-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 35.9 |
- D2B6F1 |
- |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-121404.73-070706 |
- 2 |
- 07/06/02 |
- 0.76 |
- 36.3 |
- D2B6F1 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-010705.38-051206 |
- 5 |
- 05/09/02 |
- 0.81 |
- 39.9 |
- BXD1 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060905.19 |
- 5 |
- 06/05/02 |
- 0.75 |
- 42.3 |
- BXD1 |
- |
- M |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-051206.13-070706 |
- 3 |
- 07/06/02 |
- 0.71 |
- 36.3 |
- BXD1 |
- |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-021304.10-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 39.1 |
- BXD2 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-04-050406 |
- 3 |
- 05/01/02 |
- 0.80 |
- 37.6 |
- BXD5 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-010705-53-050306 |
- 5 |
- 05/01/02 |
- 0.76 |
- 37.1 |
- BXD5 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031103.01-062206 |
- 3 |
- 06/21/02 |
- 0.75 |
- 37.1 |
- BXD5 |
- |
- M |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-040505-51-050306 |
- 5 |
- 05/01/02 |
- 0.71 |
- 35.5 |
- BXD6 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-092705-29--050406 |
- 5 |
- 05/02/02 |
- 0.75 |
- 36.1 |
- BXD6 |
- 160 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_092404.01-042106 |
- 4 |
- 04/18/02 |
- 0.71 |
- 36.3 |
- BXD8 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051205-25-042706 |
- 5 |
- 04/23/02 |
- 0.92 |
- 37.9 |
- BXD8 |
- |
- F |
- 77 |
- UTM RW |
-
-
- | KS-021605-17-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 40.8 |
- BXD9 |
- |
- F |
- 67 |
- UTM RW |
-
-
- | KS-032905-32-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 36.8 |
- BXD9 |
- |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-062006.08-070706 |
- 3 |
- 07/06/02 |
- 0.74 |
- 36.3 |
- BXD9 |
- |
- M |
- 78 |
- UTM RW |
-
-
- | GKHI-KS-031505.22-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 39.5 |
- BXD11 |
- |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031605.01 |
- 5 |
- 06/05/02 |
- 0.74 |
- 43.4 |
- BXD11 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI_KS_102104.40-042106 |
- 4 |
- 04/18/02 |
- 0.72 |
- 38.5 |
- BXD12 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-112002.07-051106 |
- 2 |
- 05/08/02 |
- 0.77 |
- 42.0 |
- BXD12 |
- |
- F |
- 64 |
- UMemphis |
-
-
- | GKHI-KS-120904.33-051206 |
- 4 |
- 05/09/02 |
- 0.71 |
- 38.4 |
- BXD13 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-042304.01 |
- 4 |
- 06/05/02 |
- 0.71 |
- 44.1 |
- BXD13 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020905.34-051106 |
- 5 |
- 05/08/02 |
- 0.75 |
- 40.7 |
- BXD14 |
- |
- F |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-022405.46-051106 |
- 5 |
- 05/08/02 |
- 0.71 |
- 40.2 |
- BXD14 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-091704.09-062206 |
- 4 |
- 06/21/02 |
- 0.73 |
- 39.0 |
- BXD14 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-013004.45-062206 |
- 4 |
- 06/21/02 |
- 0.76 |
- 38.5 |
- BXD15 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022405.43-051106 |
- 5 |
- 05/08/02 |
- 0.73 |
- 40.5 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-041604.10-051106 |
- 4 |
- 05/08/02 |
- 0.73 |
- 42.6 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.01-051106 |
- 5 |
- 05/08/02 |
- 0.79 |
- 42.4 |
- BXD16 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.04-051106 |
- 5 |
- 05/08/02 |
- 0.77 |
- 39.9 |
- BXD16 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.10-051006 |
- 5 |
- 05/05/02 |
- 0.93 |
- 38.7 |
- BXD18 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052804.09-051106 |
- 4 |
- 05/05/02 |
- 0.67 |
- 37.6 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.47-051106 |
- 5 |
- 05/05/02 |
- 0.73 |
- 42.3 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.44-070706 |
- 3 |
- 07/06/02 |
- 0.73 |
- 36.1 |
- BXD19 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-062905.07-051106 |
- 5 |
- 05/05/02 |
- 0.72 |
- 37.9 |
- BXD20 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-072104.58-051106 |
- 4 |
- 05/05/02 |
- 0.73 |
- 37.0 |
- BXD20 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-050405.21-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 35.1 |
- BXD21 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040705.24 |
- 5 |
- 06/05/02 |
- 0.80 |
- 40.2 |
- BXD21 |
- |
- F |
- 99 |
- UAB |
-
-
- | GKHI-KS-110405.01-051006 |
- 5 |
- 05/05/02 |
- 0.71 |
- 42.1 |
- BXD22 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-110405.04-051006 |
- 5 |
- 05/05/02 |
- 0.76 |
- 40.6 |
- BXD22 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.01-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 36.4 |
- BXD23 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.04-051006 |
- 5 |
- 05/05/02 |
- 0.73 |
- 39.3 |
- BXD23 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI_KS_091704.13-042106 |
- 4 |
- 04/18/02 |
- 0.73 |
- 37.7 |
- BXD24 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-20-050206 |
- 3 |
- 04/30/02 |
- 0.77 |
- 36.3 |
- BXD24 |
- |
- F |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-021805.20-051006 |
- 5 |
- 05/05/02 |
- 0.83 |
- 40.5 |
- BXD25 |
- |
- F |
- 67 |
- UAB |
-
-
- | GKHI-KS-090705.05-062206 |
- 5 |
- 06/21/02 |
- 0.76 |
- 38.4 |
- BXD25 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-090705.03-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 40.1 |
- BXD25 |
- |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-022105.42-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 41.8 |
- BXD27 |
- |
- M |
- 70 |
- UAB |
-
-
- | GKHI-KS-032205.31-051006 |
- 5 |
- 05/05/02 |
- 0.74 |
- 39.0 |
- BXD27 |
- |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-060706.10-070706 |
- 3 |
- 07/06/02 |
- 0.69 |
- 37.8 |
- BXD27 |
- |
- F |
- 85 |
- UTM RW |
-
-
- | GKHI-KS-012805-41-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 34.2 |
- BXD28 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-44-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 35.8 |
- BXD28 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-38-050506 |
- 5 |
- 05/04/02 |
- 0.77 |
- 42.7 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-35-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 35.8 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-32-050506 |
- 5 |
- 05/04/02 |
- 0.74 |
- 39.9 |
- BXD31 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-100604-07-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 40.2 |
- BXD31 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-021605.26-051706 |
- 5 |
- 05/14/02 |
- 1.11 |
- 39.0 |
- BXD32 |
- |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-112002.01-051206 |
- 2 |
- 05/09/02 |
- 0.76 |
- 38.1 |
- BXD32 |
- |
- F |
- 60 |
- UMemphis |
-
-
- | GKHI-KS-072605-01-050506 |
- 5 |
- 05/04/02 |
- 0.79 |
- 41.3 |
- BXD33 |
- 50 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-091405-23-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 38.4 |
- BXD33 |
- 50 |
- M |
- 76 |
- UTM RW |
-
-
- | GKHI-KS-111104-18-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 42.2 |
- BXD36 |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031804-07-050506 |
- 4 |
- 05/04/02 |
- 0.85 |
- 42.5 |
- BXD36 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-092005.16-051206 |
- 5 |
- 05/09/02 |
- 0.72 |
- 37.2 |
- BXD38 |
- 46 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031403.01-060806 |
- 1 |
- 06/07/02 |
- 0.69 |
- 39.6 |
- BXD38 |
- |
- M |
- 69 |
- UMemphis |
-
-
- | GKHI-KS-090104.21-051106 |
- 4 |
- 05/08/02 |
- 0.72 |
- 36.3 |
- BXD39 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040204.30 |
- 4 |
- 06/05/02 |
- 0.77 |
- 43.9 |
- BXD39 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051805-16-050506 |
- 5 |
- 05/04/02 |
- 2.16 |
- 43.8 |
- BXD40 |
- |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-111902-04-050506 |
- 2 |
- 05/04/02 |
- 0.84 |
- 41.0 |
- BXD40 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-050604-01-050406 |
- 4 |
- 05/01/02 |
- 0.85 |
- 35.6 |
- BXD43 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-080905-43-050406 |
- 5 |
- 05/01/02 |
- 0.78 |
- 33.7 |
- BXD43 |
- 28 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-031004-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 36.2 |
- BXD44 |
- 21 |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-020504-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 30.8 |
- BXD44 |
- 20 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-071504-01-050406 |
- 4 |
- 05/01/02 |
- 0.74 |
- 37.7 |
- BXD45 |
- 20 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-081104-05-050406 |
- 4 |
- 05/01/02 |
- 0.78 |
- 34.2 |
- BXD45 |
- 20 |
- M |
- 93 |
- UTM RW |
-
-
- | GKHI-KS-031204-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 35.6 |
- BXD48 |
- 22 |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-021104.06-051706 |
- 4 |
- 05/14/02 |
- 0.75 |
- 41.1 |
- BXD48 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-033005-21-050306 |
- 5 |
- 05/01/02 |
- 0.78 |
- 34.9 |
- BXD51 |
- 27 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-090204-01-050306 |
- 4 |
- 05/01/02 |
- 0.72 |
- 38.3 |
- BXD51 |
- 24 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI_KS-010704.01-040606 |
- 4 |
- 04/03/02 |
- 0.75 |
- 37.5 |
- BXD60 |
- 21 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_013004.38-042006 |
- 4 |
- 04/17/02 |
- 0.78 |
- 40.1 |
- BXD60 |
- 21 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-030905-28-050206 |
- 5 |
- 04/30/02 |
- 0.73 |
- 36.6 |
- BXD61 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-050305-18-050206 |
- 5 |
- 04/30/02 |
- 0.83 |
- 35.8 |
- BXD61 |
- 21 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-121803.01-040706 |
- 3 |
- 04/03/02 |
- 0.80 |
- 40.0 |
- BXD62 |
- 20 |
- M |
- 54 |
- UTM RW |
-
-
- | GKHI_KS_021204.01-042006 |
- 4 |
- 04/17/02 |
- 0.85 |
- 39.8 |
- BXD62 |
- 21 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-020905-25-050206 |
- 5 |
- 04/30/02 |
- 0.84 |
- 35.2 |
- BXD63 |
- 21 |
- M |
- 70 |
- UTM RW |
-
-
- | GKHI-KS-040705.49-060806 |
- 2 |
- 06/07/02 |
- 0.85 |
- 39.4 |
- BXD65 |
- 20 |
- F |
- 55 |
- UTM RW |
-
-
- | GKHI-KS-040406.12-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 40.4 |
- BXD65 |
- 23 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-052405-36-050406 |
- 5 |
- 05/02/02 |
- 0.84 |
- 36.8 |
- BXD67 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-041205-01-050206 |
- 5 |
- 04/30/02 |
- 0.77 |
- 39.7 |
- BXD67 |
- 20 |
- F |
- 54 |
- UTM RW |
-
-
- | GKHI-KS-062305-01-050206 |
- 5 |
- 04/30/02 |
- 0.76 |
- 36.0 |
- BXD68 |
- 20 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-062305-09-050206 |
- 5 |
- 04/30/02 |
- 0.93 |
- 37.4 |
- BXD68 |
- 20 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_110105.30-042006 |
- 5 |
- 04/17/02 |
- 0.80 |
- 39.0 |
- BXD69 |
- 26 |
- F |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-061504.64-062206 |
- 4 |
- 06/21/02 |
- 0.72 |
- 39.3 |
- BXD69 |
- 20 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS-050404.04-040606 |
- 4 |
- 04/03/02 |
- 0.77 |
- 38.3 |
- BXD69 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-042705-01-042706 |
- 5 |
- 04/23/02 |
- 0.83 |
- 38.6 |
- BXD70 |
- 21 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-051705-59-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 38.5 |
- BXD70 |
- 22 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-030805-40-042706 |
- 5 |
- 04/23/02 |
- 0.86 |
- 38.5 |
- BXD73 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-041905.172-062206 |
- 5 |
- 06/21/02 |
- 0.79 |
- 37.6 |
- BXD73 |
- 24 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-072605-03-042706 |
- 5 |
- 04/23/02 |
- 0.87 |
- 38.2 |
- BXD73 |
- 25 |
- F |
- 72 |
- UTM RW |
-
-
- | GKHI-KS-041205-04-050406 |
- 5 |
- 05/02/02 |
- 0.83 |
- 41.4 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-041205.07 |
- 5 |
- 06/05/02 |
- 0.79 |
- 45.8 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-101805-35-050406 |
- 5 |
- 05/02/02 |
- 0.79 |
- 38.4 |
- BXD77 |
- 24 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-070605.43 |
- 5 |
- 06/05/02 |
- 0.77 |
- 42.8 |
- BXD77 |
- 23 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-071205-31-042706 |
- 5 |
- 04/23/02 |
- 0.91 |
- 37.7 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-071205-2-042706 |
- 5 |
- 04/23/02 |
- 0.90 |
- 38.1 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | KS-011305-11-042606 |
- 5 |
- 04/22/02 |
- 0.82 |
- 39.0 |
- BXD85 |
- 22 |
- M |
- 91 |
- UTM RW |
-
-
- | KS-110805-27-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 35.2 |
- BXD85 |
- 25 |
- F |
- 63 |
- UTM RW |
-
-
- | KS-080404-28-042606 |
- 4 |
- 04/22/02 |
- 0.84 |
- 36.8 |
- BXD86 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | KS-080504-04-042606 |
- 4 |
- 04/22/02 |
- 0.81 |
- 33.4 |
- BXD86 |
- 20 |
- M |
- 77 |
- UTM RW |
-
-
- | KS-051705-57-042606 |
- 5 |
- 04/22/02 |
- 1.11 |
- 35.6 |
- BXD87 |
- 20 |
- M |
- 63 |
- UTM RW |
-
-
- | KS-032905-46-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 36.1 |
- BXD87 |
- 20 |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-080905-49-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 37.6 |
- BXD90 |
- 23 |
- F |
- 71 |
- UTM RW |
-
-
- | GKHI-KS-101105.26 |
- 5 |
- 06/05/02 |
- 0.84 |
- 43.6 |
- BXD90 |
- 25 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-062304.02-040606 |
- 4 |
- 04/03/02 |
- 0.85 |
- 40.9 |
- BXD92 |
- 21 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS_071404.01-042006 |
- 4 |
- 04/17/02 |
- 0.77 |
- 39.5 |
- BXD92 |
- 21 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI_KS_031005.17-042006 |
- 5 |
- 04/17/02 |
- 0.77 |
- 38.1 |
- BXD96 |
- 20 |
- M |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-111505.12 |
- 5 |
- 06/05/02 |
- 0.77 |
- 44.1 |
- BXD96 |
- 23 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-012406.21-060806 |
- 3 |
- 06/07/02 |
- 0.73 |
- 36.6 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.24-060806 |
- 3 |
- 06/07/02 |
- 1.28 |
- 39.2 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.13-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 41.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.16-060806 |
- 3 |
- 06/07/02 |
- 0.66 |
- 37.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.31-060806 |
- 3 |
- 06/07/02 |
- 0.80 |
- 37.2 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.34-060806 |
- 3 |
- 06/07/02 |
- 0.76 |
- 38.5 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060806.04-070706 |
- 3 |
- 07/06/02 |
- 0.68 |
- 37.3 |
- C3H/HeJ |
- |
- F |
- 76 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-071505.08-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-071505.11-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 39.2 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-030305.15-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- CAST/Ei |
- |
- F |
- 64 |
- JAX |
-
-
- | GKHI-KS-031005.35-060906 |
- 3 |
- 06/08/02 |
- 0.70 |
- 35.7 |
- CAST/Ei |
- |
- M |
- 64 |
- JAX |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 37.9 |
- KK/HlJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.07-060906 |
- 3 |
- 06/08/02 |
- 0.72 |
- 35.5 |
- KK/HlJ |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031606.01-060906 |
- 3 |
- 06/08/02 |
- 0.86 |
- 35.9 |
- MOLF/Ei |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.87 |
- 37.4 |
- MOLF/Ei |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.25-060906 |
- 3 |
- 06/08/02 |
- 0.75 |
- 38.3 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.28-061306 |
- 3 |
- 06/11/02 |
- 0.82 |
- 37.1 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.04.060906 |
- 3 |
- 06/08/02 |
- 0.73 |
- 40.2 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.07-060906 |
- 3 |
- 06/08/02 |
- 0.74 |
- 39.4 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020706.04-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 41.6 |
- NZW/LacJ |
- |
- F |
- 65 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.19-060906 |
- 3 |
- 06/08/02 |
- 0.77 |
- 36.7 |
- NZW/LacJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.33-061306 |
- 3 |
- 06/11/02 |
- 0.95 |
- 35.3 |
- PWD/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.30-062006 |
- 3 |
- 06/18/02 |
- 0.88 |
- 36.3 |
- PWD/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.01-062206 |
- 3 |
- 06/21/02 |
- 1.02 |
- 35.9 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.04-062206 |
- 3 |
- 06/21/02 |
- 0.96 |
- 38.7 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.07-062206 |
- 3 |
- 06/21/02 |
- 0.98 |
- 36.6 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.10-062206 |
- 3 |
- 06/21/02 |
- 0.87 |
- 35.2 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052705.01-061306 |
- 2 |
- 06/11/02 |
- 0.72 |
- 38.3 |
- WSB/EiJ |
- |
- F |
- 52 |
- UTM RW |
-
-
- | GKHI-KS-051005.07-061306 |
- 3 |
- 06/11/02 |
- 0.77 |
- 38.0 |
- WSB/EiJ |
- |
- M |
- 58 |
- JAX |
-
-
-
-
diff --git a/general/datasets/MA_M2_0706_R/notes.rtf b/general/datasets/MA_M2_0706_R/notes.rtf
deleted file mode 100644
index d41fda1..0000000
--- a/general/datasets/MA_M2_0706_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.
-
diff --git a/general/datasets/MA_M2_0706_R/platform.rtf b/general/datasets/MA_M2_0706_R/platform.rtf
deleted file mode 100644
index cb0e8d5..0000000
--- a/general/datasets/MA_M2_0706_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
-
diff --git a/general/datasets/MA_M2_0706_R/processing.rtf b/general/datasets/MA_M2_0706_R/processing.rtf
deleted file mode 100644
index b313d60..0000000
--- a/general/datasets/MA_M2_0706_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/MA_M2_0706_R/summary.rtf b/general/datasets/MA_M2_0706_R/summary.rtf
deleted file mode 100644
index 9055ba0..0000000
--- a/general/datasets/MA_M2_0706_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/MA_M2_0706_R/tissue.rtf b/general/datasets/MA_M2_0706_R/tissue.rtf
deleted file mode 100644
index 5bc52e9..0000000
--- a/general/datasets/MA_M2_0706_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).
-
diff --git a/general/datasets/MA_M2_0806_P/acknowledgment.rtf b/general/datasets/MA_M2_0806_P/acknowledgment.rtf
deleted file mode 100644
index fea38e8..0000000
--- a/general/datasets/MA_M2_0806_P/acknowledgment.rtf
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:
-
-
- - Erwin Bottinger, M.D.
- Grant Support: R01 DK60043-04
- - Russell Chesney, M.D.
- Grant Support: Le Bonheur Chair of Excellence in Pediatrics II
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Peter Mundel
- Grant Support: NIH R01DK57683, NIH R01 DK 62472
- - Paul Klotman
- Grant Support: PO1 DK56492, PO1 DK56492.
- - Matthew Breyer
- Grant Support: DK-38226
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/MA_M2_0806_P/cases.rtf b/general/datasets/MA_M2_0806_P/cases.rtf
deleted file mode 100644
index 465b87c..0000000
--- a/general/datasets/MA_M2_0806_P/cases.rtf
+++ /dev/null
@@ -1,44 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-
- - BTBR T+tf/J
- Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - D2B6F1
- F1 hybrid generated by crossing C57BL/6J with DBA/2J
-
-
-These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>
-
-
diff --git a/general/datasets/MA_M2_0806_P/experiment-design.rtf b/general/datasets/MA_M2_0806_P/experiment-design.rtf
deleted file mode 100644
index 464e50d..0000000
--- a/general/datasets/MA_M2_0806_P/experiment-design.rtf
+++ /dev/null
@@ -1,1864 +0,0 @@
-
-Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
-
-Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
-
-
-This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
-
-
-
-
-
- | Microarray_ID |
- # mice |
- Microarray Date |
- GAPDH (3`/5`) |
- % present |
- strains |
- generation |
- sex |
- age |
- Mice Source |
-
-
- | GKHI-KS-050603.07-051706 |
- 3 |
- 05/14/02 |
- 0.73 |
- 37.6 |
- C57BL/6J |
- |
- M |
- 56 |
- UTM RW |
-
-
- | GKHI-KS-070803.01-051706 |
- 3 |
- 05/14/02 |
- 0.75 |
- 41.6 |
- C57BL/6J |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-DBA-Male-070706 |
- 2 |
- 07/06/02 |
- 0.71 |
- 37.3 |
- DBA/2J |
- |
- M |
- 56 |
- JAX |
-
-
- | GKHI_KS_121404.75-042106 |
- 4 |
- 04/18/02 |
- |
- |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.75-033006 |
- 4 |
- 03/19/02 |
- 0.73 |
- 48.5 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.78-042006 |
- 4 |
- 04/17/02 |
- 0.83 |
- 40.6 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_070804.39-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 39.0 |
- D2B6F1 |
- |
- M |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_030904.01-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 35.9 |
- D2B6F1 |
- |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-121404.73-070706 |
- 2 |
- 07/06/02 |
- 0.76 |
- 36.3 |
- D2B6F1 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-010705.38-051206 |
- 5 |
- 05/09/02 |
- 0.81 |
- 39.9 |
- BXD1 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060905.19 |
- 5 |
- 06/05/02 |
- 0.75 |
- 42.3 |
- BXD1 |
- |
- M |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-051206.13-070706 |
- 3 |
- 07/06/02 |
- 0.71 |
- 36.3 |
- BXD1 |
- |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-021304.10-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 39.1 |
- BXD2 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-04-050406 |
- 3 |
- 05/01/02 |
- 0.80 |
- 37.6 |
- BXD5 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-010705-53-050306 |
- 5 |
- 05/01/02 |
- 0.76 |
- 37.1 |
- BXD5 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031103.01-062206 |
- 3 |
- 06/21/02 |
- 0.75 |
- 37.1 |
- BXD5 |
- |
- M |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-040505-51-050306 |
- 5 |
- 05/01/02 |
- 0.71 |
- 35.5 |
- BXD6 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-092705-29--050406 |
- 5 |
- 05/02/02 |
- 0.75 |
- 36.1 |
- BXD6 |
- 160 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_092404.01-042106 |
- 4 |
- 04/18/02 |
- 0.71 |
- 36.3 |
- BXD8 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051205-25-042706 |
- 5 |
- 04/23/02 |
- 0.92 |
- 37.9 |
- BXD8 |
- |
- F |
- 77 |
- UTM RW |
-
-
- | KS-021605-17-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 40.8 |
- BXD9 |
- |
- F |
- 67 |
- UTM RW |
-
-
- | KS-032905-32-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 36.8 |
- BXD9 |
- |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-062006.08-070706 |
- 3 |
- 07/06/02 |
- 0.74 |
- 36.3 |
- BXD9 |
- |
- M |
- 78 |
- UTM RW |
-
-
- | GKHI-KS-031505.22-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 39.5 |
- BXD11 |
- |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031605.01 |
- 5 |
- 06/05/02 |
- 0.74 |
- 43.4 |
- BXD11 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI_KS_102104.40-042106 |
- 4 |
- 04/18/02 |
- 0.72 |
- 38.5 |
- BXD12 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-112002.07-051106 |
- 2 |
- 05/08/02 |
- 0.77 |
- 42.0 |
- BXD12 |
- |
- F |
- 64 |
- UMemphis |
-
-
- | GKHI-KS-120904.33-051206 |
- 4 |
- 05/09/02 |
- 0.71 |
- 38.4 |
- BXD13 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-042304.01 |
- 4 |
- 06/05/02 |
- 0.71 |
- 44.1 |
- BXD13 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020905.34-051106 |
- 5 |
- 05/08/02 |
- 0.75 |
- 40.7 |
- BXD14 |
- |
- F |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-022405.46-051106 |
- 5 |
- 05/08/02 |
- 0.71 |
- 40.2 |
- BXD14 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-091704.09-062206 |
- 4 |
- 06/21/02 |
- 0.73 |
- 39.0 |
- BXD14 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-013004.45-062206 |
- 4 |
- 06/21/02 |
- 0.76 |
- 38.5 |
- BXD15 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022405.43-051106 |
- 5 |
- 05/08/02 |
- 0.73 |
- 40.5 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-041604.10-051106 |
- 4 |
- 05/08/02 |
- 0.73 |
- 42.6 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.01-051106 |
- 5 |
- 05/08/02 |
- 0.79 |
- 42.4 |
- BXD16 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.04-051106 |
- 5 |
- 05/08/02 |
- 0.77 |
- 39.9 |
- BXD16 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.10-051006 |
- 5 |
- 05/05/02 |
- 0.93 |
- 38.7 |
- BXD18 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052804.09-051106 |
- 4 |
- 05/05/02 |
- 0.67 |
- 37.6 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.47-051106 |
- 5 |
- 05/05/02 |
- 0.73 |
- 42.3 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.44-070706 |
- 3 |
- 07/06/02 |
- 0.73 |
- 36.1 |
- BXD19 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-062905.07-051106 |
- 5 |
- 05/05/02 |
- 0.72 |
- 37.9 |
- BXD20 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-072104.58-051106 |
- 4 |
- 05/05/02 |
- 0.73 |
- 37.0 |
- BXD20 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-050405.21-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 35.1 |
- BXD21 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040705.24 |
- 5 |
- 06/05/02 |
- 0.80 |
- 40.2 |
- BXD21 |
- |
- F |
- 99 |
- UAB |
-
-
- | GKHI-KS-110405.01-051006 |
- 5 |
- 05/05/02 |
- 0.71 |
- 42.1 |
- BXD22 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-110405.04-051006 |
- 5 |
- 05/05/02 |
- 0.76 |
- 40.6 |
- BXD22 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.01-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 36.4 |
- BXD23 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.04-051006 |
- 5 |
- 05/05/02 |
- 0.73 |
- 39.3 |
- BXD23 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI_KS_091704.13-042106 |
- 4 |
- 04/18/02 |
- 0.73 |
- 37.7 |
- BXD24 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-20-050206 |
- 3 |
- 04/30/02 |
- 0.77 |
- 36.3 |
- BXD24 |
- |
- F |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-021805.20-051006 |
- 5 |
- 05/05/02 |
- 0.83 |
- 40.5 |
- BXD25 |
- |
- F |
- 67 |
- UAB |
-
-
- | GKHI-KS-090705.05-062206 |
- 5 |
- 06/21/02 |
- 0.76 |
- 38.4 |
- BXD25 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-090705.03-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 40.1 |
- BXD25 |
- |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-022105.42-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 41.8 |
- BXD27 |
- |
- M |
- 70 |
- UAB |
-
-
- | GKHI-KS-032205.31-051006 |
- 5 |
- 05/05/02 |
- 0.74 |
- 39.0 |
- BXD27 |
- |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-060706.10-070706 |
- 3 |
- 07/06/02 |
- 0.69 |
- 37.8 |
- BXD27 |
- |
- F |
- 85 |
- UTM RW |
-
-
- | GKHI-KS-012805-41-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 34.2 |
- BXD28 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-44-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 35.8 |
- BXD28 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-38-050506 |
- 5 |
- 05/04/02 |
- 0.77 |
- 42.7 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-35-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 35.8 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-32-050506 |
- 5 |
- 05/04/02 |
- 0.74 |
- 39.9 |
- BXD31 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-100604-07-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 40.2 |
- BXD31 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-021605.26-051706 |
- 5 |
- 05/14/02 |
- 1.11 |
- 39.0 |
- BXD32 |
- |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-112002.01-051206 |
- 2 |
- 05/09/02 |
- 0.76 |
- 38.1 |
- BXD32 |
- |
- F |
- 60 |
- UMemphis |
-
-
- | GKHI-KS-072605-01-050506 |
- 5 |
- 05/04/02 |
- 0.79 |
- 41.3 |
- BXD33 |
- 50 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-091405-23-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 38.4 |
- BXD33 |
- 50 |
- M |
- 76 |
- UTM RW |
-
-
- | GKHI-KS-111104-18-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 42.2 |
- BXD36 |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031804-07-050506 |
- 4 |
- 05/04/02 |
- 0.85 |
- 42.5 |
- BXD36 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-092005.16-051206 |
- 5 |
- 05/09/02 |
- 0.72 |
- 37.2 |
- BXD38 |
- 46 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031403.01-060806 |
- 1 |
- 06/07/02 |
- 0.69 |
- 39.6 |
- BXD38 |
- |
- M |
- 69 |
- UMemphis |
-
-
- | GKHI-KS-090104.21-051106 |
- 4 |
- 05/08/02 |
- 0.72 |
- 36.3 |
- BXD39 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040204.30 |
- 4 |
- 06/05/02 |
- 0.77 |
- 43.9 |
- BXD39 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051805-16-050506 |
- 5 |
- 05/04/02 |
- 2.16 |
- 43.8 |
- BXD40 |
- |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-111902-04-050506 |
- 2 |
- 05/04/02 |
- 0.84 |
- 41.0 |
- BXD40 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-050604-01-050406 |
- 4 |
- 05/01/02 |
- 0.85 |
- 35.6 |
- BXD43 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-080905-43-050406 |
- 5 |
- 05/01/02 |
- 0.78 |
- 33.7 |
- BXD43 |
- 28 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-031004-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 36.2 |
- BXD44 |
- 21 |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-020504-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 30.8 |
- BXD44 |
- 20 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-071504-01-050406 |
- 4 |
- 05/01/02 |
- 0.74 |
- 37.7 |
- BXD45 |
- 20 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-081104-05-050406 |
- 4 |
- 05/01/02 |
- 0.78 |
- 34.2 |
- BXD45 |
- 20 |
- M |
- 93 |
- UTM RW |
-
-
- | GKHI-KS-031204-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 35.6 |
- BXD48 |
- 22 |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-021104.06-051706 |
- 4 |
- 05/14/02 |
- 0.75 |
- 41.1 |
- BXD48 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-033005-21-050306 |
- 5 |
- 05/01/02 |
- 0.78 |
- 34.9 |
- BXD51 |
- 27 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-090204-01-050306 |
- 4 |
- 05/01/02 |
- 0.72 |
- 38.3 |
- BXD51 |
- 24 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI_KS-010704.01-040606 |
- 4 |
- 04/03/02 |
- 0.75 |
- 37.5 |
- BXD60 |
- 21 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_013004.38-042006 |
- 4 |
- 04/17/02 |
- 0.78 |
- 40.1 |
- BXD60 |
- 21 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-030905-28-050206 |
- 5 |
- 04/30/02 |
- 0.73 |
- 36.6 |
- BXD61 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-050305-18-050206 |
- 5 |
- 04/30/02 |
- 0.83 |
- 35.8 |
- BXD61 |
- 21 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-121803.01-040706 |
- 3 |
- 04/03/02 |
- 0.80 |
- 40.0 |
- BXD62 |
- 20 |
- M |
- 54 |
- UTM RW |
-
-
- | GKHI_KS_021204.01-042006 |
- 4 |
- 04/17/02 |
- 0.85 |
- 39.8 |
- BXD62 |
- 21 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-020905-25-050206 |
- 5 |
- 04/30/02 |
- 0.84 |
- 35.2 |
- BXD63 |
- 21 |
- M |
- 70 |
- UTM RW |
-
-
- | GKHI-KS-040705.49-060806 |
- 2 |
- 06/07/02 |
- 0.85 |
- 39.4 |
- BXD65 |
- 20 |
- F |
- 55 |
- UTM RW |
-
-
- | GKHI-KS-040406.12-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 40.4 |
- BXD65 |
- 23 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-052405-36-050406 |
- 5 |
- 05/02/02 |
- 0.84 |
- 36.8 |
- BXD67 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-041205-01-050206 |
- 5 |
- 04/30/02 |
- 0.77 |
- 39.7 |
- BXD67 |
- 20 |
- F |
- 54 |
- UTM RW |
-
-
- | GKHI-KS-062305-01-050206 |
- 5 |
- 04/30/02 |
- 0.76 |
- 36.0 |
- BXD68 |
- 20 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-062305-09-050206 |
- 5 |
- 04/30/02 |
- 0.93 |
- 37.4 |
- BXD68 |
- 20 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_110105.30-042006 |
- 5 |
- 04/17/02 |
- 0.80 |
- 39.0 |
- BXD69 |
- 26 |
- F |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-061504.64-062206 |
- 4 |
- 06/21/02 |
- 0.72 |
- 39.3 |
- BXD69 |
- 20 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS-050404.04-040606 |
- 4 |
- 04/03/02 |
- 0.77 |
- 38.3 |
- BXD69 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-042705-01-042706 |
- 5 |
- 04/23/02 |
- 0.83 |
- 38.6 |
- BXD70 |
- 21 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-051705-59-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 38.5 |
- BXD70 |
- 22 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-030805-40-042706 |
- 5 |
- 04/23/02 |
- 0.86 |
- 38.5 |
- BXD73 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-041905.172-062206 |
- 5 |
- 06/21/02 |
- 0.79 |
- 37.6 |
- BXD73 |
- 24 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-072605-03-042706 |
- 5 |
- 04/23/02 |
- 0.87 |
- 38.2 |
- BXD73 |
- 25 |
- F |
- 72 |
- UTM RW |
-
-
- | GKHI-KS-041205-04-050406 |
- 5 |
- 05/02/02 |
- 0.83 |
- 41.4 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-041205.07 |
- 5 |
- 06/05/02 |
- 0.79 |
- 45.8 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-101805-35-050406 |
- 5 |
- 05/02/02 |
- 0.79 |
- 38.4 |
- BXD77 |
- 24 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-070605.43 |
- 5 |
- 06/05/02 |
- 0.77 |
- 42.8 |
- BXD77 |
- 23 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-071205-31-042706 |
- 5 |
- 04/23/02 |
- 0.91 |
- 37.7 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-071205-2-042706 |
- 5 |
- 04/23/02 |
- 0.90 |
- 38.1 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | KS-011305-11-042606 |
- 5 |
- 04/22/02 |
- 0.82 |
- 39.0 |
- BXD85 |
- 22 |
- M |
- 91 |
- UTM RW |
-
-
- | KS-110805-27-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 35.2 |
- BXD85 |
- 25 |
- F |
- 63 |
- UTM RW |
-
-
- | KS-080404-28-042606 |
- 4 |
- 04/22/02 |
- 0.84 |
- 36.8 |
- BXD86 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | KS-080504-04-042606 |
- 4 |
- 04/22/02 |
- 0.81 |
- 33.4 |
- BXD86 |
- 20 |
- M |
- 77 |
- UTM RW |
-
-
- | KS-051705-57-042606 |
- 5 |
- 04/22/02 |
- 1.11 |
- 35.6 |
- BXD87 |
- 20 |
- M |
- 63 |
- UTM RW |
-
-
- | KS-032905-46-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 36.1 |
- BXD87 |
- 20 |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-080905-49-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 37.6 |
- BXD90 |
- 23 |
- F |
- 71 |
- UTM RW |
-
-
- | GKHI-KS-101105.26 |
- 5 |
- 06/05/02 |
- 0.84 |
- 43.6 |
- BXD90 |
- 25 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-062304.02-040606 |
- 4 |
- 04/03/02 |
- 0.85 |
- 40.9 |
- BXD92 |
- 21 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS_071404.01-042006 |
- 4 |
- 04/17/02 |
- 0.77 |
- 39.5 |
- BXD92 |
- 21 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI_KS_031005.17-042006 |
- 5 |
- 04/17/02 |
- 0.77 |
- 38.1 |
- BXD96 |
- 20 |
- M |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-111505.12 |
- 5 |
- 06/05/02 |
- 0.77 |
- 44.1 |
- BXD96 |
- 23 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-012406.21-060806 |
- 3 |
- 06/07/02 |
- 0.73 |
- 36.6 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.24-060806 |
- 3 |
- 06/07/02 |
- 1.28 |
- 39.2 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.13-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 41.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.16-060806 |
- 3 |
- 06/07/02 |
- 0.66 |
- 37.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.31-060806 |
- 3 |
- 06/07/02 |
- 0.80 |
- 37.2 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.34-060806 |
- 3 |
- 06/07/02 |
- 0.76 |
- 38.5 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060806.04-070706 |
- 3 |
- 07/06/02 |
- 0.68 |
- 37.3 |
- C3H/HeJ |
- |
- F |
- 76 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-071505.08-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-071505.11-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 39.2 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-030305.15-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- CAST/Ei |
- |
- F |
- 64 |
- JAX |
-
-
- | GKHI-KS-031005.35-060906 |
- 3 |
- 06/08/02 |
- 0.70 |
- 35.7 |
- CAST/Ei |
- |
- M |
- 64 |
- JAX |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 37.9 |
- KK/HlJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.07-060906 |
- 3 |
- 06/08/02 |
- 0.72 |
- 35.5 |
- KK/HlJ |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031606.01-060906 |
- 3 |
- 06/08/02 |
- 0.86 |
- 35.9 |
- MOLF/Ei |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.87 |
- 37.4 |
- MOLF/Ei |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.25-060906 |
- 3 |
- 06/08/02 |
- 0.75 |
- 38.3 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.28-061306 |
- 3 |
- 06/11/02 |
- 0.82 |
- 37.1 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.04.060906 |
- 3 |
- 06/08/02 |
- 0.73 |
- 40.2 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.07-060906 |
- 3 |
- 06/08/02 |
- 0.74 |
- 39.4 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020706.04-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 41.6 |
- NZW/LacJ |
- |
- F |
- 65 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.19-060906 |
- 3 |
- 06/08/02 |
- 0.77 |
- 36.7 |
- NZW/LacJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.33-061306 |
- 3 |
- 06/11/02 |
- 0.95 |
- 35.3 |
- PWD/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.30-062006 |
- 3 |
- 06/18/02 |
- 0.88 |
- 36.3 |
- PWD/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.01-062206 |
- 3 |
- 06/21/02 |
- 1.02 |
- 35.9 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.04-062206 |
- 3 |
- 06/21/02 |
- 0.96 |
- 38.7 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.07-062206 |
- 3 |
- 06/21/02 |
- 0.98 |
- 36.6 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.10-062206 |
- 3 |
- 06/21/02 |
- 0.87 |
- 35.2 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052705.01-061306 |
- 2 |
- 06/11/02 |
- 0.72 |
- 38.3 |
- WSB/EiJ |
- |
- F |
- 52 |
- UTM RW |
-
-
- | GKHI-KS-051005.07-061306 |
- 3 |
- 06/11/02 |
- 0.77 |
- 38.0 |
- WSB/EiJ |
- |
- M |
- 58 |
- JAX |
-
-
-
-
diff --git a/general/datasets/MA_M2_0806_P/notes.rtf b/general/datasets/MA_M2_0806_P/notes.rtf
deleted file mode 100644
index d41fda1..0000000
--- a/general/datasets/MA_M2_0806_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.
-
diff --git a/general/datasets/MA_M2_0806_P/platform.rtf b/general/datasets/MA_M2_0806_P/platform.rtf
deleted file mode 100644
index cb0e8d5..0000000
--- a/general/datasets/MA_M2_0806_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
-
diff --git a/general/datasets/MA_M2_0806_P/processing.rtf b/general/datasets/MA_M2_0806_P/processing.rtf
deleted file mode 100644
index b313d60..0000000
--- a/general/datasets/MA_M2_0806_P/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/MA_M2_0806_P/summary.rtf b/general/datasets/MA_M2_0806_P/summary.rtf
deleted file mode 100644
index 9055ba0..0000000
--- a/general/datasets/MA_M2_0806_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/MA_M2_0806_P/tissue.rtf b/general/datasets/MA_M2_0806_P/tissue.rtf
deleted file mode 100644
index 5bc52e9..0000000
--- a/general/datasets/MA_M2_0806_P/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).
-
diff --git a/general/datasets/MA_M2_0806_R/acknowledgment.rtf b/general/datasets/MA_M2_0806_R/acknowledgment.rtf
deleted file mode 100644
index fea38e8..0000000
--- a/general/datasets/MA_M2_0806_R/acknowledgment.rtf
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort:
-
-
- - Erwin Bottinger, M.D.
- Grant Support: R01 DK60043-04
- - Russell Chesney, M.D.
- Grant Support: Le Bonheur Chair of Excellence in Pediatrics II
- - Lu Lu, M.D.
- Grant Support: NIH U01AA13499, U24AA13513
- - Peter Mundel
- Grant Support: NIH R01DK57683, NIH R01 DK 62472
- - Paul Klotman
- Grant Support: PO1 DK56492, PO1 DK56492.
- - Matthew Breyer
- Grant Support: DK-38226
- - Kenneth F. Manly, Ph.D.
- Grant Support: NIH P20MH062009 and U01CA105417
- - Robert W. Williams, Ph.D.
- Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513
-
-
-
-
diff --git a/general/datasets/MA_M2_0806_R/cases.rtf b/general/datasets/MA_M2_0806_R/cases.rtf
deleted file mode 100644
index 465b87c..0000000
--- a/general/datasets/MA_M2_0806_R/cases.rtf
+++ /dev/null
@@ -1,44 +0,0 @@
-
-The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs.
-
-
-Mouse Diversity Panel (MDP). We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants.
-
-
- - genetic and phenotypic diversity, including use by the Phenome Project
- - their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains
- - their use by the Complex Trait Consortium to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)
- - genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)
- - availability from The Jackson Laboratory
-
-
-
- - BTBR T+tf/J
- Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body.
- - C3H/HeJ
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list
- - C57BL/6J
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list
- - C57BL/6ByJ
- Paternal substrain of B6 used to generate the CXB panel
- - CAST/Ei
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list
- - DBA/2J
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list
- - KK/HlJ
- Sequenced by Perlegen/NIEHS
- - NOD/LtJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic
- - PWD/PhJ
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues
- - PWK/PhJ
- Collaborative Cross strain; Phenome Project D list
- - WSB/EiJ
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list
- - D2B6F1
- F1 hybrid generated by crossing C57BL/6J with DBA/2J
-
-
-These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.P>
-
-
diff --git a/general/datasets/MA_M2_0806_R/experiment-design.rtf b/general/datasets/MA_M2_0806_R/experiment-design.rtf
deleted file mode 100644
index 464e50d..0000000
--- a/general/datasets/MA_M2_0806_R/experiment-design.rtf
+++ /dev/null
@@ -1,1864 +0,0 @@
-
-Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
-
-Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
-
-Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
-
-
-This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
-
-
-
-
-
- | Microarray_ID |
- # mice |
- Microarray Date |
- GAPDH (3`/5`) |
- % present |
- strains |
- generation |
- sex |
- age |
- Mice Source |
-
-
- | GKHI-KS-050603.07-051706 |
- 3 |
- 05/14/02 |
- 0.73 |
- 37.6 |
- C57BL/6J |
- |
- M |
- 56 |
- UTM RW |
-
-
- | GKHI-KS-070803.01-051706 |
- 3 |
- 05/14/02 |
- 0.75 |
- 41.6 |
- C57BL/6J |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-DBA-Male-070706 |
- 2 |
- 07/06/02 |
- 0.71 |
- 37.3 |
- DBA/2J |
- |
- M |
- 56 |
- JAX |
-
-
- | GKHI_KS_121404.75-042106 |
- 4 |
- 04/18/02 |
- |
- |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.75-033006 |
- 4 |
- 03/19/02 |
- 0.73 |
- 48.5 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_121404.78-042006 |
- 4 |
- 04/17/02 |
- 0.83 |
- 40.6 |
- DBA/2J |
- |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_070804.39-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 39.0 |
- D2B6F1 |
- |
- M |
- 59 |
- UTM RW |
-
-
- | GKHI_KS_030904.01-042006 |
- 4 |
- 04/17/02 |
- 0.82 |
- 35.9 |
- D2B6F1 |
- |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-121404.73-070706 |
- 2 |
- 07/06/02 |
- 0.76 |
- 36.3 |
- D2B6F1 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI-KS-010705.38-051206 |
- 5 |
- 05/09/02 |
- 0.81 |
- 39.9 |
- BXD1 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060905.19 |
- 5 |
- 06/05/02 |
- 0.75 |
- 42.3 |
- BXD1 |
- |
- M |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-051206.13-070706 |
- 3 |
- 07/06/02 |
- 0.71 |
- 36.3 |
- BXD1 |
- |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-021304.10-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 39.1 |
- BXD2 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-04-050406 |
- 3 |
- 05/01/02 |
- 0.80 |
- 37.6 |
- BXD5 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-010705-53-050306 |
- 5 |
- 05/01/02 |
- 0.76 |
- 37.1 |
- BXD5 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031103.01-062206 |
- 3 |
- 06/21/02 |
- 0.75 |
- 37.1 |
- BXD5 |
- |
- M |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-040505-51-050306 |
- 5 |
- 05/01/02 |
- 0.71 |
- 35.5 |
- BXD6 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-092705-29--050406 |
- 5 |
- 05/02/02 |
- 0.75 |
- 36.1 |
- BXD6 |
- 160 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_092404.01-042106 |
- 4 |
- 04/18/02 |
- 0.71 |
- 36.3 |
- BXD8 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051205-25-042706 |
- 5 |
- 04/23/02 |
- 0.92 |
- 37.9 |
- BXD8 |
- |
- F |
- 77 |
- UTM RW |
-
-
- | KS-021605-17-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 40.8 |
- BXD9 |
- |
- F |
- 67 |
- UTM RW |
-
-
- | KS-032905-32-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 36.8 |
- BXD9 |
- |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-062006.08-070706 |
- 3 |
- 07/06/02 |
- 0.74 |
- 36.3 |
- BXD9 |
- |
- M |
- 78 |
- UTM RW |
-
-
- | GKHI-KS-031505.22-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 39.5 |
- BXD11 |
- |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031605.01 |
- 5 |
- 06/05/02 |
- 0.74 |
- 43.4 |
- BXD11 |
- |
- F |
- 69 |
- UTM RW |
-
-
- | GKHI_KS_102104.40-042106 |
- 4 |
- 04/18/02 |
- 0.72 |
- 38.5 |
- BXD12 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-112002.07-051106 |
- 2 |
- 05/08/02 |
- 0.77 |
- 42.0 |
- BXD12 |
- |
- F |
- 64 |
- UMemphis |
-
-
- | GKHI-KS-120904.33-051206 |
- 4 |
- 05/09/02 |
- 0.71 |
- 38.4 |
- BXD13 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-042304.01 |
- 4 |
- 06/05/02 |
- 0.71 |
- 44.1 |
- BXD13 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020905.34-051106 |
- 5 |
- 05/08/02 |
- 0.75 |
- 40.7 |
- BXD14 |
- |
- F |
- 68 |
- UTM RW |
-
-
- | GKHI-KS-022405.46-051106 |
- 5 |
- 05/08/02 |
- 0.71 |
- 40.2 |
- BXD14 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-091704.09-062206 |
- 4 |
- 06/21/02 |
- 0.73 |
- 39.0 |
- BXD14 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-013004.45-062206 |
- 4 |
- 06/21/02 |
- 0.76 |
- 38.5 |
- BXD15 |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022405.43-051106 |
- 5 |
- 05/08/02 |
- 0.73 |
- 40.5 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-041604.10-051106 |
- 4 |
- 05/08/02 |
- 0.73 |
- 42.6 |
- BXD15 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.01-051106 |
- 5 |
- 05/08/02 |
- 0.79 |
- 42.4 |
- BXD16 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031805.04-051106 |
- 5 |
- 05/08/02 |
- 0.77 |
- 39.9 |
- BXD16 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.10-051006 |
- 5 |
- 05/05/02 |
- 0.93 |
- 38.7 |
- BXD18 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052804.09-051106 |
- 4 |
- 05/05/02 |
- 0.67 |
- 37.6 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.47-051106 |
- 5 |
- 05/05/02 |
- 0.73 |
- 42.3 |
- BXD19 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-010705.44-070706 |
- 3 |
- 07/06/02 |
- 0.73 |
- 36.1 |
- BXD19 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-062905.07-051106 |
- 5 |
- 05/05/02 |
- 0.72 |
- 37.9 |
- BXD20 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-072104.58-051106 |
- 4 |
- 05/05/02 |
- 0.73 |
- 37.0 |
- BXD20 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-050405.21-051206 |
- 4 |
- 05/09/02 |
- 0.81 |
- 35.1 |
- BXD21 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040705.24 |
- 5 |
- 06/05/02 |
- 0.80 |
- 40.2 |
- BXD21 |
- |
- F |
- 99 |
- UAB |
-
-
- | GKHI-KS-110405.01-051006 |
- 5 |
- 05/05/02 |
- 0.71 |
- 42.1 |
- BXD22 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-110405.04-051006 |
- 5 |
- 05/05/02 |
- 0.76 |
- 40.6 |
- BXD22 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.01-051206 |
- 5 |
- 05/09/02 |
- 0.74 |
- 36.4 |
- BXD23 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040805.04-051006 |
- 5 |
- 05/05/02 |
- 0.73 |
- 39.3 |
- BXD23 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI_KS_091704.13-042106 |
- 4 |
- 04/18/02 |
- 0.73 |
- 37.7 |
- BXD24 |
- |
- M |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040303-20-050206 |
- 3 |
- 04/30/02 |
- 0.77 |
- 36.3 |
- BXD24 |
- |
- F |
- 71 |
- UMemphis |
-
-
- | GKHI-KS-021805.20-051006 |
- 5 |
- 05/05/02 |
- 0.83 |
- 40.5 |
- BXD25 |
- |
- F |
- 67 |
- UAB |
-
-
- | GKHI-KS-090705.05-062206 |
- 5 |
- 06/21/02 |
- 0.76 |
- 38.4 |
- BXD25 |
- |
- M |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-090705.03-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 40.1 |
- BXD25 |
- |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-022105.42-051006 |
- 5 |
- 05/05/02 |
- 0.81 |
- 41.8 |
- BXD27 |
- |
- M |
- 70 |
- UAB |
-
-
- | GKHI-KS-032205.31-051006 |
- 5 |
- 05/05/02 |
- 0.74 |
- 39.0 |
- BXD27 |
- |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-060706.10-070706 |
- 3 |
- 07/06/02 |
- 0.69 |
- 37.8 |
- BXD27 |
- |
- F |
- 85 |
- UTM RW |
-
-
- | GKHI-KS-012805-41-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 34.2 |
- BXD28 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-44-050506 |
- 5 |
- 05/04/02 |
- 0.81 |
- 35.8 |
- BXD28 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-38-050506 |
- 5 |
- 05/04/02 |
- 0.77 |
- 42.7 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-35-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 35.8 |
- BXD29 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012805-32-050506 |
- 5 |
- 05/04/02 |
- 0.74 |
- 39.9 |
- BXD31 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-100604-07-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 40.2 |
- BXD31 |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-021605.26-051706 |
- 5 |
- 05/14/02 |
- 1.11 |
- 39.0 |
- BXD32 |
- |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-112002.01-051206 |
- 2 |
- 05/09/02 |
- 0.76 |
- 38.1 |
- BXD32 |
- |
- F |
- 60 |
- UMemphis |
-
-
- | GKHI-KS-072605-01-050506 |
- 5 |
- 05/04/02 |
- 0.79 |
- 41.3 |
- BXD33 |
- 50 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-091405-23-050506 |
- 5 |
- 05/04/02 |
- 0.84 |
- 38.4 |
- BXD33 |
- 50 |
- M |
- 76 |
- UTM RW |
-
-
- | GKHI-KS-111104-18-050506 |
- 4 |
- 05/04/02 |
- 0.79 |
- 42.2 |
- BXD36 |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031804-07-050506 |
- 4 |
- 05/04/02 |
- 0.85 |
- 42.5 |
- BXD36 |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-092005.16-051206 |
- 5 |
- 05/09/02 |
- 0.72 |
- 37.2 |
- BXD38 |
- 46 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-031403.01-060806 |
- 1 |
- 06/07/02 |
- 0.69 |
- 39.6 |
- BXD38 |
- |
- M |
- 69 |
- UMemphis |
-
-
- | GKHI-KS-090104.21-051106 |
- 4 |
- 05/08/02 |
- 0.72 |
- 36.3 |
- BXD39 |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-040204.30 |
- 4 |
- 06/05/02 |
- 0.77 |
- 43.9 |
- BXD39 |
- |
- F |
- 59 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-051805-16-050506 |
- 5 |
- 05/04/02 |
- 2.16 |
- 43.8 |
- BXD40 |
- |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-111902-04-050506 |
- 2 |
- 05/04/02 |
- 0.84 |
- 41.0 |
- BXD40 |
- |
- F |
- 56 |
- UMemphis |
-
-
- | GKHI-KS-050604-01-050406 |
- 4 |
- 05/01/02 |
- 0.85 |
- 35.6 |
- BXD43 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-080905-43-050406 |
- 5 |
- 05/01/02 |
- 0.78 |
- 33.7 |
- BXD43 |
- 28 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-031004-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 36.2 |
- BXD44 |
- 21 |
- F |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-020504-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 30.8 |
- BXD44 |
- 20 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-071504-01-050406 |
- 4 |
- 05/01/02 |
- 0.74 |
- 37.7 |
- BXD45 |
- 20 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-081104-05-050406 |
- 4 |
- 05/01/02 |
- 0.78 |
- 34.2 |
- BXD45 |
- 20 |
- M |
- 93 |
- UTM RW |
-
-
- | GKHI-KS-031204-01-050406 |
- 4 |
- 05/01/02 |
- 0.75 |
- 35.6 |
- BXD48 |
- 22 |
- M |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-021104.06-051706 |
- 4 |
- 05/14/02 |
- 0.75 |
- 41.1 |
- BXD48 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | GKHI-KS-033005-21-050306 |
- 5 |
- 05/01/02 |
- 0.78 |
- 34.9 |
- BXD51 |
- 27 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-090204-01-050306 |
- 4 |
- 05/01/02 |
- 0.72 |
- 38.3 |
- BXD51 |
- 24 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI_KS-010704.01-040606 |
- 4 |
- 04/03/02 |
- 0.75 |
- 37.5 |
- BXD60 |
- 21 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_013004.38-042006 |
- 4 |
- 04/17/02 |
- 0.78 |
- 40.1 |
- BXD60 |
- 21 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-030905-28-050206 |
- 5 |
- 04/30/02 |
- 0.73 |
- 36.6 |
- BXD61 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-050305-18-050206 |
- 5 |
- 04/30/02 |
- 0.83 |
- 35.8 |
- BXD61 |
- 21 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-121803.01-040706 |
- 3 |
- 04/03/02 |
- 0.80 |
- 40.0 |
- BXD62 |
- 20 |
- M |
- 54 |
- UTM RW |
-
-
- | GKHI_KS_021204.01-042006 |
- 4 |
- 04/17/02 |
- 0.85 |
- 39.8 |
- BXD62 |
- 21 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-020905-25-050206 |
- 5 |
- 04/30/02 |
- 0.84 |
- 35.2 |
- BXD63 |
- 21 |
- M |
- 70 |
- UTM RW |
-
-
- | GKHI-KS-040705.49-060806 |
- 2 |
- 06/07/02 |
- 0.85 |
- 39.4 |
- BXD65 |
- 20 |
- F |
- 55 |
- UTM RW |
-
-
- | GKHI-KS-040406.12-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 40.4 |
- BXD65 |
- 23 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-052405-36-050406 |
- 5 |
- 05/02/02 |
- 0.84 |
- 36.8 |
- BXD67 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-041205-01-050206 |
- 5 |
- 04/30/02 |
- 0.77 |
- 39.7 |
- BXD67 |
- 20 |
- F |
- 54 |
- UTM RW |
-
-
- | GKHI-KS-062305-01-050206 |
- 5 |
- 04/30/02 |
- 0.76 |
- 36.0 |
- BXD68 |
- 20 |
- F |
- 59 |
- UTM RW |
-
-
- | GKHI-KS-062305-09-050206 |
- 5 |
- 04/30/02 |
- 0.93 |
- 37.4 |
- BXD68 |
- 20 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI_KS_110105.30-042006 |
- 5 |
- 04/17/02 |
- 0.80 |
- 39.0 |
- BXD69 |
- 26 |
- F |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-061504.64-062206 |
- 4 |
- 06/21/02 |
- 0.72 |
- 39.3 |
- BXD69 |
- 20 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS-050404.04-040606 |
- 4 |
- 04/03/02 |
- 0.77 |
- 38.3 |
- BXD69 |
- 20 |
- F |
- 63 |
- UTM RW |
-
-
- | GKHI-KS-042705-01-042706 |
- 5 |
- 04/23/02 |
- 0.83 |
- 38.6 |
- BXD70 |
- 21 |
- F |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-051705-59-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 38.5 |
- BXD70 |
- 22 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-030805-40-042706 |
- 5 |
- 04/23/02 |
- 0.86 |
- 38.5 |
- BXD73 |
- 23 |
- F |
- 61 |
- UTM RW |
-
-
- | GKHI-KS-041905.172-062206 |
- 5 |
- 06/21/02 |
- 0.79 |
- 37.6 |
- BXD73 |
- 24 |
- M |
- 64 |
- UTM RW |
-
-
- | GKHI-KS-072605-03-042706 |
- 5 |
- 04/23/02 |
- 0.87 |
- 38.2 |
- BXD73 |
- 25 |
- F |
- 72 |
- UTM RW |
-
-
- | GKHI-KS-041205-04-050406 |
- 5 |
- 05/02/02 |
- 0.83 |
- 41.4 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-041205.07 |
- 5 |
- 06/05/02 |
- 0.79 |
- 45.8 |
- BXD75 |
- 22 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-101805-35-050406 |
- 5 |
- 05/02/02 |
- 0.79 |
- 38.4 |
- BXD77 |
- 24 |
- F |
- 60 |
- UTM RW |
-
-
- | GKHI-KS-070605.43 |
- 5 |
- 06/05/02 |
- 0.77 |
- 42.8 |
- BXD77 |
- 23 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI-KS-071205-31-042706 |
- 5 |
- 04/23/02 |
- 0.91 |
- 37.7 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-071205-2-042706 |
- 5 |
- 04/23/02 |
- 0.90 |
- 38.1 |
- BXD80 |
- 20 |
- F |
- 65 |
- UTM RW |
-
-
- | KS-011305-11-042606 |
- 5 |
- 04/22/02 |
- 0.82 |
- 39.0 |
- BXD85 |
- 22 |
- M |
- 91 |
- UTM RW |
-
-
- | KS-110805-27-042606 |
- 5 |
- 04/22/02 |
- 0.91 |
- 35.2 |
- BXD85 |
- 25 |
- F |
- 63 |
- UTM RW |
-
-
- | KS-080404-28-042606 |
- 4 |
- 04/22/02 |
- 0.84 |
- 36.8 |
- BXD86 |
- 21 |
- F |
- 58 |
- UTM RW |
-
-
- | KS-080504-04-042606 |
- 4 |
- 04/22/02 |
- 0.81 |
- 33.4 |
- BXD86 |
- 20 |
- M |
- 77 |
- UTM RW |
-
-
- | KS-051705-57-042606 |
- 5 |
- 04/22/02 |
- 1.11 |
- 35.6 |
- BXD87 |
- 20 |
- M |
- 63 |
- UTM RW |
-
-
- | KS-032905-46-042606 |
- 5 |
- 04/22/02 |
- 0.85 |
- 36.1 |
- BXD87 |
- 20 |
- M |
- 57 |
- UTM RW |
-
-
- | GKHI-KS-080905-49-042706 |
- 5 |
- 04/23/02 |
- 0.89 |
- 37.6 |
- BXD90 |
- 23 |
- F |
- 71 |
- UTM RW |
-
-
- | GKHI-KS-101105.26 |
- 5 |
- 06/05/02 |
- 0.84 |
- 43.6 |
- BXD90 |
- 25 |
- F |
- 70 |
- UTM RW |
-
-
- | GKHI_KS-062304.02-040606 |
- 4 |
- 04/03/02 |
- 0.85 |
- 40.9 |
- BXD92 |
- 21 |
- M |
- 55 |
- UTM RW |
-
-
- | GKHI_KS_071404.01-042006 |
- 4 |
- 04/17/02 |
- 0.77 |
- 39.5 |
- BXD92 |
- 21 |
- F |
- 62 |
- UTM RW |
-
-
- | GKHI_KS_031005.17-042006 |
- 5 |
- 04/17/02 |
- 0.77 |
- 38.1 |
- BXD96 |
- 20 |
- M |
- 65 |
- UTM RW |
-
-
- | GKHI-KS-111505.12 |
- 5 |
- 06/05/02 |
- 0.77 |
- 44.1 |
- BXD96 |
- 23 |
- M |
- 66 |
- UTM RW |
-
-
- | GKHI-KS-012406.21-060806 |
- 3 |
- 06/07/02 |
- 0.73 |
- 36.6 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.24-060806 |
- 3 |
- 06/07/02 |
- 1.28 |
- 39.2 |
- BTBR T+tf/J |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.13-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 41.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-030206.16-060806 |
- 3 |
- 06/07/02 |
- 0.66 |
- 37.2 |
- BXSB/MpJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.31-060806 |
- 3 |
- 06/07/02 |
- 0.80 |
- 37.2 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-011906.34-060806 |
- 3 |
- 06/07/02 |
- 0.76 |
- 38.5 |
- C3H/HeJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-060806.04-070706 |
- 3 |
- 07/06/02 |
- 0.68 |
- 37.3 |
- C3H/HeJ |
- |
- F |
- 76 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-071505.08-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-071505.11-060806 |
- 2 |
- 06/07/02 |
- 0.73 |
- 39.2 |
- C57BL/6ByJ |
- |
- F |
- 51 |
- JAX |
-
-
- | GKHI-KS-030305.15-060806 |
- 3 |
- 06/07/02 |
- 0.71 |
- 37.4 |
- CAST/Ei |
- |
- F |
- 64 |
- JAX |
-
-
- | GKHI-KS-031005.35-060906 |
- 3 |
- 06/08/02 |
- 0.70 |
- 35.7 |
- CAST/Ei |
- |
- M |
- 64 |
- JAX |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 37.9 |
- KK/HlJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.07-060906 |
- 3 |
- 06/08/02 |
- 0.72 |
- 35.5 |
- KK/HlJ |
- |
- M |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-031606.01-060906 |
- 3 |
- 06/08/02 |
- 0.86 |
- 35.9 |
- MOLF/Ei |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-022206.16-060906 |
- 3 |
- 06/08/02 |
- 0.87 |
- 37.4 |
- MOLF/Ei |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.25-060906 |
- 3 |
- 06/08/02 |
- 0.75 |
- 38.3 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012006.28-061306 |
- 3 |
- 06/11/02 |
- 0.82 |
- 37.1 |
- NOD/LtJ |
- |
- F |
- 58 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.04.060906 |
- 3 |
- 06/08/02 |
- 0.73 |
- 40.2 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-032306.07-060906 |
- 3 |
- 06/08/02 |
- 0.74 |
- 39.4 |
- NZB/BlNJ |
- |
- F |
- 61 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020706.04-060906 |
- 3 |
- 06/08/02 |
- 0.71 |
- 41.6 |
- NZW/LacJ |
- |
- F |
- 65 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.19-060906 |
- 3 |
- 06/08/02 |
- 0.77 |
- 36.7 |
- NZW/LacJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.33-061306 |
- 3 |
- 06/11/02 |
- 0.95 |
- 35.3 |
- PWD/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-012406.30-062006 |
- 3 |
- 06/18/02 |
- 0.88 |
- 36.3 |
- PWD/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.01-062206 |
- 3 |
- 06/21/02 |
- 1.02 |
- 35.9 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.04-062206 |
- 3 |
- 06/21/02 |
- 0.96 |
- 38.7 |
- PWK/PhJ |
- |
- F |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.07-062206 |
- 3 |
- 06/21/02 |
- 0.98 |
- 36.6 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-020206.10-062206 |
- 3 |
- 06/21/02 |
- 0.87 |
- 35.2 |
- PWK/PhJ |
- |
- M |
- 60 |
- Harvard/BIDMC |
-
-
- | GKHI-KS-052705.01-061306 |
- 2 |
- 06/11/02 |
- 0.72 |
- 38.3 |
- WSB/EiJ |
- |
- F |
- 52 |
- UTM RW |
-
-
- | GKHI-KS-051005.07-061306 |
- 3 |
- 06/11/02 |
- 0.77 |
- 38.0 |
- WSB/EiJ |
- |
- M |
- 58 |
- JAX |
-
-
-
-
diff --git a/general/datasets/MA_M2_0806_R/notes.rtf b/general/datasets/MA_M2_0806_R/notes.rtf
deleted file mode 100644
index d41fda1..0000000
--- a/general/datasets/MA_M2_0806_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by Kremena Star on July 22 ,2006. Updated by KS on July 25, 2006.
-
diff --git a/general/datasets/MA_M2_0806_R/platform.rtf b/general/datasets/MA_M2_0806_R/platform.rtf
deleted file mode 100644
index cb0e8d5..0000000
--- a/general/datasets/MA_M2_0806_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.
-
diff --git a/general/datasets/MA_M2_0806_R/processing.rtf b/general/datasets/MA_M2_0806_R/processing.rtf
deleted file mode 100644
index b313d60..0000000
--- a/general/datasets/MA_M2_0806_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Probe set data from the CHP file: The expression values were generated using RMA. The same simple steps described above were also applied to these values.
-
-
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients.
-
-Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain.
-
-Sex of the samples was validated using sex-specific probe sets such as Xist and Dby.
-
-
-
-All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on Data Sharing Policies, and Conditions and Limitations, and Contacts. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access probelms.
-
diff --git a/general/datasets/MA_M2_0806_R/summary.rtf b/general/datasets/MA_M2_0806_R/summary.rtf
deleted file mode 100644
index 9055ba0..0000000
--- a/general/datasets/MA_M2_0806_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The July 2006 Kidney QTL Consortium data set provides estimates of mRNA expression in the adult kidney of 70 genetically diverse strains of mice including 54 BXD recombinant inbred strains, a set of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were processed using a total of 153 Affymetrix Mouse Expression 430 2.0 microarrays (M430v2.0). This particular data set was processed using the RMA protocol. CAUTION: This dataset is not sex-balanced.
diff --git a/general/datasets/MA_M2_0806_R/tissue.rtf b/general/datasets/MA_M2_0806_R/tissue.rtf
deleted file mode 100644
index 5bc52e9..0000000
--- a/general/datasets/MA_M2_0806_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1).
-
diff --git a/general/datasets/MA_M_0704_M/acknowledgment.rtf b/general/datasets/MA_M_0704_M/acknowledgment.rtf
deleted file mode 100644
index 2408013..0000000
--- a/general/datasets/MA_M_0704_M/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All of the NCI mammary mRNA M430A and M430B data sets have been generated by Kent Hunter at the Laboratory of Population Genetics at the National Cancer Institute in Bethesda. For contact and citations and other information on these data sets please review the INFO pages and contact Dr. Hunter regarding use of this data set in publications or projects.
diff --git a/general/datasets/MA_M_0704_M/cases.rtf b/general/datasets/MA_M_0704_M/cases.rtf
deleted file mode 100644
index 615a0f3..0000000
--- a/general/datasets/MA_M_0704_M/cases.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-The lines of mice used in this NCI-sponsored project consist of 18 groups of isogenic F1 progeny made by crossing females from each of 18 AKXD recombinant inbred strains (AKXD2, 3, 7, 9, 10, 11, 13, 14, 16, 18, 20, 21, 22, 23, 24, 25, 27, and 28) to male FVB/N mice that carry a transgene that consistently leads to the development of mammary tumors in females (e.g. Le Voyer et al., 2001). The formal nomenclature of the male transgenic line is FVB/N-TgN(MMTV-PyMT)634Mul. The genomes of each AKXD x FVB F1 consist of one set of FVB chromosomes (including the transgene) and one set of chromosomes inherited from one of the 18 AKXD RI strain mothers. Only the AKXD chromosomes are "recombinant" across this panel of F1 progeny, and the set therefore has a genetic architecture similar to backcross progeny. It is possible to map modifiers that influence tumor characteristics and expression patterns. It is also possible to study covariance of transcript expression levels in tumor tissue. For further background on this special mapping design please see Hunter and Williams (2002).
-
-The ancestral strains from which all AKXD strains are derived are AKR/J (AKR) and DBA/2J (D2 or D). DBA/2J has been partially sequenced (approximately 1.5x coverage by D by Celera Genomics). Significant genomic sequence data for AKR is not currently available. Chromosomes of the two parental strains have recombined in the different AKXD strains. All of these strains are available from The Jackson Laboratory as cryopreserved stocks. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/MA_M_0704_M/notes.rtf b/general/datasets/MA_M_0704_M/notes.rtf
deleted file mode 100644
index 4e0118b..0000000
--- a/general/datasets/MA_M_0704_M/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Text originally written by Kent Hunter and Robert W. Williams, July 2004. Updated by RWW, Nov 6, 2004.
diff --git a/general/datasets/MA_M_0704_M/platform.rtf b/general/datasets/MA_M_0704_M/platform.rtf
deleted file mode 100644
index 4b22e44..0000000
--- a/general/datasets/MA_M_0704_M/platform.rtf
+++ /dev/null
@@ -1,643 +0,0 @@
-All samples were processed and arrayed in the Laboratory of Population Genetics at the NCI. The table below lists the arrays by Samples, AKXD strain and Age.
-
-
-
-
-
-
-
-
-
- |
- Sample
- |
-
- AKXD strain
- |
-
- Age
- |
-
-
- |
- AKXD2957
- |
-
- 2
- |
-
- 98
- |
-
-
- |
- AKXD2959
- |
-
- 2
- |
-
- 96
- |
-
-
- |
- AKXD1747
- |
-
- 3
- |
-
- 84
- |
-
-
- |
- AKXD3446
- |
-
- 3
- |
-
- 91
- |
-
-
- |
- AKXD4225
- |
-
- 3
- |
-
- 83
- |
-
-
- |
- AKXD2543
- |
-
- 7
- |
-
- 82
- |
-
-
- |
- AKXD2967
- |
-
- 7
- |
-
- 88
- |
-
-
- |
- AKXD3336
- |
-
- 7
- |
-
- 95
- |
-
-
- |
- AKXD2685
- |
-
- 9
- |
-
- 113
- |
-
-
- |
- AKXD2710
- |
-
- 9
- |
-
- 109
- |
-
-
- |
- AKXD2949
- |
-
- 9
- |
-
- 115
- |
-
-
- |
- AKXD2618
- |
-
- 10
- |
-
- 99
- |
-
-
- |
- AKXD2620
- |
-
- 10
- |
-
- 99
- |
-
-
- |
- AKXD3023
- |
-
- 10
- |
-
- 94
- |
-
-
- |
- AKXD1910
- |
-
- 11
- |
-
- 87
- |
-
-
- |
- AKXD2824
- |
-
- 11
- |
-
- 92
- |
-
-
- |
- AKXD2825
- |
-
- 11
- |
-
- 103
- |
-
-
- |
- AKXD2635
- |
-
- 13
- |
-
- 83
- |
-
-
- |
- AKXD2718
- |
-
- 13
- |
-
- 100
- |
-
-
- |
- AKXD2721
- |
-
- 13
- |
-
- 91
- |
-
-
- |
- AKXD2632
- |
-
- 14
- |
-
- 99
- |
-
-
- |
- AKXD2640
- |
-
- 14
- |
-
- 100
- |
-
-
- |
- AKXD3444
- |
-
- 14
- |
-
- 96
- |
-
-
- |
- AKXD1636
- |
-
- 16
- |
-
- 112
- |
-
-
- |
- AKXD3688
- |
-
- 16
- |
-
- 80
- |
-
-
- |
- AKXD4152
- |
-
- 16
- |
-
- 91
- |
-
-
- |
- AKXD1647
- |
-
- 18
- |
-
- 91
- |
-
-
- |
- AKXD2616
- |
-
- 18
- |
-
- 91
- |
-
-
- |
- AKXD2804
- |
-
- 18
- |
-
- 80
- |
-
-
- |
- AKXD2456
- |
-
- 20
- |
-
- 100
- |
-
-
- |
- AKXD2554
- |
-
- 20
- |
-
- 107
- |
-
-
- |
- AKXD2829
- |
-
- 20
- |
-
- 105
- |
-
-
- |
- AKXD1610
- |
-
- 21
- |
-
- 98
- |
-
-
- |
- AKXD2611
- |
-
- 21
- |
-
- 88
- |
-
-
- |
- AKXD2918
- |
-
- 21
- |
-
- 98
- |
-
-
- |
- AKXD2460
- |
-
- 22
- |
-
- 107
- |
-
-
- |
- AKXD2461
- |
-
- 22
- |
-
- 94
- |
-
-
- |
- AKXD2463
- |
-
- 22
- |
-
- 110
- |
-
-
- |
- AKXD2975
- |
-
- 23
- |
-
- 82
- |
-
-
- |
- AKXD2976
- |
-
- 23
- |
-
- 86
- |
-
-
- |
- AKXD3955
- |
-
- 23
- |
-
- 90
- |
-
-
- |
- AKXD1494
- |
-
- 24
- |
-
- 103
- |
-
-
- |
- AKXD1880
- |
-
- 24
- |
-
- 104
- |
-
-
- |
- AKXD3030
- |
-
- 24
- |
-
- 89
- |
-
-
- |
- AKXD1607
- |
-
- 25
- |
-
- 110
- |
-
-
- |
- AKXD2326
- |
-
- 25
- |
-
- 92
- |
-
-
- |
- AKXD2328
- |
-
- 25
- |
-
- 90
- |
-
-
- |
- AKXD2629
- |
-
- 25
- |
-
- 96
- |
-
-
- |
- AKXD1756
- |
-
- 27
- |
-
- 100
- |
-
-
- |
- AKXD1757
- |
-
- 27
- |
-
- 98
- |
-
-
- |
- AKXD1948
- |
-
- 27
- |
-
- 99
- |
-
-
- |
- AKXD1950
- |
-
- 27
- |
-
- 97
- |
-
-
- |
- AKXD2968
- |
-
- 27
- |
-
- 94
- |
-
-
- |
- AKXD2809
- |
-
- 28
- |
-
- 88
- |
-
-
- |
- AKXD2815
- |
-
- 28
- |
-
- 90
- |
-
-
- |
- AKXD3432
- |
-
- 28
- |
-
- 91
- |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/MA_M_0704_M/processing.rtf b/general/datasets/MA_M_0704_M/processing.rtf
deleted file mode 100644
index 0d11078..0000000
--- a/general/datasets/MA_M_0704_M/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the .CEL file: These .CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 to the .CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z scores for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-Probe set data from the .CHP file: The expression data were generated using MAS5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/MA_M_0704_M/summary.rtf b/general/datasets/MA_M_0704_M/summary.rtf
deleted file mode 100644
index 6423e7c..0000000
--- a/general/datasets/MA_M_0704_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Used the Affymetrix M430A and M430B pair of arrays (total of 45,137 probe sets). Data available as CEL files from GeneNetwork upon request.
diff --git a/general/datasets/MA_M_0704_M/tissue.rtf b/general/datasets/MA_M_0704_M/tissue.rtf
deleted file mode 100644
index 01385cb..0000000
--- a/general/datasets/MA_M_0704_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Mammary tumors used in this array experiment were derived from 18 sets of AKXD x FVB/N F1 females as described above. After the primary tumor was diagnosed, the animals were aged an additional 40 days to permit metastatic progression. Females were sacrificed and mammary tumors were harvested. Samples were processed and arrayed on Affymetrix M430A and M430B arrays. The majority of the samples were assayed on arrays obtained from the same lot number.
diff --git a/general/datasets/MA_M_0704_R/acknowledgment.rtf b/general/datasets/MA_M_0704_R/acknowledgment.rtf
deleted file mode 100644
index 2408013..0000000
--- a/general/datasets/MA_M_0704_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All of the NCI mammary mRNA M430A and M430B data sets have been generated by Kent Hunter at the Laboratory of Population Genetics at the National Cancer Institute in Bethesda. For contact and citations and other information on these data sets please review the INFO pages and contact Dr. Hunter regarding use of this data set in publications or projects.
diff --git a/general/datasets/MA_M_0704_R/cases.rtf b/general/datasets/MA_M_0704_R/cases.rtf
deleted file mode 100644
index 615a0f3..0000000
--- a/general/datasets/MA_M_0704_R/cases.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-The lines of mice used in this NCI-sponsored project consist of 18 groups of isogenic F1 progeny made by crossing females from each of 18 AKXD recombinant inbred strains (AKXD2, 3, 7, 9, 10, 11, 13, 14, 16, 18, 20, 21, 22, 23, 24, 25, 27, and 28) to male FVB/N mice that carry a transgene that consistently leads to the development of mammary tumors in females (e.g. Le Voyer et al., 2001). The formal nomenclature of the male transgenic line is FVB/N-TgN(MMTV-PyMT)634Mul. The genomes of each AKXD x FVB F1 consist of one set of FVB chromosomes (including the transgene) and one set of chromosomes inherited from one of the 18 AKXD RI strain mothers. Only the AKXD chromosomes are "recombinant" across this panel of F1 progeny, and the set therefore has a genetic architecture similar to backcross progeny. It is possible to map modifiers that influence tumor characteristics and expression patterns. It is also possible to study covariance of transcript expression levels in tumor tissue. For further background on this special mapping design please see Hunter and Williams (2002).
-
-The ancestral strains from which all AKXD strains are derived are AKR/J (AKR) and DBA/2J (D2 or D). DBA/2J has been partially sequenced (approximately 1.5x coverage by D by Celera Genomics). Significant genomic sequence data for AKR is not currently available. Chromosomes of the two parental strains have recombined in the different AKXD strains. All of these strains are available from The Jackson Laboratory as cryopreserved stocks. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
diff --git a/general/datasets/MA_M_0704_R/notes.rtf b/general/datasets/MA_M_0704_R/notes.rtf
deleted file mode 100644
index 4e0118b..0000000
--- a/general/datasets/MA_M_0704_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Text originally written by Kent Hunter and Robert W. Williams, July 2004. Updated by RWW, Nov 6, 2004.
diff --git a/general/datasets/MA_M_0704_R/platform.rtf b/general/datasets/MA_M_0704_R/platform.rtf
deleted file mode 100644
index 4b22e44..0000000
--- a/general/datasets/MA_M_0704_R/platform.rtf
+++ /dev/null
@@ -1,643 +0,0 @@
-All samples were processed and arrayed in the Laboratory of Population Genetics at the NCI. The table below lists the arrays by Samples, AKXD strain and Age.
-
-
-
-
-
-
-
-
-
- |
- Sample
- |
-
- AKXD strain
- |
-
- Age
- |
-
-
- |
- AKXD2957
- |
-
- 2
- |
-
- 98
- |
-
-
- |
- AKXD2959
- |
-
- 2
- |
-
- 96
- |
-
-
- |
- AKXD1747
- |
-
- 3
- |
-
- 84
- |
-
-
- |
- AKXD3446
- |
-
- 3
- |
-
- 91
- |
-
-
- |
- AKXD4225
- |
-
- 3
- |
-
- 83
- |
-
-
- |
- AKXD2543
- |
-
- 7
- |
-
- 82
- |
-
-
- |
- AKXD2967
- |
-
- 7
- |
-
- 88
- |
-
-
- |
- AKXD3336
- |
-
- 7
- |
-
- 95
- |
-
-
- |
- AKXD2685
- |
-
- 9
- |
-
- 113
- |
-
-
- |
- AKXD2710
- |
-
- 9
- |
-
- 109
- |
-
-
- |
- AKXD2949
- |
-
- 9
- |
-
- 115
- |
-
-
- |
- AKXD2618
- |
-
- 10
- |
-
- 99
- |
-
-
- |
- AKXD2620
- |
-
- 10
- |
-
- 99
- |
-
-
- |
- AKXD3023
- |
-
- 10
- |
-
- 94
- |
-
-
- |
- AKXD1910
- |
-
- 11
- |
-
- 87
- |
-
-
- |
- AKXD2824
- |
-
- 11
- |
-
- 92
- |
-
-
- |
- AKXD2825
- |
-
- 11
- |
-
- 103
- |
-
-
- |
- AKXD2635
- |
-
- 13
- |
-
- 83
- |
-
-
- |
- AKXD2718
- |
-
- 13
- |
-
- 100
- |
-
-
- |
- AKXD2721
- |
-
- 13
- |
-
- 91
- |
-
-
- |
- AKXD2632
- |
-
- 14
- |
-
- 99
- |
-
-
- |
- AKXD2640
- |
-
- 14
- |
-
- 100
- |
-
-
- |
- AKXD3444
- |
-
- 14
- |
-
- 96
- |
-
-
- |
- AKXD1636
- |
-
- 16
- |
-
- 112
- |
-
-
- |
- AKXD3688
- |
-
- 16
- |
-
- 80
- |
-
-
- |
- AKXD4152
- |
-
- 16
- |
-
- 91
- |
-
-
- |
- AKXD1647
- |
-
- 18
- |
-
- 91
- |
-
-
- |
- AKXD2616
- |
-
- 18
- |
-
- 91
- |
-
-
- |
- AKXD2804
- |
-
- 18
- |
-
- 80
- |
-
-
- |
- AKXD2456
- |
-
- 20
- |
-
- 100
- |
-
-
- |
- AKXD2554
- |
-
- 20
- |
-
- 107
- |
-
-
- |
- AKXD2829
- |
-
- 20
- |
-
- 105
- |
-
-
- |
- AKXD1610
- |
-
- 21
- |
-
- 98
- |
-
-
- |
- AKXD2611
- |
-
- 21
- |
-
- 88
- |
-
-
- |
- AKXD2918
- |
-
- 21
- |
-
- 98
- |
-
-
- |
- AKXD2460
- |
-
- 22
- |
-
- 107
- |
-
-
- |
- AKXD2461
- |
-
- 22
- |
-
- 94
- |
-
-
- |
- AKXD2463
- |
-
- 22
- |
-
- 110
- |
-
-
- |
- AKXD2975
- |
-
- 23
- |
-
- 82
- |
-
-
- |
- AKXD2976
- |
-
- 23
- |
-
- 86
- |
-
-
- |
- AKXD3955
- |
-
- 23
- |
-
- 90
- |
-
-
- |
- AKXD1494
- |
-
- 24
- |
-
- 103
- |
-
-
- |
- AKXD1880
- |
-
- 24
- |
-
- 104
- |
-
-
- |
- AKXD3030
- |
-
- 24
- |
-
- 89
- |
-
-
- |
- AKXD1607
- |
-
- 25
- |
-
- 110
- |
-
-
- |
- AKXD2326
- |
-
- 25
- |
-
- 92
- |
-
-
- |
- AKXD2328
- |
-
- 25
- |
-
- 90
- |
-
-
- |
- AKXD2629
- |
-
- 25
- |
-
- 96
- |
-
-
- |
- AKXD1756
- |
-
- 27
- |
-
- 100
- |
-
-
- |
- AKXD1757
- |
-
- 27
- |
-
- 98
- |
-
-
- |
- AKXD1948
- |
-
- 27
- |
-
- 99
- |
-
-
- |
- AKXD1950
- |
-
- 27
- |
-
- 97
- |
-
-
- |
- AKXD2968
- |
-
- 27
- |
-
- 94
- |
-
-
- |
- AKXD2809
- |
-
- 28
- |
-
- 88
- |
-
-
- |
- AKXD2815
- |
-
- 28
- |
-
- 90
- |
-
-
- |
- AKXD3432
- |
-
- 28
- |
-
- 91
- |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/MA_M_0704_R/processing.rtf b/general/datasets/MA_M_0704_R/processing.rtf
deleted file mode 100644
index 0d11078..0000000
--- a/general/datasets/MA_M_0704_R/processing.rtf
+++ /dev/null
@@ -1,15 +0,0 @@
-Probe (cell) level data from the .CEL file: These .CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
- - Step 1: We added an offset of 1.0 to the .CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z scores for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B GeneChips include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the two GeneChips to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-Probe set data from the .CHP file: The expression data were generated using MAS5. The same simple steps described above were also applied to these values. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 (mm5) assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.
diff --git a/general/datasets/MA_M_0704_R/summary.rtf b/general/datasets/MA_M_0704_R/summary.rtf
deleted file mode 100644
index 6423e7c..0000000
--- a/general/datasets/MA_M_0704_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Used the Affymetrix M430A and M430B pair of arrays (total of 45,137 probe sets). Data available as CEL files from GeneNetwork upon request.
diff --git a/general/datasets/MA_M_0704_R/tissue.rtf b/general/datasets/MA_M_0704_R/tissue.rtf
deleted file mode 100644
index 01385cb..0000000
--- a/general/datasets/MA_M_0704_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Mammary tumors used in this array experiment were derived from 18 sets of AKXD x FVB/N F1 females as described above. After the primary tumor was diagnosed, the animals were aged an additional 40 days to permit metastatic progression. Females were sacrificed and mammary tumors were harvested. Samples were processed and arrayed on Affymetrix M430A and M430B arrays. The majority of the samples were assayed on arrays obtained from the same lot number.
diff --git a/general/datasets/MDPPublish/summary.rtf b/general/datasets/MDPPublish/summary.rtf
deleted file mode 100644
index a5cb4f6..0000000
--- a/general/datasets/MDPPublish/summary.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-MDP: The great majority of data on the Mouse Diversity Panel is taken from the Phenome Project. Unlike the PHone Project, the MDP also includes limited data from the older literature.
-
-These data were downloaded from the Mouse Phenome Database at The Jackson Laboratory in June 2006 and implemented in GeneNetwork July 2006.
-
-The Mouse Phenome Database (MPD) and several other large data sets are being integrated into the GeneNetwork's Mouse Diversity Panel. To access these new data sets please select "MOUSE-GROUP-Mouse Diversity Panel". The Mouse Diversity Panel will eventually includes the MPD, additional strain data sets extracted from the published literature, the Wellcome Trust-CTC SNP collection, and several large gene expression data sets, including those for whole brain, hippocampus, cerebellum, and eye. (Implemented by Jintao Wang and Evan G. Williams.)
-
-
-
-
-
-Legend: Access to the new Mouse Diversity Panel data sets.
-
-
-
-
-
-Legend: Bar chart of white blood cell counts across 43 strains of mice taken from the Mouse Diversity Panel. Virutally all of the phenotype data are provided from the Mouse Phenome Project.
diff --git a/general/datasets/NCI_Agil_Mam_Tum_RMA_0409/summary.rtf b/general/datasets/NCI_Agil_Mam_Tum_RMA_0409/summary.rtf
deleted file mode 100644
index adb7c9d..0000000
--- a/general/datasets/NCI_Agil_Mam_Tum_RMA_0409/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 71, Name: NCI Mammary LMT miRNA v2 (Apr09) RMA
\ No newline at end of file
diff --git a/general/datasets/NCI_Mam_Tum_RMA_0409/summary.rtf b/general/datasets/NCI_Mam_Tum_RMA_0409/summary.rtf
deleted file mode 100644
index bc18abd..0000000
--- a/general/datasets/NCI_Mam_Tum_RMA_0409/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 72, Name: NCI Mammary M430v2 (Apr09) RMA
\ No newline at end of file
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/acknowledgment.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/acknowledgment.rtf
deleted file mode 100644
index 3a00fd4..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Mackay laboratory: http://mackay.gnets.ncsu.edu/MackaySite/Homepage.html
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/cases.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/cases.rtf
deleted file mode 100644
index 333a904..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-The raw microarray data are deposited in the ArrayExpress database (www.ebi.ac.uk/arrayexpress,) under accession number E-MEXP-1594
-
-We have derived a population of 192 inbred lines by 20 generations of full sib inbreeding of isofemale lines collected from the Raleigh, NC population. A White Paper to obtain complete genome sequences of these lines (link to pdf of White Paper) has been approved by the National Institutes of Health National Human Genome Research Institute, using a combination of 454 XLR long read pyrosequencing and paired end Solexa short read (currently 45 bp) technology. The sequencing is being done at the Baylor College of Medicine Sequencing Center, in collaboration with Richard Gibbs and Stephen Richards.
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/experiment-design.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/experiment-design.rtf
deleted file mode 100644
index 387a16a..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-We derived inbred lines from the Raleigh, USA population by 20 generations of full-sib mating. We used the C(2L)RM-P1, b1; C(2R)RM-SKIA, cn1bw1 compound autosome (CA) stock for fitness assays. P-element mutations and co-isogenic control lines were a gift of H. Bellen (Howard Hughes Medical Institute, Baylor College of Medicine). We reared flies on cornmeal-molasses-agar medium at 25 °C, 60–75% relative humidity and a 12-h light-dark cycle unless otherwise specified.
-
-Organismal phenotypes.
-
-For the starvation stress resistance group, we placed ten same-sex, 2-d-old flies in vials containing 1.5% agar and 5 ml water, and scored survival every eight hours (N = 5 vials/sex/line). For the chill coma recovery group, we placed 3- to 7-d-old flies in empty vials on ice for three hours, and recorded the time for each individual to right itself after transfer to room temperature (N = 20 flies/sex/line). For longevity, we placed five 1- to 2-d-old same-sex virgin flies into vials containing 5 ml medium, and recorded survival every two days (N = 5 vials/sex/line). For locomotor reactivity, we placed single 3- to 7-d-old flies into vials containing 5 ml medium. The following day, between 8 am and 12 pm, we mechanically disturbed each fly19, and recorded the total activity in the 45 s immediately following the disturbance. We obtained two replicate measurements of 20 flies/sex/replicate/line. For the copulation latency group, we aspirated pairs of 3- to 7-d-old virgin flies into vials containing 5 ml medium between 8 am and 12 pm, and recorded the number of minutes until initiation of copulation, for a maximum of 120 min (N = 24 pairs/line). For the reproductive fitness group, we used the competitive index technique45, 46. We reared all wild-type and CA parents in constant density (10 pairs) vials. We placed six 3- to 4-d-old virgin CA males and females and three 3- to 4-d-old wild-type males and females in a vial containing 10 ml medium, discarding the flies after 7 d. The competitive index was the ratio of the number of wild type to the total number of progeny emerging by day 17 (N = 20 replicate vials/line).
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/notes.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/notes.rtf
deleted file mode 100644
index 790f36a..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Please see Mackay lab link: http://mackay.gnets.ncsu.edu/MackaySite/DGRP_files/The40ExpressionDataMatrix10096.txt
-
-ArrayExpress: accession number E-MEXP-1594
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/platform.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/platform.rtf
deleted file mode 100644
index 74f3b36..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-We used Affymetrix Drosophila 2.0 arrays to assess transcript profiles of 3- to 5-d-old flies from the inbred lines. All samples were frozen between 1 and 3 pm. We extracted RNA from two independent pools (25 flies/sex/line), and hybridized 10 g fragmented cRNA to each array. We randomized RNA extraction, labeling and array hybridization across all samples, and normalized the raw array data across sexes and lines using a median standardization.
-
-Each transcript is represented by 14 perfect-match 25-bp oligonucleotides. To identify perfect-match probes with SFPs between the wild-derived lines and the strain used to design the array, we quantified the maximal degree to which the variation between lines could be reduced by partitioning the lines into two allelic classes. We computed the sum of squared deviations from each class mean and expressed their sum as a fraction of the total sum of squares. The smallest fraction across all bipartitions was used to score each probe. We identified 3,136 candidate SFPs with scores 0.1 (a tenfold reduction in the sum of squares). We validated polymorphisms in 20 of 21 of these SFPs by designing primers flanking the SFP and sequencing the PCR products (data not shown).
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/processing.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/processing.rtf
deleted file mode 100644
index 33266b5..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Our measure of expression for each probe set was the median log2 signal intensity of perfect-match probes without SFPs. We used negative control probes to estimate the background intensity, and removed probes below this threshold.
-
-Data may have been normalized prior to entry into GeneNetwork using 2z + 8 transform. This method simply stabilizes the variance of all array data sets, and resets the z score to 8 (rather than 0).
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/summary.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/summary.rtf
deleted file mode 100644
index 68b99df..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/summary.rtf
+++ /dev/null
@@ -1,2 +0,0 @@
-Determining the genetic architecture of complex traits is challenging because phenotypic variation arises from interactions between multiple, environmentally sensitive alleles. We quantified genomewide transcript abundance and phenotypes for six ecologically relevant traits in D. melanogaster wild-derived inbred lines. We observed 10,096 genetically variable transcripts and high heritabilities for all organismal phenotypes. The transcriptome is highly genetically inter-correlated, forming 241 transcriptional modules. Modules are enriched for transcripts in common pathways, gene ontology categories, tissue-specific expression, and transcription factor binding sites. The high transcriptional connectivity allows us to infer genetic networks and the function of predicted genes based on annotations of other genes in the network. Regressions of organismal phenotypes on transcript abundance implicate several hundred candidate genes that form modules of biologically meaningful correlated transcripts affecting each phenotype. Overlapping transcripts in modules associated with different traits provides insight into the molecular basis of pleiotropy between complex traits.
-Full Article
diff --git a/general/datasets/NCSU_DrosWB_LC_RMA_0111/tissue.rtf b/general/datasets/NCSU_DrosWB_LC_RMA_0111/tissue.rtf
deleted file mode 100644
index 0ba4e81..0000000
--- a/general/datasets/NCSU_DrosWB_LC_RMA_0111/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Whole body. 3- to 5-d-old flies from the inbred lines. All samples were frozen between 1 and 3 pm. We extracted RNA from two independent pools (25 flies/sex/line)We derived inbred lines from the Raleigh, USA population by 20 generations of full-sib mating. We used the C(2L)RM-P1, b1; C(2R)RM-SKIA, cn1bw1 compound autosome (CA) stock for fitness assays. P-element mutations and co-isogenic control lines were a gift of H. Bellen (Howard Hughes Medical Institute, Baylor College of Medicine). We reared flies on cornmeal-molasses-agar medium at 25 °C, 60–75% relative humidity and a 12-h light-dark cycle unless otherwise specified.
diff --git a/general/datasets/Nci_mam_tum_rma_0409/experiment-type.rtf b/general/datasets/Nci_mam_tum_rma_0409/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Nci_mam_tum_rma_0409/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/OHSU_HS-CC_ILMStr_0211/summary.rtf b/general/datasets/OHSU_HS-CC_ILMStr_0211/summary.rtf
deleted file mode 100644
index e096b10..0000000
--- a/general/datasets/OHSU_HS-CC_ILMStr_0211/summary.rtf
+++ /dev/null
@@ -1,2 +0,0 @@
-The current study focused on the extent genetic diversity within a species (Mus musculus) affects gene co-expression network structure. To examine this issue, we have created a new mouse resource, a heterogeneous stock (HS) formed from the same eight inbred strains that have been used to create the collaborative cross (CC). The eight inbred strains capture > 90% of the genetic diversity available within the species. For contrast with the HS-CC, a C57BL/6J (B6) × DBA/2J (D2) F2 intercross and the HS4, derived from crossing the B6, D2, BALB/cJ and LP/J strains, were used. Brain (striatum) gene expression data were obtained using the Illumina Mouse WG 6.1 array, and the data sets were interrogated using a weighted gene co-expression network analysis (WGCNA).
-Read full article: Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse.
diff --git a/general/datasets/ONCRetILM6_0412/acknowledgment.rtf b/general/datasets/ONCRetILM6_0412/acknowledgment.rtf
deleted file mode 100644
index a41ff76..0000000
--- a/general/datasets/ONCRetILM6_0412/acknowledgment.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-The HEI Retinal Database is supported by National Eye Institute Grants:
-
-
-
-
- - R01EY017841 (Dr. Eldon E. Geisert, PI)
-
-
- - P030EY13080 (NEI Vision Core Grant), and
-
-
- - A Unrestricted Grand from Research to Prevent Blindness (Dr. Barrett Haik, PI)
-
diff --git a/general/datasets/ONCRetILM6_0412/cases.rtf b/general/datasets/ONCRetILM6_0412/cases.rtf
deleted file mode 100644
index b37d700..0000000
--- a/general/datasets/ONCRetILM6_0412/cases.rtf
+++ /dev/null
@@ -1,14 +0,0 @@
-
-Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 48 and maximum age is 118 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J.
-
-BXD strains:
-
-
- - The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s.
- - In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset.
- - The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set.
-
-
-
-
-What Makes the G2 HEI Retina Database different from the HEI Retina Database Examination of Gfap expression across all of the strains in the HEI Retinal Dataset, reveals that some strains express very high levels of Gfap relative to others. For example, BXD24 expresses Gfap at a 9-fold higher level, than BXD22. It has been established that BXD24 acquired a mutation in Cep290 that results in early onset photoreceptor degeneration (Chang et al., 2006). This degeneration results in reactive gliosis throughout the retina. In addition to BXD24, other BXD strains expressed very high levels of Gfap including: BXD32, BXD49, BXD70, BXD83 and BXD89. For the G2 dataset all of these strains with potential reactive gliosis were removed from the dataset.
diff --git a/general/datasets/ONCRetILM6_0412/experiment-design.rtf b/general/datasets/ONCRetILM6_0412/experiment-design.rtf
deleted file mode 100644
index 4fff707..0000000
--- a/general/datasets/ONCRetILM6_0412/experiment-design.rtf
+++ /dev/null
@@ -1,12 +0,0 @@
-Expression profiling by array
-
-We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.
-
-All normalization was performed by William E. Orr in the HEI Vision Core Facility
-
-
- - Computed the log base 2 of each raw signal value
- - Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
- - Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
-
diff --git a/general/datasets/ONCRetILM6_0412/notes.rtf b/general/datasets/ONCRetILM6_0412/notes.rtf
deleted file mode 100644
index 13ff99a..0000000
--- a/general/datasets/ONCRetILM6_0412/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This data set is available as a bulk download in several formats. The data are available as either strain means or the individual arrays. Due to the involved normalization procedures required to correct for batch effects we strongly recommend not using the raw CEL files without special statistical procedures.
diff --git a/general/datasets/ONCRetILM6_0412/platform.rtf b/general/datasets/ONCRetILM6_0412/platform.rtf
deleted file mode 100644
index 2c52707..0000000
--- a/general/datasets/ONCRetILM6_0412/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina MouseWG-6 v2.0 arrays: The Illumina Sentrix Mouse-6 BeadChip uses 50-nucleotide probes to interrogate approximately 46,000 sequences from the mouse transcriptome. For each array, the RNA was pooled from two retinas.
diff --git a/general/datasets/ONCRetILM6_0412/processing.rtf b/general/datasets/ONCRetILM6_0412/processing.rtf
deleted file mode 100644
index 97cc2be..0000000
--- a/general/datasets/ONCRetILM6_0412/processing.rtf
+++ /dev/null
@@ -1,2654 +0,0 @@
-Values of all 45,281 probe sets in this data set range from a low of 6.25 (Rho GTPase activating protein 11A, Arhgap11a, probe ID ILMN_2747167) to a high of 18.08 (Ubiquitin B, Ubb, probe ID ILMN_2516699). This corresponds to 11.83 units or a 1 to 3641 dynamic range of expression (2^11.83). We normalized raw signal values using Beadstudio’s rank invariant normalization algorithm. BXD62 was the strain used as the control group
-
-
-
-Sample Processing: Drs. Natalie E. Freeman-Anderson and Justin P. Templeton extracted the retinas from the mice and Dr. Natalie Freeman-Anderson processed all samples in the HEI Vision Core Facility. The tissue was homogenized and extracted according to the RNA-Stat-60 protocol as described by the manufacturer (Tel-Test, Friendswood, TX) listed above. The quality and purity of RNA was assessed using an Agilent Bioanalyzer 2100 system. The RNA from each sample was processed with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) to produce labeled cRNA. The cRNA for each sample was then hybridized to an Illumina Sentrix® Mouse-6-V2 BeadChip (Illumina, San Diego, CA)
-
-
-
-
-
-Quality control analysis of the raw image data was performed using the Illumina BeadStudio software. MIAME standards were used for all microarray data. Rank invariant normalization with BeadStudio software was used to calculate the data. Once this data was collected, the data was globally normalized across all samples using the formula 2 (z-score of log2 [intensity]) + 8.
-
-Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.
-
-Table 1: HEI Retina case IDs, including sample tube ID, strain, age, sex, and source of mice
-
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain |
- Age |
- Sex |
- Source of Animal |
-
-
- | 1 |
- 121608_11-C57BL/6JcFA |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 2 |
- 121608_12-C57BL/6JcFB |
- C57BL/6J |
- 69 |
- F |
- JAX |
-
-
- | 3 |
- KA7444-C57BL/6JcMC |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 4 |
- KA7444-C57BL/6JcMD |
- C57BL/6J |
- 97 |
- M |
- UTHSC RW |
-
-
- | 5 |
- 31209.05-DBA2JcFA |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 6 |
- 31209.05-DBA2JcFB |
- DBA2J |
- 75 |
- F |
- UTHSC RW |
-
-
- | 7 |
- 121608_13-DBA/2JcMA |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 8 |
- 121608_14-DBA/2JcMB |
- DBA/2J |
- 89 |
- M |
- UTHSC RW |
-
-
- | 9 |
- KA7446-B6D2F1cFA |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 10 |
- KA7446-B6D2F1cFB |
- B6D2F1 |
- 92 |
- F |
- UTHSC RW |
-
-
- | 11 |
- KA7446-B6D2F1cMC |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 12 |
- KA7446-B6D2F1cMD |
- B6D2F1 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 13 |
- KA7466-D2B6F1cFA |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 14 |
- KA7466-D2B6F1cFB |
- D2B6F1 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 15 |
- KA7466-D2B6F1cMC |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 16 |
- KA7466-D2B6F1cMD |
- D2B6F1 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 17 |
- 82609.13-1cFA |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 18 |
- 82609.14-1cFB |
- BXD01 |
- 62 |
- F |
- JAX |
-
-
- | 19 |
- KA7389-1cFA |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 20 |
- KA7389-1cFB |
- BXD01 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 21 |
- KA7389-1cMC |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 22 |
- KA7389-1cMD |
- BXD01 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 23 |
- KA7300-2cFA |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 24 |
- KA7300-2cFB |
- BXD02 |
- 75 |
- F |
- UTHSC RW |
-
-
- | 25 |
- 100909.01-2cMA |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 26 |
- 100909.02-2cMB |
- BXD02 |
- 65 |
- M |
- JAX |
-
-
- | 27 |
- KA6699-5cFA |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 28 |
- KA6699-5cFB |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 29 |
- KA6699-5cFC |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 30 |
- KA6699-5cFD |
- BXD05 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 31 |
- 82609.09-5cMA |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 32 |
- 82609.1-5cMB |
- BXD05 |
- 60 |
- M |
- JAX |
-
-
- | 33 |
- KA6763-6cFA |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 34 |
- KA6763-6cFB |
- BXD06 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 35 |
- 81209.06-6cMA |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 36 |
- 81209.07-6cMB |
- BXD06 |
- 69 |
- M |
- VAMC |
-
-
- | 37 |
- 82609.07-8cFA |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 38 |
- 82609.08-8cFB |
- BXD08 |
- 68 |
- F |
- JAX |
-
-
- | 39 |
- JAX-8cMA |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 40 |
- JAX-8cMB |
- BXD08 |
- 76 |
- M |
- JAX |
-
-
- | 41 |
- KA7289-9cFA |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 42 |
- KA7289-9cFB |
- BXD09 |
- 87 |
- F |
- UTHSC RW |
-
-
- | 43 |
- KA7289-9cMC |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 44 |
- KA7289-9cMD |
- BXD09 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 45 |
- JAX-11cFA |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 46 |
- JAX-11cFB |
- BXD11 |
- 84 |
- F |
- JAX |
-
-
- | 47 |
- JAX-11cMC |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 48 |
- JAX-11cMD |
- BXD11 |
- 71 |
- M |
- JAX |
-
-
- | 49 |
- 40209.07-12cFA |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 50 |
- 40209.08-12cFB |
- BXD12 |
- 65 |
- F |
- VAMC |
-
-
- | 51 |
- 011309.01-12cMA |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 52 |
- 011309.02-12cMB |
- BXD12 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 53 |
- KA7286-13cFA |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 54 |
- KA7286-13cFB |
- BXD13 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 55 |
- KA7286-13cMC |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 56 |
- KA7286-13cMD |
- BXD13 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 57 |
- KA7302-14cFA |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 58 |
- KA7302-14cFB |
- BXD14 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 59 |
- 100909.05-14cMA |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 60 |
- 100909.06-14cMB |
- BXD14 |
- 66 |
- M |
- JAX |
-
-
- | 61 |
- KA7288-15cFA |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 62 |
- KA7288-15cFB |
- BXD15 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 63 |
- KA7288-15cMC |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 64 |
- KA7288-15cMD |
- BXD15 |
- 89 |
- M |
- UTHSC RW |
-
-
- | 65 |
- 062509.01-16cFA |
- BXD16 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 66 |
- KA7267-16cMA |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 67 |
- KA7267-16cMB |
- BXD16 |
- 91 |
- M |
- UTHSC RW |
-
-
- | 68 |
- KA6686-18cFB |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 69 |
- KA6686-18cFC |
- BXD18 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 70 |
- KA6686-18cME |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 71 |
- KA6686-18cMF |
- BXD18 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 72 |
- KA6676-19cFB |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 73 |
- KA6676-19cFC |
- BXD19 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 74 |
- KA6676-19cME |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 75 |
- KA6676-19cMF |
- BXD19 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 76 |
- 060409.05-20cFA |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 77 |
- 060409.06-20cFB |
- BXD20 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 78 |
- 021909.03-20cMA |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 79 |
- 021909.04-20cMB |
- BXD20 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 80 |
- 82609.02-21cFC |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 81 |
- 82609.03-21cFD |
- BXD21 |
- 65 |
- F |
- JAX |
-
-
- | 82 |
- 121709.01-21cMA |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 83 |
- 121709.02-21cMB |
- BXD21 |
- 80 |
- M |
- JAX |
-
-
- | 84 |
- 121709.03-22cFA |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 85 |
- 121709.04-22cFB |
- BXD22 |
- 62 |
- F |
- JAX |
-
-
- | 86 |
- 092308_03-22cMA |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 87 |
- 092308_04-22cMB |
- BXD22 |
- 118 |
- M |
- UTHSC RW |
-
-
- | 88 |
- 80409.01-24AcFA |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 89 |
- 080409_02_24AcFB |
- BXD24A |
- 72 |
- F |
- UTHSC RW |
-
-
- | 90 |
- 82609.26-24AcFC |
- BXD24A |
- 64 |
- F |
- UTHSC RW |
-
-
- | 91 |
- 81209.03-24AcMC |
- BXD24A |
- 62 |
- M |
- UTHSC RW |
-
-
- | 92 |
- KA6678-24cFA |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 93 |
- KA6678-24cFB |
- BXD24 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 94 |
- KA6678-24cME |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 95 |
- KA6678-24cMF |
- BXD24 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 96 |
- 060409.07-27cFA |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 97 |
- 060409.08-27cFB |
- BXD27 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 98 |
- 80409.03-27cMA |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 99 |
- 80409.04-27cMB |
- BXD27 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 100 |
- JAX-28cFA |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 101 |
- JAX-28cFB |
- BXD28 |
- 67 |
- F |
- JAX |
-
-
- | 102 |
- JAX-28cMC |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 103 |
- JAX-28cMD |
- BXD28 |
- 67 |
- M |
- JAX |
-
-
- | 104 |
- 82609.11-29cFA |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 105 |
- 82609.12-29cFB |
- BXD29 |
- 66 |
- F |
- JAX |
-
-
- | 106 |
- 82609.04-29cMA |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 107 |
- 82609.05-29cMB |
- BXD29 |
- 66 |
- M |
- JAX |
-
-
- | 108 |
- JAX-31cMB |
- BXD 31 |
- 56 |
- M |
- JAX |
-
-
- | 109 |
- JAX-31cFC |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 110 |
- JAX-31cFD |
- BXD 31 |
- 69 |
- F |
- JAX |
-
-
- | 111 |
- 011309.03-32cFA |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 112 |
- 011309.04-32cFB |
- BXD32 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 113 |
- KA7318-32cFC |
- BXD32 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 114 |
- KA7319-32cMA |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 115 |
- KA7319-32cMB |
- BXD32 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 116 |
- 100909.07-33cFA |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 117 |
- 100909.08-33cFB |
- BXD33 |
- 65 |
- F |
- JAX |
-
-
- | 118 |
- 022609.01-33cMA |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 119 |
- 022609.02-33cMB |
- BXD33 |
- 92 |
- M |
- UTHSC RW |
-
-
- | 120 |
- KA7416-34cFA |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 121 |
- KA7416-34cFB |
- BXD34 |
- 97 |
- F |
- UTHSC RW |
-
-
- | 122 |
- KA6321-34cMA |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 123 |
- KA6321-34cMB |
- BXD34 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 124 |
- 060409.01-36cFA |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 125 |
- 060409.02-36cFB |
- BXD36 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 126 |
- 060409.03-36cMC |
- BXD36 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 127 |
- KA6702-38cFA |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 128 |
- KA6702-38cFB |
- BXD38 |
- 63 |
- F |
- UTHSC RW |
-
-
- | 129 |
- 82609.24-38cFA |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 130 |
- 82609.25-38cFB |
- BXD38 |
- 85 |
- F |
- UTHSC RW |
-
-
- | 131 |
- 100909.03-38cMA |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 132 |
- 100909.04-38cMB |
- BXD38 |
- 61 |
- M |
- JAX |
-
-
- | 133 |
- 022609.05-39cFA |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 134 |
- 022609.06-39cFB |
- BXD39 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 135 |
- 31209.01-39cMC |
- BXD39 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 136 |
- 92409.01-40cFA |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 137 |
- 92409.02-40cFB |
- BXD40 |
- 64 |
- F |
- UTHSC RW |
-
-
- | 138 |
- KA6173-40cMA |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 139 |
- KA6173-40cMB |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 140 |
- KA6173-40cMC |
- BXD40 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 141 |
- 091809.01-42cFA |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 142 |
- 091809.02-42cFB |
- BXD42 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 143 |
- 021909.01-42cFA |
- BXD42 |
- 89 |
- F |
- UTHSC RW |
-
-
- | 144 |
- 011309.06-42cMA |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 145 |
- 011309.07-42cMB |
- BXD42 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 146 |
- 110408_02-43cFA |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 147 |
- 110408_03-43cFB |
- BXD43 |
- 61 |
- F |
- UTHSC RW |
-
-
- | 148 |
- KA6158-43cMA |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 149 |
- KA6158-43cMB |
- BXD43 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 150 |
- 100308_01-44cFA |
- BXD44 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 151 |
- 102208_02-44cMD |
- BXD44 |
- 64 |
- M |
- UTHSC RW |
-
-
- | 152 |
- 103009.03-45cFA |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 153 |
- 103009.04-45cFB |
- BXD45 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 154 |
- 022609.03-45cFA |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 155 |
- 022609.04-45cFB |
- BXD45 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 156 |
- 40309.05-45cMB |
- BXD45 |
- 65 |
- M |
- UTHSC RW |
-
-
- | 157 |
- 40209.05-48cFB |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 158 |
- 40209.06-48cFC |
- BXD48 |
- 58 |
- F |
- VAMC |
-
-
- | 159 |
- 81209.04-48cMA |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 160 |
- 81209.05-48cMB |
- BXD48 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 161 |
- 81209.08-49cFA |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 162 |
- 81209.09-49cFB |
- BXD49 |
- 70 |
- F |
- VAMC |
-
-
- | 163 |
- 40209.01-49cMA |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 164 |
- 40209.02-49cMB |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 165 |
- 40209.03-49cMC |
- BXD49 |
- 87 |
- M |
- VAMC |
-
-
- | 166 |
- KA737850cFA |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 167 |
- KA737850cFB |
- BXD50 |
- 50 |
- F |
- UTHSC RW |
-
-
- | 168 |
- 121908_01-50cMA |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 169 |
- 121908_02-50cMB |
- BXD50 |
- 49 |
- M |
- UTHSC RW |
-
-
- | 170 |
- 111208_01-51cFA |
- BXD51 |
- 99 |
- F |
- UTHSC RW |
-
-
- | 171 |
- 102208_03-51cMA |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 172 |
- 102208_04-51cMB |
- BXD51 |
- 56 |
- M |
- UTHSC RW |
-
-
- | 173 |
- 090208_14-53BcFA |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 174 |
- 090208_15-53BcFB |
- BXD53B |
- 93 |
- F |
- UTHSC RW |
-
-
- | 175 |
- 090208_16-53BcMC |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 176 |
- 090208_17-53BcMD |
- BXD53B |
- 93 |
- M |
- UTHSC RW |
-
-
- | 177 |
- 111208_05-55cFB |
- BXD55 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 178 |
- KA6183-55cMA |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 179 |
- KA6183-55cMB |
- BXD55 |
- 63 |
- M |
- UTHSC RW |
-
-
- | 180 |
- KA7362-56cFB |
- BXD 56 |
- 54 |
- F |
- UTHSC RW |
-
-
- | 181 |
- KA6088-56cMA |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 182 |
- KA6088-56cMB |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 183 |
- KA6088-56cMC |
- BXD56 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 184 |
- 21810.01-60RFA |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 185 |
- 21810.02-60RFB |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 186 |
- 21810.02-60RFC |
- BXD 60 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 187 |
- SQ7325-60cMA |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 188 |
- SQ7325-60cMB |
- BXD60 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 189 |
- 092308_10-61cFA |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 190 |
- 092308_11-61cFB |
- BXD61 |
- 110 |
- F |
- UTHSC RW |
-
-
- | 191 |
- 31909.01-61cMA |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 192 |
- 31909.02-61cMB |
- BXD61 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 193 |
- KA7462-62cFA |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 194 |
- KA7462-62cFB |
- BXD62 |
- 76 |
- F |
- UTHSC RW |
-
-
- | 195 |
- KA5996-62cMA |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 196 |
- KA5996-62cMB |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 197 |
- KA5996-62cMC |
- BXD62 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 198 |
- 090309.01-63cFA |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 199 |
- 090309.02-63cFB |
- BXD63 |
- 69 |
- F |
- UTHSC RW |
-
-
- | 200 |
- 110609.01-63cMA |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 201 |
- 110609.02-63cMB |
- BXD63 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 202 |
- 091809.03-65cFA |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 203 |
- 091809.04-65cFB |
- BXD65 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 204 |
- 103009.01-65cMA |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 205 |
- 103009.02-65cMB |
- BXD65 |
- 74 |
- M |
- UTHSC RW |
-
-
- | 206 |
- 110408_05-66cFB |
- BXD66 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 207 |
- KA7165-66cMA |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 208 |
- KA7165-66cMB |
- BXD66 |
- 95 |
- M |
- UTHSC RW |
-
-
- | 209 |
- 90809.01-67cMA |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 210 |
- 90809.02-67cMB |
- BXD67 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 211 |
- 110609.03-67cFA |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 212 |
- 110609.04-67cFB |
- BXD67 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 213 |
- 120408_01-68cFA |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 214 |
- 120408_02-68cFB |
- BXD68 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 215 |
- SQ7205-68cMA |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 216 |
- SQ7205-68cMB |
- BXD68 |
- 87 |
- M |
- UTHSC RW |
-
-
- | 217 |
- KA6316-68cMA |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 218 |
- KA6316-68cMB |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 219 |
- KA6316-68cMC |
- BXD68 |
- 76 |
- M |
- UTHSC RW |
-
-
- | 220 |
- KA76-69cFA |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 221 |
- KA76-69cFB |
- BXD69 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 222 |
- KA6074-69cMA |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 223 |
- KA6074-69cMB |
- BXD69 |
- 90 |
- M |
- UTHSC RW |
-
-
- | 224 |
- 121608_01-70cFA |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 225 |
- 121608_02-70cFB |
- BXD70 |
- 80 |
- F |
- UTHSC RW |
-
-
- | 226 |
- KA7394-70cMA |
- BXD70 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 227 |
- 81209.08-70cMA |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 228 |
- 81209.09-70cMB |
- BXD70 |
- 71 |
- M |
- VAMC |
-
-
- | 229 |
- 052809.01-71cFA |
- BXD71 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 230 |
- 060409.09-71cMA |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 231 |
- 060409.10-71cMB |
- BXD71 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 232 |
- 40809.01-73cFA |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 233 |
- 40809.02-73cFB |
- BXD73 |
- 83 |
- F |
- UTHSC RW |
-
-
- | 234 |
- 111708_01-73cFA |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 235 |
- 111708_01-73cFB |
- BXD73 |
- 55 |
- F |
- UTHSC RW |
-
-
- | 236 |
- KA6164-73cMB |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 237 |
- KA6164-73cMC |
- BXD73 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 238 |
- 82609.22-74cFA |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 239 |
- 82609.23-74cFB |
- BXD74 |
- 68 |
- F |
- VAMC |
-
-
- | 240 |
- 82609.20-74cMA |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 241 |
- 82609.21-74cMB |
- BXD74 |
- 68 |
- M |
- VAMC |
-
-
- | 242 |
- KA733675cFA |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 243 |
- KA733675cFB |
- BXD75 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 244 |
- KA38-75cMB |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 245 |
- KA38-75cMC |
- BXD75 |
- 62 |
- M |
- UTHSC RW |
-
-
- | 246 |
- 41509.01-77cFA |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 247 |
- 41509.02-77cFB |
- BXD77 |
- 70 |
- F |
- UTHSC RW |
-
-
- | 248 |
- 41509.03-77cMC |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 249 |
- 41509.04-77cMD |
- BXD77 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 250 |
- 121608_03-80cFA |
- BXD80 |
- 77 |
- F |
- UTHSC RW |
-
-
- | 251 |
- 121608_05-80cMC |
- BXD80 |
- 70 |
- M |
- UTHSC RW |
-
-
- | 252 |
- KA23-80cMC |
- BXD80 |
- 77 |
- M |
- UTHSC RW |
-
-
- | 253 |
- KA7305-81cFA |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 254 |
- KA7305-81cFB |
- BXD81 |
- 51 |
- F |
- UTHSC RW |
-
-
- | 255 |
- KA7305-81cMD |
- BXD81 |
- 51 |
- M |
- UTHSC RW |
-
-
- | 256 |
- 060409.11-83cFA |
- BXD83 |
- 65 |
- F |
- UTHSC RW |
-
-
- | 257 |
- KA24-83cFA |
- BXD83 |
- 78 |
- F |
- UTHSC RW |
-
-
- | 258 |
- 121608_07-83cMA |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 259 |
- 121608_08-83cMB |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 260 |
- KA24-83cMD |
- BXD83 |
- 78 |
- M |
- UTHSC RW |
-
-
- | 261 |
- 090409.05-84cFA |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 262 |
- 090409.06-84cFB |
- BXD84 |
- 65 |
- F |
- VAMC |
-
-
- | 263 |
- KA6203-84cMA |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 264 |
- KA6203-84cMB |
- BXD84 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 265 |
- 40309.02-85cFD |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 266 |
- 40309.03-85cFE |
- BXD85 |
- 58 |
- F |
- UTHSC RW |
-
-
- | 267 |
- 32609.01-85cMA |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 268 |
- 32609.02-85cMB |
- BXD85 |
- 67 |
- M |
- UTHSC RW |
-
-
- | 269 |
- 41509.05-86cFA |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 270 |
- 41509.06-86cFB |
- BXD86 |
- 73 |
- F |
- UTHSC RW |
-
-
- | 271 |
- KA6101-86cMA |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 272 |
- KA6101-86cMC |
- BXD86 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 273 |
- 070909.02-87cFA |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 274 |
- 070909.03-87cFB |
- BXD87 |
- 86 |
- F |
- UTHSC RW |
-
-
- | 275 |
- KA7407-87cMA |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 276 |
- KA7407-87cMB |
- BXD87 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 277 |
- 102208_05-89cFA |
- BXD89 |
- 82 |
- F |
- UTHSC RW |
-
-
- | 278 |
- KA5974-89cMA |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 279 |
- KA5974-89cMB |
- BXD89 |
- 113 |
- M |
- UTHSC RW |
-
-
- | 280 |
- 102208_06-89cMC |
- BXD89 |
- 82 |
- M |
- UTHSC RW |
-
-
- | 281 |
- 72309.01-90cFA |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 282 |
- 72309.02-90cFB |
- BXD90 |
- 67 |
- F |
- UTHSC RW |
-
-
- | 283 |
- 090409.03-90cMA |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 284 |
- 090409.04-90cMB |
- BXD90 |
- 64 |
- M |
- VAMC |
-
-
- | 285 |
- KA6094-92cMA |
- BXD92 |
- 85 |
- M |
- UTHSC RW |
-
-
- | 286 |
- 020609.01-95cFA |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 287 |
- 020609.02-95cFB |
- BXD95 |
- 71 |
- F |
- UTHSC RW |
-
-
- | 288 |
- KA6181-95cMA |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 289 |
- KA6181-95cMB |
- BXD95 |
- 61 |
- M |
- UTHSC RW |
-
-
- | 290 |
- 31209.03-96cFA |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 291 |
- 31209.04-96cFB |
- BXD96 |
- 62 |
- F |
- UTHSC RW |
-
-
- | 292 |
- KA7246-96cMA |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 293 |
- KA7246-96cMB |
- BXD96 |
- 73 |
- M |
- UTHSC RW |
-
-
- | 294 |
- 81209.10-97cFA |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 295 |
- 81209.11-97cFB |
- BXD97 |
- 83 |
- F |
- VAMC |
-
-
- | 296 |
- 81209.1-97cMA |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 297 |
- 81209.11-97cMB |
- BXD97 |
- 83 |
- M |
- VAMC |
-
-
- | 298 |
- SQ7520-98cFA |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 299 |
- SQ7520-98cFB |
- BXD98 |
- 59 |
- F |
- UTHSC RW |
-
-
- | 300 |
- SQ7520-98cMC |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 301 |
- SQ7520-98cMD |
- BXD98 |
- 59 |
- M |
- UTHSC RW |
-
-
- | 302 |
- 82609.17-99cFA |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 303 |
- 82609.18-99cFB |
- BXD99 |
- 64 |
- F |
- VAMC |
-
-
- | 304 |
- 81409.01-99cMA |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 305 |
- 81409.02-99cMB |
- BXD99 |
- 66 |
- M |
- UTHSC RW |
-
-
- | 306 |
- 121608_09-100cFA |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 307 |
- 121608_10-100cFB |
- BXD100 |
- 81 |
- F |
- UTHSC RW |
-
-
- | 308 |
- KA6001-100cMA |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 309 |
- KA6001-100cMB |
- BXD100 |
- 111 |
- M |
- UTHSC RW |
-
-
- | 310 |
- 81209.12-101cFA |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 311 |
- 81209.13-101cFB |
- BXD101 |
- 72 |
- F |
- VAMC |
-
-
- | 312 |
- KA7296-101cMA |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 313 |
- KA7296-101cMB |
- BXD101 |
- 75 |
- M |
- UTHSC RW |
-
-
- | 314 |
- 92409.03-102cFA |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 315 |
- 92409.04-102cFB |
- BXD102 |
- 71 |
- F |
- VAMC |
-
-
- | 316 |
- KA7380-102cMA |
- BXD102 |
- 115 |
- M |
- UTHSC RW |
-
-
- | 317 |
- 43009.01-103cFA |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 318 |
- 43009.02-103cFB |
- BXD103 |
- 68 |
- F |
- UTHSC RW |
-
-
- | 319 |
- KA79-103cFA |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 320 |
- KA79-103cFB |
- BXD103 |
- 48 |
- F |
- UTHSC RW |
-
-
- | 321 |
- KA79-103cMC |
- BXD103 |
- 48 |
- M |
- UTHSC RW |
-
-
- | 322 |
- 82609.15-103cMA |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 323 |
- 82609.16-103cMB |
- BXD103 |
- 69 |
- M |
- VAMC |
-
-
- | 324 |
- 102909.01-BALBCcFA |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 325 |
- 102909.02-BALBCcFB |
- BALB/cByJ |
- 78 |
- F |
- JAX |
-
-
- | 326 |
- 102909.03-BALBCcMA |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
- | 327 |
- 102909.04-BALBCcMB |
- BALB/cByJ |
- 78 |
- M |
- JAX |
-
-
-
- |
-
-
-
diff --git a/general/datasets/ONCRetILM6_0412/summary.rtf b/general/datasets/ONCRetILM6_0412/summary.rtf
deleted file mode 100644
index 44e98a7..0000000
--- a/general/datasets/ONCRetILM6_0412/summary.rtf
+++ /dev/null
@@ -1,50 +0,0 @@
-
-This is a subtractive dataset. The Normal retina dataset was subtracted from the ONC data set probe by probe to create a data set of the changes occurring following ONC. This data set can be used to define gene changes following ONC. It is not compatible with most of the bioinformatic tools available on GeneNetwork.
-
-HEI Retina Illumina V6.2 (April 2010) RankInv was normalized and scaled by William E. Orr and uploaded by Arthur Centeno and Xiaodong Zhou on April 7, 2010. This data set consists of either 69 BXD strains (Normal data set) or 75 BXD strains (Full data set), C57BL/6J, DBA/2J, both reciprocal F1s, and BALB/cByJ. A total of either 74 strains (Normal data set) or 80 strains (Full data set) were quantified.
-
-COMMENT on FULL versus NORMAL data sets: For many general uses there is no significant difference between FULL and NORMAL data sets. However, the FULL data set includes strains with high endogenous Gfap mRNA expression, indicative of reactive gliosis. For that reason, and to compare to OPTIC NERVE CRUSH (ONC), we removed data from six strains to make the NORMAL data set.
-
-The NORMAL data set exludes data from BXD24, BXD32, BXD49, BXD70, BXD83, and BXD89. BXD24 has known retinal degeneration and is now known officially as BXD24/TyJ-Cep290/J, JAX Stock number 000031. BXD32 has mild retinal degeneration. The NORMAL data set does include BXD24a, now also known as BXD24/TyJ (JAX Stock number 005243).
-
-The data are now open and available for analysis.
-
-Please cite: Freeman NE, Templeton JP, Orr WE, Lu L, Williams RW, Geisert EE (2011) Genetic networks in the mouse retina: Growth Associated Protein 43 and Phosphate Tensin Homology network. Molecular Vision 17:1355-1372. Full Text PDF or HTML
-
-This is rank invariant expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 6.25 to 18.08 (11.83 units), a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.
-
-The lowest level of expression is 6.254 for ILMN_2747167 (Arhgap11a) from HEI Retina Illumina V6.2 (April 2010) RankInv **. Lowest single data about 5.842.
-
-The highest level of expression is 18.077 for ILMN_2516699 (Ubb). Highest single value is about 18.934.
-
-
-
-
-Other Related Publications
-
-
-
-
-
- - Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW.:Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Molecular Vision 2009 Aug 31;15:1730-63, (Link)
- - Geisert EE, Jr., Williams RW: The Mouse Eye Transcriptome: Cellular Signatures, Molecular Networks, and Candidate Genes for Human Disease. In Eye, Retina, and Visual System of the Mouse. Edited by Chalupa LM, Williams RW. Cambridge: The MIT Press; 2008:659-674
- - Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7. (Link)
- - Templeton JP, Nassr M, Vazquez-Chona F, Freeman-Anderson NE, Orr WE, Williams RW, Geisert EE: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. BMC Neurosci. 2009, July 30;10:90.(Link)
-
-
-
-
-
-
-
-Other Data Sets Users of these mouse retina data may also find the following complementary resources useful:
-
-
- - NEIBank collection of ESTs and SAGE data.
- - RetNet: the Retinal Information Network--tables of genes and loci causing inherited retinal diseases
- - Mouse Retina SAGE Library from the Cepko laboratory. This site provides extensive developmental data from as early as embryonic day E12.5.
- - Digital reference of ophthalmology from Columbia provides high quality photographs of human ocular diseases, case studies, and short explanations. This reference does not have a molecular focus.
- - Mouse Retinal Developmental Gene Expression data sets from the Friedlander laboratory. This site provides extensive developmental data using the Affymetrix U74 v 2 array (predecessor of the M430).
- - Data sets on differential gene expression in anatomical compartments of the human eye from Pat Brown's lab. View expression signatures for different ocular tissues using the geneXplorer 2.0.
-
-
diff --git a/general/datasets/ONCRetILM6_0412/tissue.rtf b/general/datasets/ONCRetILM6_0412/tissue.rtf
deleted file mode 100644
index 766ab59..0000000
--- a/general/datasets/ONCRetILM6_0412/tissue.rtf
+++ /dev/null
@@ -1,32 +0,0 @@
-
-Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RNAlater at room temperature. Two retinas from one mouse were stored in a single tube.
-
-Each array was hybridized with a pool of cRNA from 2 retinas (1 mouse). Natalie Freeman-Anderson extracted RNA at UTHSC.
-
-
-
-Dissecting and preparing eyes for RNA extraction
-
-
-
-Retinas for RNA extraction were placed in RNA STAT-60 (Tel-Test Inc.) and processed per manufacturer’s instructions (in brief form below). Total RNA was extracted with RNA STAT-60 (Tel-Test Inc.) according to the manufacturer's instructions. Briefly we:
-
-
-
-
- - Homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue via syringe)
- - Allow the homogenate to stand for 5-10 min at room temperature
- - Add 0.2 ml of chloroform per 1 ml RNA STAT-60
- - Mix the sample vigorously for 15 sec and let the sample incubate at room temperature for 5-10 min
- - Centrifuge at 12,000 g for 1 hr at 4°C
- - Transfer the aqueous phase to a clean centrifuge tube
- - Add 0.5 ml of isopropanol per 1 ml RNA STAT-60
- - Vortex and incubate the sample at -20°C for 1 hr or overnight
- - Centrifuge at 12,000 g for 1 hr
- - Remove the supernatant and wash the RNA pellet with 75% ethanol
- - Remove ethanol, let air dry (5-10 min)
- - Dissolve the pellet in 50 μl of nuclease free water.
-
-
-
-
diff --git a/general/datasets/OXUKHS_ILMHipp_RI0510/cases.rtf b/general/datasets/OXUKHS_ILMHipp_RI0510/cases.rtf
deleted file mode 100644
index d216153..0000000
--- a/general/datasets/OXUKHS_ILMHipp_RI0510/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-HS Northport stock (see https://www.nature.com/articles/ng1840) descended from eight inbred progenitor strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and LP/J). For details, please see Demarest, K., Koyner, J., McCaughran, J. Jr., Cipp, L. & Hitzemann, R. Further characterization and high-resolution mapping of quantitative trait loci for ethanol-induced locomotor activity. Behav. Genet. 31, 79–91 (2001).
diff --git a/general/datasets/OXUKHS_ILMHipp_RI0510/platform.rtf b/general/datasets/OXUKHS_ILMHipp_RI0510/platform.rtf
deleted file mode 100644
index c8db2c0..0000000
--- a/general/datasets/OXUKHS_ILMHipp_RI0510/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Array design: A-MEXP-533 - Illumina Mouse-6 v1 Expression BeadChip
diff --git a/general/datasets/OXUKHS_ILMHipp_RI0510/summary.rtf b/general/datasets/OXUKHS_ILMHipp_RI0510/summary.rtf
deleted file mode 100644
index 5b53e35..0000000
--- a/general/datasets/OXUKHS_ILMHipp_RI0510/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in _30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3_ end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.
diff --git a/general/datasets/OXUKHS_ILMLiver_RI0510/cases.rtf b/general/datasets/OXUKHS_ILMLiver_RI0510/cases.rtf
deleted file mode 100644
index fcc2f2d..0000000
--- a/general/datasets/OXUKHS_ILMLiver_RI0510/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-HS Northport stock (see https://www.nature.com/articles/ng1840) descended from eight inbred progenitor strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and LP/J). For details, please see Demarest, K., Koyner, J., McCaughran, J. Jr., Cipp, L. & Hitzemann, R. Further characterization and high-resolution mapping of quantitative trait loci for ethanol-induced locomotor activity. Behav. Genet.31, 79–91 (2001).
diff --git a/general/datasets/OXUKHS_ILMLiver_RI0510/platform.rtf b/general/datasets/OXUKHS_ILMLiver_RI0510/platform.rtf
deleted file mode 100644
index add8a75..0000000
--- a/general/datasets/OXUKHS_ILMLiver_RI0510/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Organism: Mus musculus. Tissue: Liver. Array design: A-MEXP-533 - Illumina Mouse-6 v1 Expression BeadChip
diff --git a/general/datasets/OXUKHS_ILMLiver_RI0510/summary.rtf b/general/datasets/OXUKHS_ILMLiver_RI0510/summary.rtf
deleted file mode 100644
index 5b53e35..0000000
--- a/general/datasets/OXUKHS_ILMLiver_RI0510/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in _30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3_ end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.
diff --git a/general/datasets/OXUKHS_ILMLung_RI0510/cases.rtf b/general/datasets/OXUKHS_ILMLung_RI0510/cases.rtf
deleted file mode 100644
index fcc2f2d..0000000
--- a/general/datasets/OXUKHS_ILMLung_RI0510/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-HS Northport stock (see https://www.nature.com/articles/ng1840) descended from eight inbred progenitor strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and LP/J). For details, please see Demarest, K., Koyner, J., McCaughran, J. Jr., Cipp, L. & Hitzemann, R. Further characterization and high-resolution mapping of quantitative trait loci for ethanol-induced locomotor activity. Behav. Genet.31, 79–91 (2001).
diff --git a/general/datasets/OXUKHS_ILMLung_RI0510/platform.rtf b/general/datasets/OXUKHS_ILMLung_RI0510/platform.rtf
deleted file mode 100644
index 56e6161..0000000
--- a/general/datasets/OXUKHS_ILMLung_RI0510/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Organism: Mus musculus. Tissue: Lung. Array design: A-MEXP-533 - Illumina Mouse-6 v1 Expression BeadChip
diff --git a/general/datasets/OXUKHS_ILMLung_RI0510/summary.rtf b/general/datasets/OXUKHS_ILMLung_RI0510/summary.rtf
deleted file mode 100644
index 5b53e35..0000000
--- a/general/datasets/OXUKHS_ILMLung_RI0510/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in _30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3_ end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.
diff --git a/general/datasets/Oxukhs_ilmhipp_ri0510/experiment-type.rtf b/general/datasets/Oxukhs_ilmhipp_ri0510/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Oxukhs_ilmhipp_ri0510/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Psu_b6d2f2_0812/experiment-type.rtf b/general/datasets/Psu_b6d2f2_0812/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Psu_b6d2f2_0812/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/RTC_1106_R/acknowledgment.rtf b/general/datasets/RTC_1106_R/acknowledgment.rtf
deleted file mode 100644
index 3246da5..0000000
--- a/general/datasets/RTC_1106_R/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-These data were generated by Prof. Dr. Klaus Schughart (Department of Experimental Mouse Genetics) and Dr. Dunja Bruder (Research Group Immune Regulation) at the Helmholtz Center for Infection Research with the help of Dr. Lothar Gröbe (FACS sorting, Research Group Mucosal Immunity).
-
-Funding was provided by the Helmholtz Association and publicly funded research projects awarded to Drs. Klaus Schughart and Dunja Bruder.
-
diff --git a/general/datasets/RTC_1106_R/cases.rtf b/general/datasets/RTC_1106_R/cases.rtf
deleted file mode 100644
index 5ae01c7..0000000
--- a/general/datasets/RTC_1106_R/cases.rtf
+++ /dev/null
@@ -1,914 +0,0 @@
-
-Parental and 31 BXD lines were studied. Mice were received from The Jackson Laboratory, or from The Oak Ridge National and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). The data set includes expression values for 18 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40), as well as the two parental strains, C57BL/6J and DBA/2J. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding.
-
-BXD spleen sample pools (from 2-3 mice) were obtained from a pathogen-free mice of the Dutch Mouse Phenomics Consortium (MPC) in Amsterdam. Mice were imported into the central animal facility at the HZI and kept in a pathogen-free vivarium. Mice were euthanized using CO2 and spleenocytes were prepared. Most mice were between 17 and 22 weeks of age when samples were collected. FACS sorting was used to select the CD4-positive T cells. These cells were further separated into CD4+CD25+ and CD4+CD25- pools.
-
-Error-checking strain identity. A set of more than 20 probe sets with Mendelian segregation patterns in this HZI data set were used to confirm strain identify in early June, 2007. Two errors were detected and rectified. As of June 22, 2007, data are registered correctly. Prior to June 22, 2007, data listed as strains BXD33 and BXD39 were essentially hybrid (mixed) data sets.
-
-On Aug 23, 2007, we loaded the final QTL Reaper data into GeneNetwork for the corrected data set. The maximum LRS generated by any probe set is 84.6 for 1436240_at (Tra2a). A total of 41 probe sets are associated with QTLs that have LRS values above 46 (LOD > 10).
-
-Sex of samples is listed below in Table 1. In brief, data for BXD14 and 23 are male-only samples, whereas BXD12, 16, 31, 34, 36 and C57BL/6J are from female-only samples. All other samples (DBA/2J, BXD1, 2, 6, 9, 11, 18, 21 32, 33, 39, 40) consist of one male and one female array. The sex of samples can be independently validated using the Xist probe set (1427262_at).
-
-
-
-Figure 1: The expression of Xist can be used as an independent marker for sex. Xist is expressed at very low levels (noise) in male samples (far left) and at high values in females (far right). Sex-balanced samples (middle) have high variance due to the inclusion of one array per sex.
-
- Table 1
-
-
-
-
-
-
-
-
-
- | Index |
- ProbeSet ID |
- Sample Description |
- Sex |
- Strain |
- cd25 |
- Microarray |
- Short Description |
- Age |
- Pool No. |
- Pool members (animal number) |
- Date of preparation |
-
-
- | 1 |
- HZI1008 |
- BXD-06f (f1) CD25+ |
- F |
- BXD6 |
- CD25+ |
- Yes |
- BXD-06f |
- 17 |
- f1 |
- 1,3,4 |
- 1-31-2006 |
-
-
- | 2 |
- HZI1009 |
- BXD-06m (m2) CD25+ |
- M |
- BXD6 |
- CD25+ |
- Yes |
- BXD-06m |
- 18 |
- m2 |
- 5,6,7 |
- 1-31-2006 |
-
-
- | 3 |
- HZI1010 |
- BXD-14m (m3) CD25+ |
- M |
- BXD14 |
- CD25+ |
- Yes |
- BXD-14m |
- 17 |
- m3 |
- 1,3,4 |
- 1-31-2006 |
-
-
- | 4 |
- HZI1013 |
- BXD-40f (f6) CD25+ |
- F |
- BXD40 |
- CD25+ |
- Yes |
- BXD-40f |
- 17 |
- f6 |
- 1,2,3 |
- 2-1-2006 |
-
-
- | 5 |
- HZI1014 |
- BXD-40m (m7) CD25+ |
- M |
- BXD40 |
- CD25+ |
- Yes |
- BXD-40m |
- 17 |
- m7 |
- 5,6,7 |
- 2-2-2006 |
-
-
- | 6 |
- HZI1015 |
- BXD-02f (f8) CD25+ |
- F |
- BXD2 |
- CD25+ |
- Yes |
- BXD-02f |
- 17 |
- f8 |
- 1,2,3 |
- 2-14-2006 |
-
-
- | 7 |
- HZI1016 |
- BXD-02m (m20) CD25+ |
- M |
- BXD2 |
- CD25+ |
- Yes |
- BXD-02m |
- 21 |
- m20 |
- 4,5,6 |
- 4-6-2006 |
-
-
- | 8 |
- HZI1017 |
- BXD-11f (f30) CD25+ |
- F |
- BXD11 |
- CD25+ |
- Yes |
- BXD-11f |
- 17 |
- f30 |
- 3,4,5 |
- 5-11-2006 |
-
-
- | 9 |
- HZI1018 |
- BXD-11m (m9) CD25+ |
- M |
- BXD11 |
- CD25+ |
- Yes |
- BXD-11m |
- 18 |
- m9 |
- 1,2 |
- 2-14-2006 |
-
-
- | 10 |
- HZI1019 |
- BXD-12f (f10) CD25+ |
- F |
- BXD12 |
- CD25+ |
- Yes |
- BXD-12f |
- 17 |
- f10 |
- 1,2,3 |
- 2-14-2006 |
-
-
- | 11 |
- HZI1020 |
- BXD-39f (f23) CD25+ |
- F |
- BXD39 |
- CD25+ |
- Yes |
- BXD-39f |
- 19 |
- f23 |
- 4,5,6 |
- 4-11-2006 |
-
-
- | 12 |
- HZI1021 |
- BXD-33m (m11) CD25+ |
- M |
- BXD33 |
- CD25+ |
- Yes |
- BXD-33m |
- 17 |
- m11 |
- 1,2 |
- 2-14-2006 |
-
-
- | 13 |
- HZI1022 |
- BXD-18f (f14) CD25+ |
- F |
- BXD18 |
- CD25+ |
- Yes |
- BXD-18f |
- 17 |
- f14 |
- 3,4,5 |
- 2-15-2006 |
-
-
- | 14 |
- HZI1023 |
- BXD-18m (m13) CD25+ |
- M |
- BXD18 |
- CD25+ |
- Yes |
- BXD-18m |
- 18 |
- m13 |
- 7,8 |
- 2-15-2006 |
-
-
- | 15 |
- HZI1024 |
- BXD-23m (m15) CD25+ |
- M |
- BXD23 |
- CD25+ |
- Yes |
- BXD-23m |
- 18 |
- m15 |
- 1,2,3 |
- 2-15-2006 |
-
-
- | 16 |
- HZI1026 |
- BXD-09f (f17) CD25+ |
- F |
- BXD9 |
- CD25+ |
- Yes |
- BXD-09f |
- 21 |
- f17 |
- 1,2,3 |
- 4-5-2006 |
-
-
- | 17 |
- HZI1028 |
- BXD-09m (m35) CD25+ |
- M |
- BXD9 |
- CD25+ |
- Yes |
- BXD-09m |
- 15 |
- m35 |
- 7,8,9 |
- 7-7-2006 |
-
-
- | 18 |
- HZI1029 |
- BXD-32f (f18) CD25+ |
- F |
- BXD32 |
- CD25+ |
- Yes |
- BXD-32f |
- 21 |
- f18 |
- 1,2,3 |
- 4-6-2006 |
-
-
- | 19 |
- HZI1030 |
- BXD-32m (m19) CD25+ |
- M |
- BXD32 |
- CD25+ |
- Yes |
- BXD-32m |
- 22 |
- m19 |
- 1,2,3 |
- 4-6-2006 |
-
-
- | 20 |
- HZI1031 |
- BXD-33f (f22) CD25+ |
- F |
- BXD33 |
- CD25+ |
- Yes |
- BXD-33f |
- 18 |
- f22 |
- 2,3,4 |
- 4-11-2006 |
-
-
- | 21 |
- HZI1032 |
- BXD-39m (m29) CD25+ |
- M |
- BXD39 |
- CD25+ |
- Yes |
- BXD-39m |
- 17 |
- m29 |
- 5,6,7 |
- 5-10-2006 |
-
-
- | 22 |
- HZI1033 |
- BXD-01f (f32) CD25+ |
- F |
- BXD1 |
- CD25+ |
- Yes |
- BXD-01f |
- 18 |
- f32 |
- 3,4 |
- 7-6-2006 |
-
-
- | 23 |
- HZI1034 |
- BXD-01m (m31) CD25+ |
- M |
- BXD1 |
- CD25+ |
- Yes |
- BXD-01m |
- 18 |
- m31 |
- 1,2 |
- 7-6-2006 |
-
-
- | 24 |
- HZI1035 |
- BXD-16f (f26) CD25+ |
- F |
- BXD16 |
- CD25+ |
- Yes |
- BXD-16f |
- 18 |
- f26 |
- 1,2,3 |
- 4-12-2006 |
-
-
- | 25 |
- HZI1036 |
- BXD-21f (f25) CD25+ |
- F |
- BXD21 |
- CD25+ |
- Yes |
- BXD-21f |
- 19 |
- f25 |
- 5,6,7 |
- 4-12-2006 |
-
-
- | 26 |
- HZI1037 |
- BXD-21m (m24) CD25+ |
- M |
- BXD21 |
- CD25+ |
- Yes |
- BXD-21m |
- 18 |
- m24 |
- 1,2,3 |
- 4-12-2006 |
-
-
- | 27 |
- HZI1039 |
- BXD-31f (f34) CD25+ |
- F |
- BXD31 |
- CD25+ |
- Yes |
- BXD-31f |
- 16 |
- f34 |
- 1,2,3 |
- 7-7-2006 |
-
-
- | 28 |
- HZI1040 |
- C57BL/6Jf (f28) CD25+ |
- F |
- C57BL/6J |
- CD25+ |
- Yes |
- C57BL/6Jf |
- 16 |
- f28 |
- 1,2,3 |
- 5-10-2006 |
-
-
- | 29 |
- HZI1041 |
- DBA/2Jf (f27) CD25+ |
- F |
- DBA/2J |
- CD25+ |
- Yes |
- DBA/2Jf |
- 16 |
- f27 |
- 5,6,7 |
- 5-10-2006 |
-
-
- | 30 |
- HZI1042 |
- DBA/2Jm (m21) CD25+ |
- M |
- DBA/2J |
- CD25+ |
- Yes |
- DBA/2Jm |
- 21 |
- m21 |
- 1,2,3 |
- 4-11-2006 |
-
-
- | 31 |
- HZI1487 |
- BXD-08f (f67) CD25+ |
- F |
- BXD8 |
- CD25+ |
- Yes |
- BXD-08f |
- 11 |
- f67 |
- 4,5,6 |
- 6-25-2007 |
-
-
- | 32 |
- HZI1488 |
- BXD-08m (m66) CD25+ |
- M |
- BXD8 |
- CD25+ |
- Yes |
- BXD-08m |
- 17 |
- m66 |
- 1,2,3 |
- 6-25-2007 |
-
-
- | 33 |
- HZI1489 |
- BXD-16m (m36) CD25+ |
- M |
- BXD16 |
- CD25+ |
- Yes |
- BXD-16m |
- 20, 16 |
- m36 |
- 5,6,7 |
- 8-28-2006 |
-
-
- | 34 |
- HZI1490 |
- BXD-12m (m42) CD25+ |
- M |
- BXD12 |
- CD25+ |
- Yes |
- BXD-12m |
- 20 |
- m42 |
- 5,6,7 |
- 10-23-2006 |
-
-
- | 35 |
- HZI1491 |
- BXD-13f (f44) CD25+ |
- F |
- BXD13 |
- CD25+ |
- Yes |
- BXD-13f |
- 15 |
- f44 |
- 1,2,3 |
- 12-13-2006 |
-
-
- | 36 |
- HZI1492 |
- BXD-13m (m45) CD25+ |
- M |
- BXD13 |
- CD25+ |
- Yes |
- BXD-13m |
- 15 |
- m45 |
- 4,5,6,7 |
- 12-13-2006 |
-
-
- | 37 |
- HZI1493 |
- BXD-14f (f48) CD25+ |
- F |
- BXD14 |
- CD25+ |
- Yes |
- BXD-14f |
- 16 |
- f48 |
- 5,6,7 |
- 2-15-2007 |
-
-
- | 38 |
- HZI1494 |
- BXD-19f (f64) CD25+ |
- F |
- BXD19 |
- CD25+ |
- Yes |
- BXD-19f |
- 19 |
- f64 |
- 7,8,9 |
- 6-20-2007 |
-
-
- | 39 |
- HZI1495 |
- BXD-19m (m46) CD25+ |
- M |
- BXD19 |
- CD25+ |
- Yes |
- BXD-19m |
- 16 |
- m46 |
- 4,5,6 |
- 12-15-2006 |
-
-
- | 40 |
- HZI1499 |
- BXD-28m (m43) CD25+ |
- M |
- BXD28 |
- CD25+ |
- Yes |
- BXD-28m |
- 17,2 |
- m43 |
- 1,2,3 |
- 10-23-2006 |
-
-
- | 41 |
- HZI1500 |
- BXD-42f (f49) CD25+ |
- F |
- BXD42 |
- CD25+ |
- Yes |
- BXD-42f |
- 17 |
- f49 |
- ?? |
- 3-8-2007 |
-
-
- | 42 |
- HZI1502 |
- F1 (BXD)m (f50) CD25+ |
- M |
- B6D2F1 |
- CD25+ |
- Yes |
- F1 (BXD)m |
- 15 |
- m51 |
- 1,2,3, |
- 4-18-2007 |
-
-
- | 43 |
- HZI1503 |
- F1 (BXD)m (m51) CD25+ |
- F |
- B6D2F1 |
- CD25+ |
- Yes |
- F1 (BXD)f |
- 15 |
- f50 |
- 1,2,3 |
- 4-18-2007 |
-
-
- | 44 |
- HZI1504 |
- BXD-86f (f52) CD25+ |
- F |
- BXD86 |
- CD25+ |
- Yes |
- BXD-86f |
- 16 |
- f52 |
- 1,2,3 |
- 4-18-2007 |
-
-
- | 45 |
- HZI1505 |
- BXD-43f (f53) CD25+ |
- F |
- BXD43 |
- CD25+ |
- Yes |
- BXD-43f |
- 16 |
- f53 |
- 1,2,3 |
- 4-23-2007 |
-
-
- | 46 |
- HZI1506 |
- BXD-44f (f54) CD25+ |
- F |
- BXD44 |
- CD25+ |
- Yes |
- BXD-44f |
- 18 |
- f54 |
- 1,2,3 |
- 4-23-2007 |
-
-
- | 47 |
- HZI1507 |
- BXD-45f (f55) CD25+ |
- F |
- BXD45 |
- CD25+ |
- Yes |
- BXD-45f |
- 19 |
- f55 |
- 1,2,3 |
- 4-23-2007 |
-
-
- | 48 |
- HZI1508 |
- BXD-62f (f56) CD25+ |
- F |
- BXD62 |
- CD25+ |
- Yes |
- BXD-62f |
- 17 |
- f56 |
- 1,2,3 |
- 4-26-2007 |
-
-
- | 49 |
- HZI1509 |
- BXD-73f (f57) CD25+ |
- F |
- BXD73 |
- CD25+ |
- Yes |
- BXD-73f |
- 18 |
- f57 |
- 1,2,3 |
- 4-26-2007 |
-
-
- | 50 |
- HZI1510 |
- BXD-51f (f59) CD25+ |
- F |
- BXD51 |
- CD25+ |
- Yes |
- BXD-51f |
- 22 |
- f59 |
- 1,2,3 |
- 6-18-2007 |
-
-
- | 51 |
- HZI1523 |
- BXD-75f (f58) CD25+ |
- F |
- BXD75 |
- CD25+ |
- Yes |
- BXD-75f |
- 15,17 |
- f58 |
- 1,2,3 |
- 4-26-2007 |
-
-
- | 52 |
- HZI1525 |
- BXD-29m (m37) CD25+ |
- M |
- BXD29 |
- CD25+ |
- Yes |
- BXD-29m |
- 20, 16 |
- m37 |
- 1,2,3 |
- 8-29-2006 |
-
-
- | 53 |
- HZI1526 |
- BXD-34f (f4) CD25+ |
- F |
- BXD34 |
- CD25+ |
- Yes |
- BXD-34f |
- 17 |
- f4 |
- 1,2,3 |
- 2-1-2006 |
-
-
- | 54 |
- HZI1940 |
- BXD-27m (m39) CD25+ |
- M |
- BXD27 |
- CD25+ |
- Yes |
- BXD-27m |
- 18 - 20 |
- m39 |
- 1,3,4 |
- 9-1-2006 |
-
-
- | 55 |
- HZI1941 |
- BXD-42m (m47) CD25+ |
- M |
- BXD42 |
- CD25+ |
- Yes |
- BXD-42m |
- 15,16 |
- m47 |
- 1,2,3 |
- 12-15-2006 |
-
-
- | 56 |
- HZI1942 |
- BXD-34m (m5) CD25+ |
- M |
- BXD34 |
- CD25+ |
- Yes |
- BXD-34m |
- 17 |
- m5 |
- 5,7,8 |
- 2-1-2006 |
-
-
- | 57 |
- HZI1943 |
- BXD-38f (f70) CD25+ |
- F |
- BXD38 |
- CD25+ |
- Yes |
- BXD-38f |
- 13 |
- f70 |
- 4,5,6,7 |
- 2-1-2008 |
-
-
- | 58 |
- HZI1944 |
- BXD-31m (m69) CD25+ |
- M |
- BXD31 |
- CD25+ |
- Yes |
- BXD-31m |
- 14 |
- m69 |
- 4,5,6 |
- 2-1-2008 |
-
-
- | 59 |
- HZI1945 |
- BXD-27f (f12) CD25+ |
- F |
- BXD27 |
- CD25+ |
- Yes |
- BXD-27f |
- 18 |
- f12 |
- 1,2 |
- 2-15-2006 |
-
-
- | 60 |
- HZI1946 |
- BXD-38m (m63) CD25+ |
- M |
- BXD38 |
- CD25+ |
- Yes |
- BXD-38m |
- 18 |
- m63 |
- 1,2,3 |
- 6-20-2007 |
-
-
- | 61 |
- HZI1947 |
- BXD-23f (f62) CD25+ |
- F |
- BXD23 |
- CD25+ |
- Yes |
- BXD-23f |
- 21 |
- f62 |
- 1,2,3 |
- 6-20-2007 |
-
-
- | 62 |
- HZI1948 |
- BXD-28f (f61) CD25+ |
- F |
- BXD28 |
- CD25+ |
- Yes |
- BXD-28f |
- 22 |
- f61 |
- 1,2,3 |
- 6-18-2007 |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/RTC_1106_R/experiment-design.rtf b/general/datasets/RTC_1106_R/experiment-design.rtf
deleted file mode 100644
index a69dffc..0000000
--- a/general/datasets/RTC_1106_R/experiment-design.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-Parental and BXD lines were received from Jackson Laboratory, or from Oak Ridge Laboratory (BXD43, BXD51, BXD61, BXD62, BXD65, BXD68, BXD69, BXD73, BXD75, BXD87, BXD90), and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). Female mice, 3 per strain, were housed on sawdust in standard Makrolon type II cages with food (Harlan Teklad 2018) and water ad libitum under specific pathogen free conditions. For the analysis, mice were transferred to the animal facility in Braunschweig and adapted for at least two weeks to the new environment before preparing the spleen cells. All protocols involving mice were approved by national animal welfare committees.
-
-For sorting of Tregs and Th cells, splenocytes from 31 BXD recombinant inbred strains, as well as from the parental strains DBA/2J and C57BL/6J, were isolated by flushing the spleens with erythrocyte lysis buffer. Cells were collected by centrifugation, resuspended in cold FACS-buffer (PBS / 2% FCS / 0,5 mM EDTA). After passing the cells through a 100 µm cell strainer and an additional washing step with FACS-buffer, splenocytes were stained with anti-CD4-APC and anti-CD25-PE for 10 minutes at 4 °C, washed and resuspended in FACS-buffer. CD4+ T cells were separated into CD4+CD25+ Tregs and CD4+CD25- Th cells using a MoFlo cell sorter (Cytomation) and purity of the sorted T cell subsets reached 95-97%.
-
-Quality and integrity of the total RNA isolated from 1x105 cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). RNA amplification and labeling was done according to manufactures protocol (Small Sample Target Labeling Assay Version II, Affymetrix; Santa Clara, CA). The concentration of biotin-labeled cRNA was determined by UV absorbance. In all cases, 10 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix MOE430 2.0 for 16 hours at 46 °C. After hybridisation the GeneChips were washed and stained using the Affymetrix´s recommended EukGE-WS2v5 protocol for GeneChip Fluidics FS400 station. Images were scanned using GeneChip Scanner 3000 under the control of GCOS 1.3 software package (Affymetrix; Santa Clara, CA).
-
diff --git a/general/datasets/RTC_1106_R/notes.rtf b/general/datasets/RTC_1106_R/notes.rtf
deleted file mode 100644
index dbd0c60..0000000
--- a/general/datasets/RTC_1106_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file was generated by KS on July, 18 2011.
diff --git a/general/datasets/RTC_1106_R/platform.rtf b/general/datasets/RTC_1106_R/platform.rtf
deleted file mode 100644
index ed42a9b..0000000
--- a/general/datasets/RTC_1106_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-The Affymetrix M430 2.0 array consists of approximately 992,936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts, including a majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using NCBI Build 107 by Affymetrix. The UTHSC GN group continuously reannotated probe sets on this array, producing more accurate data on probe and probe set targets. All probes have also be aligned to the most recent assembly of the Mouse Genome using Jim Kent's BLAT program.
-
diff --git a/general/datasets/RTC_1106_R/processing.rtf b/general/datasets/RTC_1106_R/processing.rtf
deleted file mode 100644
index b8d49b7..0000000
--- a/general/datasets/RTC_1106_R/processing.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-
-Microarray data then was preprocessed using the RMA method [bolstad] and subsequently batch corrected [Alberts et al]. In this study, RNA was extracted at three different points in time for the Treg samples and also microarray processing was performed at three different points in time. Similarly, the Th samples were processed in two batches. Therefore, we performed a batch correction for both cell types using the following ANOVA model before further analysis of the data.
-yi = μ + Bi + ei
-Where yi is the expression level of the ith microarray, μ is the overall mean, Bi is the batch to which the ith individual belongs and ei is the residual error.
-Batch corrected data sets were then preprocessed before transferring them to the GeneNetwork (GN) database: Adding an offset of 1 unit to each signal intensity value to ensure that the logarithm of all values were positive, computing the log2 value, performing a quantile normalization of the log2 values for the total set of arrays using the same initial steps used by the RMA transform, computing the Z scores for each cell value, multiplying all Z scores by 2 and adding 8 to the value of all Z scores. The advantage of this variant of a Z transformation is that all values are positive and that 1 unit represents approximately a 2-fold difference in expression as determined using the spike-in control probe sets. The mean values were subsequently calculated if multiple samples from one BXD line were recorded (male and females or replicates).
-
diff --git a/general/datasets/RTC_1106_R/summary.rtf b/general/datasets/RTC_1106_R/summary.rtf
deleted file mode 100644
index 2094b06..0000000
--- a/general/datasets/RTC_1106_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-ERROR-CHECKED FIRST PHASE PRIVATE TEST DATA SET. This data set provides estimates of gene expression in regulatory T cells (CD4+CD25+) of BXD strains. Data were generated by Prof. Dr. Klaus Schughart and colleagues at the Helmholtz Centre for Infection Research (HZI). Samples were processed using a total of 35 Affymetrix MOE 430 2.0 short oligomer microarrays, of which 33 passed stringent quality control and error checking.
-This is a private test data set. Please contact Dr. Klaus Schughart for early access.
-
diff --git a/general/datasets/RTHC_0211_R/acknowledgment.rtf b/general/datasets/RTHC_0211_R/acknowledgment.rtf
deleted file mode 100644
index 3246da5..0000000
--- a/general/datasets/RTHC_0211_R/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-These data were generated by Prof. Dr. Klaus Schughart (Department of Experimental Mouse Genetics) and Dr. Dunja Bruder (Research Group Immune Regulation) at the Helmholtz Center for Infection Research with the help of Dr. Lothar Gröbe (FACS sorting, Research Group Mucosal Immunity).
-
-Funding was provided by the Helmholtz Association and publicly funded research projects awarded to Drs. Klaus Schughart and Dunja Bruder.
-
diff --git a/general/datasets/RTHC_0211_R/cases.rtf b/general/datasets/RTHC_0211_R/cases.rtf
deleted file mode 100644
index 5f97723..0000000
--- a/general/datasets/RTHC_0211_R/cases.rtf
+++ /dev/null
@@ -1,824 +0,0 @@
-
-Parental and 31 BXD lines were studied. Mice were received from Jackson Laboratory, or from The Oak Ridge National and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). The data set includes expression values for 18 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40, as well as the two parental strains, C57BL/6J and DBA/2J. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding.
-
-BXD spleen sample pools (from 2-3 mice) were obtained from a pathogen-free mice of the Dutch Mouse Phenomics Consortium (MPC) in Amsterdam. Mice were imported into the central animal facility at the HZI and kept in a pathogen-free vivarium. Mice were euthanized using CO2 and spleenocytes wre prepared. Most mice were between 17 and 22 weeks of age when samples were collected. FACS sorting was used to select the CD4-positive T cells. These cells were further separated into CD4+CD25+ and CD4+CD25- pools.
-
-Error-checking strain identity. A set of more than 20 probe sets with Mendelian segregation patterns in this HZI data set were used to confirm strain identify in early June, 2007. Two errors were detected and rectified. As of June 22, 2007, data are registered correctly. Prior to June 22, 2007, data listed as strains BXD33 and BXD39 were essentially hybrid (mixed) data sets.
-
-On Aug 23, 2007, we loaded the final QTL Reaper data into GeneNetwork for the corrected data set. The maximum LRS generated by any probe set is 84.6 for 1436240_at (Tra2a). A total of 41 probe sets are associated with QTLs that have LRS values above 46 (LOD > 10).
-
- Table 1
-
-
-
-
-
-
-
-
-
- | Index |
- ProbeSet ID |
- Sample Description |
- Sex |
- Strain |
- cd25 |
- Microarray |
- Short Description |
- Age |
- Pool No. |
- Pool members (animal number) |
- Date of preparation |
-
-
- | 1 |
- HZI1176 |
- BXD-06f (f1) CD25 |
- F |
- BXD6 |
- CD25- |
- Yes |
- BXD-06f |
- 17 |
- f1 |
- 1,3,4 |
- 1-31-2006 |
-
-
- | 2 |
- HZI1177 |
- BXD-06m (m2) CD25 |
- M |
- BXD6 |
- CD25- |
- Yes |
- BXD-06m |
- 18 |
- m2 |
- 5,6,7 |
- 1-31-2006 |
-
-
- | 3 |
- HZI1178 |
- BXD-14m (m3) CD25 |
- M |
- BXD14 |
- CD25- |
- Yes |
- BXD-14m |
- 17 |
- m3 |
- 1,3,4 |
- 1-31-2006 |
-
-
- | 4 |
- HZI1179 |
- BXD-34f (f4) CD25 |
- F |
- BXD34 |
- CD25- |
- Yes |
- BXD-34f |
- 17 |
- f4 |
- 1,2,3 |
- 2-1-2006 |
-
-
- | 5 |
- HZI1180 |
- BXD-34m (m5) CD25 |
- M |
- BXD34 |
- CD25- |
- Yes |
- BXD-34m |
- 17 |
- m5 |
- 5,7,8 |
- 2-1-2006 |
-
-
- | 6 |
- HZI1181 |
- BXD-40f (f6) CD25 |
- F |
- BXD40 |
- CD25- |
- Yes |
- BXD-40f |
- 17 |
- f6 |
- 1,2,3 |
- 2-1-2006 |
-
-
- | 7 |
- HZI1182 |
- BXD-40m (m7) CD25 |
- M |
- BXD40 |
- CD25- |
- Yes |
- BXD-40m |
- 17 |
- m7 |
- 5,6,7 |
- 2-2-2006 |
-
-
- | 8 |
- HZI1183 |
- BXD-02f (f8) CD25 |
- F |
- BXD2 |
- CD25- |
- Yes |
- BXD-02f |
- 17 |
- f8 |
- 1,2,3 |
- 2-14-2006 |
-
-
- | 9 |
- HZI1184 |
- BXD-02m (m20) CD25 |
- M |
- BXD2 |
- CD25- |
- Yes |
- BXD-02m |
- 21 |
- m20 |
- 4,5,6 |
- 4-6-2006 |
-
-
- | 10 |
- HZI1185 |
- BXD-11f (f30) CD25 |
- F |
- BXD11 |
- CD25- |
- Yes |
- BXD-11f |
- 17 |
- f30 |
- 3,4,5 |
- 5-11-2006 |
-
-
- | 11 |
- HZI1186 |
- BXD-11m (m9) CD25 |
- M |
- BXD11 |
- CD25- |
- Yes |
- BXD-11m |
- 18 |
- m9 |
- 1,2 |
- 2-14-2006 |
-
-
- | 12 |
- HZI1187 |
- BXD-12f (f10) CD25 |
- F |
- BXD12 |
- CD25- |
- Yes |
- BXD-12f |
- 17 |
- f10 |
- 1,2,3 |
- 2-14-2006 |
-
-
- | 13 |
- HZI1188 |
- BXD-39f (f23) CD25 |
- F |
- BXD39 |
- CD25- |
- Yes |
- BXD-39f |
- 19 |
- f23 |
- 4,5,6 |
- 4-11-2006 |
-
-
- | 14 |
- HZI1191 |
- BXD-18m (m13) CD25 |
- M |
- BXD18 |
- CD25- |
- Yes |
- BXD-18m |
- 18 |
- m13 |
- 7,8 |
- 2-15-2006 |
-
-
- | 15 |
- HZI1192 |
- BXD-23m (m15) CD25 |
- M |
- BXD23 |
- CD25- |
- Yes |
- BXD-23m |
- 18 |
- m15 |
- 1,2,3 |
- 2-15-2006 |
-
-
- | 16 |
- HZI1194 |
- BXD-09f (f17) CD25 |
- F |
- BXD9 |
- CD25- |
- Yes |
- BXD-09f |
- 21 |
- f17 |
- 1,2,3 |
- 4-5-2006 |
-
-
- | 17 |
- HZI1195 |
- BXD-09m (m16) CD25 |
- M |
- BXD9 |
- CD25- |
- Yes |
- BXD-09m2 |
- 21 |
- m16 |
- 5,6 |
- 4-5-2006 |
-
-
- | 18 |
- HZI1196 |
- BXD-09m (m35) CD25 |
- M |
- BXD9 |
- CD25- |
- Yes |
- BXD-09m |
- 15 |
- m35 |
- 7,8,9 |
- 7-7-2006 |
-
-
- | 19 |
- HZI1197 |
- BXD-32f (f18) CD25 |
- F |
- BXD32 |
- CD25- |
- Yes |
- BXD-32f |
- 21 |
- f18 |
- 1,2,3 |
- 4-6-2006 |
-
-
- | 20 |
- HZI1198 |
- BXD-32m (m19) CD25 |
- M |
- BXD32 |
- CD25- |
- Yes |
- BXD-32m |
- 22 |
- m19 |
- 1,2,3 |
- 4-6-2006 |
-
-
- | 21 |
- HZI1199 |
- BXD-33f (f22) CD25 |
- F |
- BXD33 |
- CD25- |
- Yes |
- BXD-33f |
- 18 |
- f22 |
- 2,3,4 |
- 4-11-2006 |
-
-
- | 22 |
- HZI1200 |
- BXD-39m (m29) CD25 |
- M |
- BXD39 |
- CD25- |
- Yes |
- BXD-39m |
- 17 |
- m29 |
- 5,6,7 |
- 5-10-2006 |
-
-
- | 23 |
- HZI1201 |
- BXD-01f (f32) CD25 |
- F |
- BXD1 |
- CD25- |
- Yes |
- BXD-01f |
- 18 |
- f32 |
- 3,4 |
- 7-6-2006 |
-
-
- | 24 |
- HZI1202 |
- BXD-01m (m31) CD25 |
- M |
- BXD1 |
- CD25- |
- Yes |
- BXD-01m |
- 18 |
- m31 |
- 1,2 |
- 7-6-2006 |
-
-
- | 25 |
- HZI1203 |
- BXD-16f (f26) CD25 |
- F |
- BXD16 |
- CD25- |
- Yes |
- BXD-16f |
- 18 |
- f26 |
- 1,2,3 |
- 4-12-2006 |
-
-
- | 26 |
- HZI1204 |
- BXD-21f (f25) CD25 |
- F |
- BXD21 |
- CD25- |
- Yes |
- BXD-21f |
- 19 |
- f25 |
- 5,6,7 |
- 4-12-2006 |
-
-
- | 27 |
- HZI1205 |
- BXD-21m (m24) CD25 |
- M |
- BXD21 |
- CD25- |
- Yes |
- BXD-21m |
- 18 |
- m24 |
- 1,2,3 |
- 4-12-2006 |
-
-
- | 28 |
- HZI1208 |
- C57BL/6Jf (f28) CD25 |
- F |
- C57BL/6J |
- CD25- |
- Yes |
- C57BL/6Jf |
- 16 |
- f28 |
- 1,2,3 |
- 5-10-2006 |
-
-
- | 29 |
- HZI1209 |
- DBA/2Jf (f27) CD25 |
- F |
- DBA/2J |
- CD25- |
- Yes |
- DBA/2Jf |
- 16 |
- f27 |
- 5,6,7 |
- 5-10-2006 |
-
-
- | 30 |
- HZI1210 |
- DBA/2Jm (m21) CD25 |
- M |
- DBA/2J |
- CD25- |
- Yes |
- DBA/2Jm |
- 21 |
- m21 |
- 1,2,3 |
- 4-11-2006 |
-
-
- | 31 |
- HZI2473 |
- BXD-13 m 45 |
- M |
- BXD13 |
- CD25- |
- Yes |
- BXD-13m |
- 15 |
- m45 |
- 4,5,6,7 |
- 12-13-2006 |
-
-
- | 32 |
- HZI2474 |
- BXD-19 m 46 |
- M |
- BXD19 |
- CD25- |
- Yes |
- BXD-19m |
- 16 |
- m46 |
- 4,5,6 |
- 12-15-2006 |
-
-
- | 33 |
- HZI2475 |
- BXD-28 m 43 |
- M |
- BXD28 |
- CD25- |
- Yes |
- BXD-28m |
- 17,2 |
- m43 |
- 1,2,3 |
- 10-23-2006 |
-
-
- | 34 |
- HZI2476 |
- BXD-29 m 37 |
- M |
- BXD29 |
- CD25- |
- Yes |
- BXD-29m |
- 20, 16 |
- m37 |
- 1,2,3 |
- 8-29-2006 |
-
-
- | 35 |
- HZI2477 |
- BXD-31 m 69 |
- M |
- BXD31 |
- CD25- |
- Yes |
- BXD-31m |
- 14 |
- m69 |
- 4,5,6 |
- 2-1-2008 |
-
-
- | 36 |
- HZI2478 |
- BXD-33 m 11 |
- M |
- BXD33 |
- CD25- |
- Yes |
- BXD-33m |
- 17 |
- m11 |
- 1,2 |
- 2-14-2006 |
-
-
- | 37 |
- HZI2479 |
- BXD-38 m 63 |
- M |
- BXD38 |
- CD25- |
- Yes |
- BXD-38m |
- 18 |
- m63 |
- 1,2,3 |
- 6-20-2007 |
-
-
- | 38 |
- HZI2480 |
- BXD-42 m 47 |
- M |
- BXD42 |
- CD25- |
- Yes |
- BXD-42m |
- 15,16 |
- m47 |
- 1,2,3 |
- 12-15-2006 |
-
-
- | 39 |
- HZI2481 |
- BXD-42 m 65 |
- M |
- BXD42 |
- CD25- |
- Yes |
- BXD-42m |
- 15,16 |
- m47 |
- 1,2,3 |
- 12-15-2006 |
-
-
- | 40 |
- HZI2482 |
- BXD-13 f 44 |
- F |
- BXD13 |
- CD25- |
- Yes |
- BXD-13f |
- 15 |
- f44 |
- 1,2,3 |
- 12-13-2006 |
-
-
- | 41 |
- HZI2483 |
- BXD-18 F 14 |
- F |
- BXD18 |
- CD25- |
- Yes |
- BXD-18f |
- 17 |
- f14 |
- 3,4,5 |
- 2-15-2006 |
-
-
- | 42 |
- HZI2484 |
- BXD-19 f 38 |
- F |
- BXD19 |
- CD25- |
- Yes |
- BXD-19f2 |
- 21 |
- f38 |
- 1,2,3 |
- 9-1-2006 |
-
-
- | 43 |
- HZI2485 |
- BXD-19 f 64 |
- F |
- BXD19 |
- CD25- |
- Yes |
- BXD-19f |
- 19 |
- f64 |
- 7,8,9 |
- 6-20-2007 |
-
-
- | 44 |
- HZI2486 |
- BXD-28 f 61 |
- F |
- BXD28 |
- CD25- |
- Yes |
- BXD-28f |
- 22 |
- f61 |
- 1,2,3 |
- 6-18-2007 |
-
-
- | 45 |
- HZI2487 |
- BXD-29 f 40 |
- F |
- BXD29 |
- CD25- |
- Yes |
- BXD-29f |
- 15 - 16 |
- f40 |
- 4,5,6 |
- 9-25-2006 |
-
-
- | 46 |
- HZI2488 |
- BXD-31 f 34 |
- F |
- BXD31 |
- CD25- |
- Yes |
- BXD-31f |
- 16 |
- f34 |
- 1,2,3 |
- 7-7-2006 |
-
-
- | 47 |
- HZI2489 |
- BXD-38 f 70 |
- F |
- BXD38 |
- CD25- |
- Yes |
- BXD-38f |
- 13 |
- f70 |
- 4,5,6,7 |
- 2-1-2008 |
-
-
- | 48 |
- HZI2490 |
- BXD-42 f 49 |
- F |
- BXD42 |
- CD25- |
- Yes |
- BXD-42f |
- 17 |
- f49 |
- ?? |
- 3-8-2007 |
-
-
- | 49 |
- HZI2491 |
- BXD-43 f 53 |
- F |
- BXD43 |
- CD25- |
- Yes |
- BXD-43f |
- 16 |
- f53 |
- 1,2,3 |
- 4-23-2007 |
-
-
- | 50 |
- HZI2492 |
- BXD-44 f 54 |
- F |
- BXD44 |
- CD25- |
- Yes |
- BXD-44f |
- 18 |
- f54 |
- 1,2,3 |
- 4-23-2007 |
-
-
- | 51 |
- HZI2493 |
- BXD-45 f 55 |
- F |
- BXD45 |
- CD25- |
- Yes |
- BXD-45f |
- 19 |
- f55 |
- 1,2,3 |
- 4-23-2007 |
-
-
- | 52 |
- HZI2494 |
- BXD-51 f 59 |
- F |
- BXD51 |
- CD25- |
- Yes |
- BXD-51f |
- 22 |
- f59 |
- 1,2,3 |
- 6-18-2007 |
-
-
- | 53 |
- HZI2495 |
- BXD-62 f 56 |
- F |
- BXD62 |
- CD25- |
- Yes |
- BXD-62f |
- 17 |
- f56 |
- 1,2,3 |
- 4-26-2007 |
-
-
- | 54 |
- HZI2496 |
- BXD-73 f 57 |
- F |
- BXD73 |
- CD25- |
- Yes |
- BXD-73f |
- 18 |
- f57 |
- 1,2,3 |
- 4-26-2007 |
-
-
- | 55 |
- HZI2497 |
- BXD-75 f 58 |
- F |
- BXD75 |
- CD25- |
- Yes |
- BXD-75f |
- 15,17 |
- f58 |
- 1,2,3 |
- 4-26-2007 |
-
-
- | 56 |
- HZI2498 |
- BXD-86 f 52 |
- F |
- BXD86 |
- CD25- |
- Yes |
- BXD-86f |
- 16 |
- f52 |
- 1,2,3 |
- 4-18-2007 |
-
-
-
- |
-
-
-
-
-
diff --git a/general/datasets/RTHC_0211_R/experiment-design.rtf b/general/datasets/RTHC_0211_R/experiment-design.rtf
deleted file mode 100644
index 2b4d4cc..0000000
--- a/general/datasets/RTHC_0211_R/experiment-design.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-
-Parental and BXD lines were received from Jackson Laboratory, or from Oak Ridge Laboratory (BXD43, BXD51, BXD61, BXD62, BXD65, BXD68, BXD69, BXD73, BXD75, BXD87, BXD90), and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). Female mice 3 per strain were housed on sawdust in standard Makrolon type II cages with food (Harlan Teklad 2018) and water ad libitum under specific pathogen free conditions. For the analysis, mice were transferred to the animal facility in Braunschweig and adapted for at least two weeks to the new environment before preparing the spleen cells. All protocols involving mice were approved by national animal welfare committees.
-
-For sorting of Tregs and Th cells, splenocytes from 31 BXD recombinant inbred strains as well as from the parental mouse lines DBA/2J and C57BL/6J were isolated by flushing the spleens with erythrocyte-lysis-buffer. Cells were collected by centrifugation, re-suspended in cold FACS-buffer (PBS / 2% FCS / 0,5 mM EDTA). After passing the cells through a 100 µm cell strainer and an additional washing step with FACS-buffer, splenocytes were stained with anti-CD4-APC and anti-CD25-PE for 10 minutes at 4°C, washed and re-suspended in FACS-buffer. CD4+ T cells were separated into CD4+CD25+ Tregs and CD4+CD25- Th cells using a MoFlo cell sorter (Cytomation) and purity of the sorted T cell subsets reached 95-97%.
-
-Quality and integrity of the total RNA isolated from 1x105 cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). RNA amplification and labeling was done according to manufactures protocol (Small Sample Target Labeling Assay Version II, Affymetrix; Santa Clara, CA). The concentration of biotin-labeled cRNA was determined by UV absorbance. In all cases, 10 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix MOE430 2.0 for 16 hours at 46°C. After hybridisation the GeneChips were washed and stained using the Affymetrix´s recommended EukGE-WS2v5 protocol for GeneChip® Fluidics FS400 station. Images were scanned using GeneChip® Scanner 3000 under the control of GCOS 1.3 software package (Affymetrix; Santa Clara, CA).
-
diff --git a/general/datasets/RTHC_0211_R/notes.rtf b/general/datasets/RTHC_0211_R/notes.rtf
deleted file mode 100644
index dbd0c60..0000000
--- a/general/datasets/RTHC_0211_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This text file was generated by KS on July, 18 2011.
diff --git a/general/datasets/RTHC_0211_R/platform.rtf b/general/datasets/RTHC_0211_R/platform.rtf
deleted file mode 100644
index ed42a9b..0000000
--- a/general/datasets/RTHC_0211_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-The Affymetrix M430 2.0 array consists of approximately 992,936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts, including a majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using NCBI Build 107 by Affymetrix. The UTHSC GN group continuously reannotated probe sets on this array, producing more accurate data on probe and probe set targets. All probes have also be aligned to the most recent assembly of the Mouse Genome using Jim Kent's BLAT program.
-
diff --git a/general/datasets/RTHC_0211_R/processing.rtf b/general/datasets/RTHC_0211_R/processing.rtf
deleted file mode 100644
index b8d49b7..0000000
--- a/general/datasets/RTHC_0211_R/processing.rtf
+++ /dev/null
@@ -1,6 +0,0 @@
-
-Microarray data then was preprocessed using the RMA method [bolstad] and subsequently batch corrected [Alberts et al]. In this study, RNA was extracted at three different points in time for the Treg samples and also microarray processing was performed at three different points in time. Similarly, the Th samples were processed in two batches. Therefore, we performed a batch correction for both cell types using the following ANOVA model before further analysis of the data.
-yi = μ + Bi + ei
-Where yi is the expression level of the ith microarray, μ is the overall mean, Bi is the batch to which the ith individual belongs and ei is the residual error.
-Batch corrected data sets were then preprocessed before transferring them to the GeneNetwork (GN) database: Adding an offset of 1 unit to each signal intensity value to ensure that the logarithm of all values were positive, computing the log2 value, performing a quantile normalization of the log2 values for the total set of arrays using the same initial steps used by the RMA transform, computing the Z scores for each cell value, multiplying all Z scores by 2 and adding 8 to the value of all Z scores. The advantage of this variant of a Z transformation is that all values are positive and that 1 unit represents approximately a 2-fold difference in expression as determined using the spike-in control probe sets. The mean values were subsequently calculated if multiple samples from one BXD line were recorded (male and females or replicates).
-
diff --git a/general/datasets/RTHC_0211_R/summary.rtf b/general/datasets/RTHC_0211_R/summary.rtf
deleted file mode 100644
index 4fd2899..0000000
--- a/general/datasets/RTHC_0211_R/summary.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-ERROR-CHECKED FIRST PHASE PRIVATE TEST DATA SET. This data set provides estimates of gene expression in helper T cells (CD4+CD25+) of BXD strains. Data were generated by Prof. Dr. Klaus Schughart and colleagues at the Helmholtz Centre for Infection Research (HZI). Samples were processed using a total of 35 Affymetrix MOE 430 2.0 short oligomer microarrays, of which 33 passed stringent quality control and error checking.
-
-This is a private test data set. Please contact Dr. Klaus Schughart for early access.
-
diff --git a/general/datasets/SA_M2_0405_M/acknowledgment.rtf b/general/datasets/SA_M2_0405_M/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_M/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_M/cases.rtf b/general/datasets/SA_M2_0405_M/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_M/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_M/experiment-design.rtf b/general/datasets/SA_M2_0405_M/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_M/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_M/notes.rtf b/general/datasets/SA_M2_0405_M/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_M/platform.rtf b/general/datasets/SA_M2_0405_M/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_M/processing.rtf b/general/datasets/SA_M2_0405_M/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_M/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_M/summary.rtf b/general/datasets/SA_M2_0405_M/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_M/tissue.rtf b/general/datasets/SA_M2_0405_M/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_M/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_MC/acknowledgment.rtf b/general/datasets/SA_M2_0405_MC/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_MC/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_MC/cases.rtf b/general/datasets/SA_M2_0405_MC/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_MC/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_MC/experiment-design.rtf b/general/datasets/SA_M2_0405_MC/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_MC/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_MC/notes.rtf b/general/datasets/SA_M2_0405_MC/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_MC/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_MC/platform.rtf b/general/datasets/SA_M2_0405_MC/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_MC/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_MC/processing.rtf b/general/datasets/SA_M2_0405_MC/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_MC/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_MC/summary.rtf b/general/datasets/SA_M2_0405_MC/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_MC/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_MC/tissue.rtf b/general/datasets/SA_M2_0405_MC/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_MC/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_P/acknowledgment.rtf b/general/datasets/SA_M2_0405_P/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_P/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_P/cases.rtf b/general/datasets/SA_M2_0405_P/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_P/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_P/experiment-design.rtf b/general/datasets/SA_M2_0405_P/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_P/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_P/notes.rtf b/general/datasets/SA_M2_0405_P/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_P/platform.rtf b/general/datasets/SA_M2_0405_P/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_P/processing.rtf b/general/datasets/SA_M2_0405_P/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_P/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_P/summary.rtf b/general/datasets/SA_M2_0405_P/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_P/tissue.rtf b/general/datasets/SA_M2_0405_P/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_P/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_PC/acknowledgment.rtf b/general/datasets/SA_M2_0405_PC/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_PC/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_PC/cases.rtf b/general/datasets/SA_M2_0405_PC/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_PC/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_PC/experiment-design.rtf b/general/datasets/SA_M2_0405_PC/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_PC/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_PC/notes.rtf b/general/datasets/SA_M2_0405_PC/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_PC/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_PC/platform.rtf b/general/datasets/SA_M2_0405_PC/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_PC/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_PC/processing.rtf b/general/datasets/SA_M2_0405_PC/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_PC/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_PC/summary.rtf b/general/datasets/SA_M2_0405_PC/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_PC/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_PC/tissue.rtf b/general/datasets/SA_M2_0405_PC/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_PC/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_R/acknowledgment.rtf b/general/datasets/SA_M2_0405_R/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_R/cases.rtf b/general/datasets/SA_M2_0405_R/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_R/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_R/experiment-design.rtf b/general/datasets/SA_M2_0405_R/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_R/notes.rtf b/general/datasets/SA_M2_0405_R/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_R/platform.rtf b/general/datasets/SA_M2_0405_R/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_R/processing.rtf b/general/datasets/SA_M2_0405_R/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_R/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_R/summary.rtf b/general/datasets/SA_M2_0405_R/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_R/tissue.rtf b/general/datasets/SA_M2_0405_R/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_R/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_RC/acknowledgment.rtf b/general/datasets/SA_M2_0405_RC/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_RC/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_RC/cases.rtf b/general/datasets/SA_M2_0405_RC/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_RC/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_RC/experiment-design.rtf b/general/datasets/SA_M2_0405_RC/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_RC/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_RC/notes.rtf b/general/datasets/SA_M2_0405_RC/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_RC/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_RC/platform.rtf b/general/datasets/SA_M2_0405_RC/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_RC/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_RC/processing.rtf b/general/datasets/SA_M2_0405_RC/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_RC/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_RC/summary.rtf b/general/datasets/SA_M2_0405_RC/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_RC/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_RC/tissue.rtf b/general/datasets/SA_M2_0405_RC/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_RC/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_RR/acknowledgment.rtf b/general/datasets/SA_M2_0405_RR/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_RR/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_RR/cases.rtf b/general/datasets/SA_M2_0405_RR/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_RR/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_RR/experiment-design.rtf b/general/datasets/SA_M2_0405_RR/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_RR/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_RR/notes.rtf b/general/datasets/SA_M2_0405_RR/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_RR/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_RR/platform.rtf b/general/datasets/SA_M2_0405_RR/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_RR/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_RR/processing.rtf b/general/datasets/SA_M2_0405_RR/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_RR/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_RR/summary.rtf b/general/datasets/SA_M2_0405_RR/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_RR/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_RR/tissue.rtf b/general/datasets/SA_M2_0405_RR/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_RR/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0405_SS/acknowledgment.rtf b/general/datasets/SA_M2_0405_SS/acknowledgment.rtf
deleted file mode 100644
index 94eec11..0000000
--- a/general/datasets/SA_M2_0405_SS/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_0405_SS/cases.rtf b/general/datasets/SA_M2_0405_SS/cases.rtf
deleted file mode 100644
index 491788f..0000000
--- a/general/datasets/SA_M2_0405_SS/cases.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 1.75 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory.
-
-
-
diff --git a/general/datasets/SA_M2_0405_SS/experiment-design.rtf b/general/datasets/SA_M2_0405_SS/experiment-design.rtf
deleted file mode 100644
index cb07f36..0000000
--- a/general/datasets/SA_M2_0405_SS/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-RNA was extracted by Rosen and colleagues and was then processed by the BIDMC Genomics Core. Labeled cRNA was generated using the Amersham Biosciences cRNA synthesis kit protocol.
-Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one sample from each sex for all BXD strains. We have not yet achieved this goal. Twenty-three of 33 strains are represented by male and female samples. The remaining 8 strains are still represented by single sex samples: BXD11 (F), BXD13 (F), BXD19 (F), BXD20 (F), BXD22 (M), BXD23 (M), BXD24 (M), BXD32 (M), C57BL/6J (M), and DBA/2J (M).
-
-Batch Structure: This data set consists of arrays processed in three batches with several reruns for the first batch. All arrays were processed using a single protocol. All data have been corrected for batch effects as described below.
-
diff --git a/general/datasets/SA_M2_0405_SS/notes.rtf b/general/datasets/SA_M2_0405_SS/notes.rtf
deleted file mode 100644
index 0af01e6..0000000
--- a/general/datasets/SA_M2_0405_SS/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ on Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004; RWW and GDR April 8, 2005.
-
diff --git a/general/datasets/SA_M2_0405_SS/platform.rtf b/general/datasets/SA_M2_0405_SS/platform.rtf
deleted file mode 100644
index 30c2f8c..0000000
--- a/general/datasets/SA_M2_0405_SS/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are near duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_0405_SS/processing.rtf b/general/datasets/SA_M2_0405_SS/processing.rtf
deleted file mode 100644
index 2e46796..0000000
--- a/general/datasets/SA_M2_0405_SS/processing.rtf
+++ /dev/null
@@ -1,17 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
-
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
- - Step 3: We computed the Z scores for each cell value.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We eliminated much of the systematic technical variance introduced by the batches at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
- - Step 7: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.
-
-
-Probe set data: The expression data were processed by Yanhua Qu (UTHSC). Probe set data were generated from the fully normalized CEL files (quantile and batch corrected) using the standard MAS 5 Tukey biweight procedure. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels. Data quality control: A total of 62 samples passed RNA quality control.
-
-Probe level QC: Log2 probe data of all arrays were inspected in DataDesk before and after quantile normalization. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients (62x61/2). Arrays with probe data that was not homogeneous when compared to any other arrays was flagged. If the correlation at the probe level was less than approximately 0.92 we deleted that array data set. Three arrays we lost during this process (BXD19_M_Str_Batch03, BXD23_F_Str_Batch03, and BXD24_F_Str_Batch03).
-
-Probe set level QC: The final normalized strain averages were evaluated for outliers. This involved counting the number of times that the probe set value for a particular strain was beyond two standard deviations of the mean of all strains. (We used the PDNN transform as our reference probe set data for this QC step.) Two strains, each represented by single arrays, generated greater than 5,000 outlier counts (10% of the number of probe sets). These two arrays generated a great number of outliers across the entire range of expression and since we do not yet have replicate arrays for either of these two strains we opted to delete them from the final April 2005 striatum data sets.
diff --git a/general/datasets/SA_M2_0405_SS/summary.rtf b/general/datasets/SA_M2_0405_SS/summary.rtf
deleted file mode 100644
index e674c86..0000000
--- a/general/datasets/SA_M2_0405_SS/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This April 2005 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of 33 lines of mice including C57BL/6J, DBA/2J, and 31 BXD recombinant inbred strains. Data were generated using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 250 brain samples (males and females) from 33 strains were used in this experiment. Samples were hybridized to a total of 59 arrays. This particular data set was processed using the Microarray Suite 5 protocol (MAS 5). To simplify comparison among different transforms, MAS5 values of each array have been adjusted to an average expression of 8 units and a standard deviation of 2 units.
diff --git a/general/datasets/SA_M2_0405_SS/tissue.rtf b/general/datasets/SA_M2_0405_SS/tissue.rtf
deleted file mode 100644
index 6503813..0000000
--- a/general/datasets/SA_M2_0405_SS/tissue.rtf
+++ /dev/null
@@ -1,440 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 20 to 25 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by GD Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25 to 30 mg of tissue) of the same strain, sex, and age was collected in one session and used to generate cRNA samples.
-
-
-The table below lists the arrays by strain, sex, sample name, and batch ID. Each array was hybridized to a pool of mRNA from 3 to 4 mice. All mice were between 55 and 62 days.
-
-
-
-
-
-
-
-
-
- | Id |
- Strain |
- Sex |
- Sample_name |
- BatchId |
-
-
- | 1 |
- C57BL/6J |
- M |
- Chip41_Batch02_B6_M_Str |
- Batch02 |
-
-
- | 2 |
- C57BL/6J |
- M |
- Chip11_Batch03_B6_M_Str |
- Batch03 |
-
-
- | 3 |
- BXD1 |
- F |
- Chip03_Batch03_BXD1_F_Str |
- Batch03 |
-
-
- | 4 |
- BXD1 |
- M |
- Chip04_Batch03_BXD1_M_Str |
- Batch03 |
-
-
- | 5 |
- BXD2 |
- F |
- Chip20_Rerun01_BXD2_F_Str |
- Rerun01 |
-
-
- | 6 |
- BXD2 |
- M |
- Chip05_Batch01_BXD2_M_Str |
- Batch01 |
-
-
- | 7 |
- BXD5 |
- F |
- Chip10_Batch03_BXD5_F_Str |
- Batch03 |
-
-
- | 8 |
- BXD5 |
- M |
- Chip12_Batch03_BXD5_M_Str |
- Batch03 |
-
-
- | 9 |
- BXD6 |
- F |
- Chip38_Batch02_BXD6_F_Str |
- Batch02 |
-
-
- | 10 |
- BXD6 |
- M |
- Chip39_Batch02_BXD6_M_Str |
- Batch02 |
-
-
- | 11 |
- BXD8 |
- F |
- Chip07_Batch03_BXD8_F_Str |
- Batch03 |
-
-
- | 12 |
- BXD8 |
- M |
- Chip02_Batch03_BXD8_M_Str |
- Batch03 |
-
-
- | 13 |
- BXD9 |
- F |
- Chip16_Batch01_BXD9_F_Str |
- Batch01 |
-
-
- | 14 |
- BXD9 |
- M |
- Chip10_Batch01_BXD9_M_Str |
- Batch01 |
-
-
- | 15 |
- BXD11 |
- F |
- Chip31_Batch02_BXD11_F_Str |
- Batch02 |
-
-
- | 16 |
- BXD12 |
- F |
- Chip11_Batch01_BXD12_F_Str |
- Batch01 |
-
-
- | 17 |
- BXD12 |
- M |
- Chip18_Batch03_BXD12_M_Str |
- Batch03 |
-
-
- | 18 |
- BXD13 |
- F |
- Chip33_Batch02_BXD13_F_Str |
- Batch02 |
-
-
- | 19 |
- BXD14 |
- F |
- Chip48_Batch02_BXD14_F_Str |
- Batch02 |
-
-
- | 20 |
- BXD14 |
- M |
- Chip47_Rerun01_BXD14_M_Str |
- Rerun01 |
-
-
- | 21 |
- BXD15 |
- F |
- Chip21_Batch01_BXD15_F_Str |
- Batch01 |
-
-
- | 22 |
- BXD15 |
- M |
- Chip13_Batch01_BXD15_M_Str |
- Batch01 |
-
-
- | 23 |
- BXD16 |
- F |
- Chip36_Batch02_BXD16_F_Str |
- Batch02 |
-
-
- | 24 |
- BXD16 |
- M |
- Chip44_Rerun01_BXD16_M_Str |
- Rerun01 |
-
-
- | 25 |
- BXD18 |
- F |
- Chip15_Batch03_BXD18_F_Str |
- Batch03 |
-
-
- | 26 |
- BXD18 |
- M |
- Chip19_Batch03_BXD18_M_Str |
- Batch03 |
-
-
- | 27 |
- BXD19 |
- F |
- Chip19_Batch01_BXD19_F_Str |
- Batch01 |
-
-
- | 28 |
- BXD20 |
- F |
- Chip14_Batch03_BXD20_F_Str |
- Batch03 |
-
-
- | 29 |
- BXD21 |
- F |
- Chip18_Batch01_BXD21_F_Str |
- Batch01 |
-
-
- | 30 |
- BXD21 |
- M |
- Chip09_Batch01_BXD21_M_Str |
- Batch01 |
-
-
- | 31 |
- BXD22 |
- M |
- Chip13_Batch03_BXD22_M_Str |
- Batch03 |
-
-
- | 32 |
- BXD23 |
- M |
- Chip01_Batch03_BXD23_M_Str |
- Batch03 |
-
-
- | 33 |
- BXD24 |
- M |
- Chip17_Batch03_BXD24_M_Str |
- Batch03 |
-
-
- | 34 |
- BXD27 |
- F |
- Chip29_Batch02_BXD27_F_Str |
- Batch02 |
-
-
- | 35 |
- BXD27 |
- M |
- Chip40_Batch02_BXD27_M_Str |
- Batch02 |
-
-
- | 36 |
- BXD28 |
- F |
- Chip06_Batch01_BXD28_F_Str |
- Batch01 |
-
-
- | 37 |
- BXD28 |
- M |
- Chip23_Batch01_BXD28_M_Str |
- Batch01 |
-
-
- | 38 |
- BXD29 |
- F |
- Chip45_Batch02_BXD29_F_Str |
- Batch02 |
-
-
- | 39 |
- BXD29 |
- M |
- Chip42_Batch02_BXD29_M_Str |
- Batch02 |
-
-
- | 40 |
- BXD31 |
- F |
- Chip14_Batch01_BXD31_F_Str |
- Batch01 |
-
-
- | 41 |
- BXD31 |
- M |
- Chip09_Batch03_BXD31_M_Str |
- Batch03 |
-
-
- | 42 |
- BXD32 |
- M |
- Chip30_Batch02_BXD32_M_Str |
- Batch02 |
-
-
- | 43 |
- BXD33 |
- F |
- Chip27_Rerun01_BXD33_F_Str |
- Rerun01 |
-
-
- | 44 |
- BXD33 |
- M |
- Chip34_Batch02_BXD33_M_Str |
- Batch02 |
-
-
- | 45 |
- BXD34 |
- F |
- Chip03_Batch01_BXD34_F_Str |
- Batch01 |
-
-
- | 46 |
- BXD34 |
- M |
- Chip07_Batch01_BXD34_M_Str |
- Batch01 |
-
-
- | 47 |
- BXD36 |
- F |
- Chip22_Batch03_BXD36_F_Str |
- Batch03 |
-
-
- | 48 |
- BXD36 |
- M |
- Chip24_Batch03_BXD36_M_Str |
- Batch03 |
-
-
- | 49 |
- BXD38 |
- F |
- Chip17_Batch01_BXD38_F_Str |
- Batch01 |
-
-
- | 50 |
- BXD38 |
- M |
- Chip24_Batch01_BXD38_M_Str |
- Batch01 |
-
-
- | 51 |
- BXD39 |
- M |
- Chip20_Batch03_BXD39_M_Str |
- Batch03 |
-
-
- | 52 |
- BXD39 |
- F |
- Chip23_Batch03_BXD39_F_Str |
- Batch03 |
-
-
- | 53 |
- BXD39 |
- M |
- Chip43_Rerun01_BXD39_M_Str |
- Rerun01 |
-
-
- | 54 |
- BXD40 |
- F |
- Chip08_Rerun01_BXD40_F_Str |
- Rerun01 |
-
-
- | 55 |
- BXD40 |
- M |
- Chip22_Batch01_BXD40_M_Str |
- Batch01 |
-
-
- | 56 |
- BXD42 |
- F |
- Chip35_Batch02_BXD42_F_Str |
- Batch02 |
-
-
- | 57 |
- BXD42 |
- M |
- Chip32_Batch02_BXD42_M_Str |
- Batch02 |
-
-
- | 58 |
- DBA/2J |
- M |
- Chip02_Batch01_D2_M_Str |
- Batch01 |
-
-
- | 59 |
- DBA/2J |
- M |
- Chip05_Batch03_D2_M_Str |
- Batch03 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SA_M2_0905_M/acknowledgment.rtf b/general/datasets/SA_M2_0905_M/acknowledgment.rtf
deleted file mode 100644
index e7f05c1..0000000
--- a/general/datasets/SA_M2_0905_M/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
-
diff --git a/general/datasets/SA_M2_0905_M/cases.rtf b/general/datasets/SA_M2_0905_M/cases.rtf
deleted file mode 100644
index 4f69ca9..0000000
--- a/general/datasets/SA_M2_0905_M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/SA_M2_0905_M/notes.rtf b/general/datasets/SA_M2_0905_M/notes.rtf
deleted file mode 100644
index 7fafba3..0000000
--- a/general/datasets/SA_M2_0905_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004, EJC June 21, 2005.
-
diff --git a/general/datasets/SA_M2_0905_M/platform.rtf b/general/datasets/SA_M2_0905_M/platform.rtf
deleted file mode 100644
index f0ee528..0000000
--- a/general/datasets/SA_M2_0905_M/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/SA_M2_0905_M/processing.rtf b/general/datasets/SA_M2_0905_M/processing.rtf
deleted file mode 100644
index 8a23d84..0000000
--- a/general/datasets/SA_M2_0905_M/processing.rtf
+++ /dev/null
@@ -1,26 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-
-About the marker set:
-
-
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
-
diff --git a/general/datasets/SA_M2_0905_M/summary.rtf b/general/datasets/SA_M2_0905_M/summary.rtf
deleted file mode 100644
index 6f477fe..0000000
--- a/general/datasets/SA_M2_0905_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/SA_M2_0905_M/tissue.rtf b/general/datasets/SA_M2_0905_M/tissue.rtf
deleted file mode 100644
index ef85488..0000000
--- a/general/datasets/SA_M2_0905_M/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
diff --git a/general/datasets/SA_M2_0905_P/acknowledgment.rtf b/general/datasets/SA_M2_0905_P/acknowledgment.rtf
deleted file mode 100644
index e7f05c1..0000000
--- a/general/datasets/SA_M2_0905_P/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
-
diff --git a/general/datasets/SA_M2_0905_P/cases.rtf b/general/datasets/SA_M2_0905_P/cases.rtf
deleted file mode 100644
index 4f69ca9..0000000
--- a/general/datasets/SA_M2_0905_P/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/SA_M2_0905_P/notes.rtf b/general/datasets/SA_M2_0905_P/notes.rtf
deleted file mode 100644
index 7fafba3..0000000
--- a/general/datasets/SA_M2_0905_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004, EJC June 21, 2005.
-
diff --git a/general/datasets/SA_M2_0905_P/platform.rtf b/general/datasets/SA_M2_0905_P/platform.rtf
deleted file mode 100644
index f0ee528..0000000
--- a/general/datasets/SA_M2_0905_P/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
- |
-
- H4
- |
-
- F
- |
-
-
- |
- 5
- |
-
- 6
- |
-
- FL14
- |
-
- L
- |
-
- K2
- |
-
- F
- |
-
-
- |
- 6
- |
-
- 10
- |
-
- FL15
- |
-
- L
- |
-
- Q2
- |
-
- F
- |
-
-
- |
- 7
- |
-
- 52
- |
-
- FL2
- |
-
- L
- |
-
- E1
- |
-
- F
- |
-
-
- |
- 8
- |
-
- 53
- |
-
- FL3
- |
-
- L
- |
-
- E2
- |
-
- F
- |
-
-
- |
- 9
- |
-
- 42
- |
-
- FL4
- |
-
- L
- |
-
- E3
- |
-
- F
- |
-
-
- |
- 10
- |
-
- 31
- |
-
- FL5
- |
-
- L
- |
-
- E4
- |
-
- F
- |
-
-
- |
- 11
- |
-
- 14
- |
-
- FL6
- |
-
- L
- |
-
- F1
- |
-
- M
- |
-
-
- |
- 12
- |
-
- 48
- |
-
- FL7
- |
-
- L
- |
-
- F2
- |
-
- F
- |
-
-
- |
- 13
- |
-
- 60
- |
-
- FL8
- |
-
- L
- |
-
- F3
- |
-
- M
- |
-
-
- |
- 14
- |
-
- 54
- |
-
- FL9
- |
-
- L
- |
-
- F4
- |
-
- F
- |
-
-
- |
- 15
- |
-
- 35
- |
-
- FR10
- |
-
- R
- |
-
- K3
- |
-
- F
- |
-
-
- |
- 16
- |
-
- 11
- |
-
- FR11
- |
-
- R
- |
-
- O1
- |
-
- F
- |
-
-
- |
- 17
- |
-
- 21
- |
-
- FR12
- |
-
- R
- |
-
- O2
- |
-
- F
- |
-
-
- |
- 18
- |
-
- 23
- |
-
- FR13
- |
-
- R
- |
-
- Q1
- |
-
- F
- |
-
-
- |
- 19
- |
-
- 15
- |
-
- FR14
- |
-
- R
- |
-
- Q3
- |
-
- F
- |
-
-
- |
- 20
- |
-
- 4
- |
-
- FR15
- |
-
- R
- |
-
- Q4
- |
-
- F
- |
-
-
- |
- 21
- |
-
- 41
- |
-
- FR2
- |
-
- R
- |
-
- A2
- |
-
- F
- |
-
-
- |
- 22
- |
-
- 44
- |
-
- FR3
- |
-
- R
- |
-
- A3
- |
-
- F
- |
-
-
- |
- 23
- |
-
- 37
- |
-
- FR4
- |
-
- R
- |
-
- C1
- |
-
- F
- |
-
-
- |
- 24
- |
-
- 8
- |
-
- FR5
- |
-
- R
- |
-
- C2
- |
-
- F
- |
-
-
- |
- 25
- |
-
- 19
- |
-
- FR6
- |
-
- R
- |
-
- C3
- |
-
- F
- |
-
-
- |
- 26
- |
-
- 40
- |
-
- FR7
- |
-
- R
- |
-
- C4
- |
-
- F
- |
-
-
- |
- 27
- |
-
- 62
- |
-
- FR8
- |
-
- R
- |
-
- D2
- |
-
- M
- |
-
-
- |
- 28
- |
-
- 39
- |
-
- FR9
- |
-
- R
- |
-
- D3
- |
-
- F
- |
-
-
- |
- 29
- |
-
- 13
- |
-
- ML1
- |
-
- L
- |
-
- B1
- |
-
- M
- |
-
-
- |
- 30
- |
-
- 22
- |
-
- ML10
- |
-
- L
- |
-
- L2
- |
-
- M
- |
-
-
- |
- 31
- |
-
- 38
- |
-
- ML11
- |
-
- L
- |
-
- L4
- |
-
- M
- |
-
-
- |
- 32
- |
-
- 43
- |
-
- ML12
- |
-
- L
- |
-
- M1
- |
-
- M
- |
-
-
- |
- 33
- |
-
- 58
- |
-
- ML13
- |
-
- L
- |
-
- N2
- |
-
- M
- |
-
-
- |
- 34
- |
-
- 7
- |
-
- ML14
- |
-
- L
- |
-
- R1
- |
-
- M
- |
-
-
- |
- 35
- |
-
- 30
- |
-
- ML15
- |
-
- L
- |
-
- R3
- |
-
- M
- |
-
-
- |
- 36
- |
-
- 46
- |
-
- ML3
- |
-
- L
- |
-
- G1
- |
-
- M
- |
-
-
- |
- 37
- |
-
- 57
- |
-
- ML4
- |
-
- L
- |
-
- G2
- |
-
- M
- |
-
-
- |
- 38
- |
-
- 51
- |
-
- ML5
- |
-
- L
- |
-
- I1
- |
-
- M
- |
-
-
- |
- 39
- |
-
- 27
- |
-
- ML6
- |
-
- L
- |
-
- I2
- |
-
- M
- |
-
-
- |
- 40
- |
-
- 50
- |
-
- ML7
- |
-
- L
- |
-
- J2
- |
-
- M
- |
-
-
- |
- 41
- |
-
- 16
- |
-
- FL1
- |
-
- L
- |
-
- O2
- |
-
- M
- |
-
-
- |
- 42
- |
-
- 3
- |
-
- ML9
- |
-
- L
- |
-
- L1
- |
-
- M
- |
-
-
- |
- 43
- |
-
- 47
- |
-
- MR10
- |
-
- R
- |
-
- R2
- |
-
- M
- |
-
-
- |
- 44
- |
-
- 56
- |
-
- MR11
- |
-
- R
- |
-
- S1
- |
-
- M
- |
-
-
- |
- 45
- |
-
- 1
- |
-
- MR12
- |
-
- R
- |
-
- S2
- |
-
- M
- |
-
-
- |
- 46
- |
-
- 55
- |
-
- MR13
- |
-
- R
- |
-
- T1
- |
-
- M
- |
-
-
- |
- 47
- |
-
- 34
- |
-
- MR14
- |
-
- R
- |
-
- U1
- |
-
- M
- |
-
-
- |
- 48
- |
-
- 25
- |
-
- MR15
- |
-
- R
- |
-
- U2
- |
-
- M
- |
-
-
- |
- 49
- |
-
- 59
- |
-
- MR2
- |
-
- R
- |
-
- J1
- |
-
- M
- |
-
-
- |
- 50
- |
-
- 32
- |
-
- MR3
- |
-
- R
- |
-
- M2
- |
-
- M
- |
-
-
- |
- 51
- |
-
- 24
- |
-
- MR4
- |
-
- R
- |
-
- M3
- |
-
- M
- |
-
-
- |
- 52
- |
-
- 12
- |
-
- MR5
- |
-
- R
- |
-
- M4
- |
-
- M
- |
-
-
- |
- 53
- |
-
- 9
- |
-
- MR6
- |
-
- R
- |
-
- N1
- |
-
- M
- |
-
-
- |
- 54
- |
-
- 36
- |
-
- MR7
- |
-
- R
- |
-
- N3
- |
-
- M
- |
-
-
- |
- 55
- |
-
- 28
- |
-
- MR8
- |
-
- R
- |
-
- P1
- |
-
- M
- |
-
-
- |
- 56
- |
-
- 33
- |
-
- MR9
- |
-
- R
- |
-
- P2
- |
-
- M
- |
-
-
-
- |
-
-
-
diff --git a/general/datasets/SA_M2_0905_P/processing.rtf b/general/datasets/SA_M2_0905_P/processing.rtf
deleted file mode 100644
index 8a23d84..0000000
--- a/general/datasets/SA_M2_0905_P/processing.rtf
+++ /dev/null
@@ -1,26 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-
-About the marker set:
-
-
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
-
diff --git a/general/datasets/SA_M2_0905_P/summary.rtf b/general/datasets/SA_M2_0905_P/summary.rtf
deleted file mode 100644
index 6f477fe..0000000
--- a/general/datasets/SA_M2_0905_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/SA_M2_0905_P/tissue.rtf b/general/datasets/SA_M2_0905_P/tissue.rtf
deleted file mode 100644
index ef85488..0000000
--- a/general/datasets/SA_M2_0905_P/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
diff --git a/general/datasets/SA_M2_0905_R/acknowledgment.rtf b/general/datasets/SA_M2_0905_R/acknowledgment.rtf
deleted file mode 100644
index e7f05c1..0000000
--- a/general/datasets/SA_M2_0905_R/acknowledgment.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-This project was supported by two Department of Veterans Affairs Merit Review Awards (to JK Belknap and R Hitzemann, respectively), AA10760 (Portland Alcohol Research Center), AA06243, AA13484, AA11034, DA05228 and MH51372.
-
-Please contact either John Belknap or Robert Hitzemann at the Dept. of Behavioral Neuroscience, Oregon Health & Science University (L470), or Research Service (R&D5), Portland VA Medical Ctr., Portland, OR 97239 USA.
-
diff --git a/general/datasets/SA_M2_0905_R/cases.rtf b/general/datasets/SA_M2_0905_R/cases.rtf
deleted file mode 100644
index 4f69ca9..0000000
--- a/general/datasets/SA_M2_0905_R/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Fifty-six B6D2F2 samples, each taken from a single brain hemisphere from an individual mouse, were assayed using 56 M430A&B Affymetrix short oligomer microarrays. [The remaining hemisphere will be used later for an anaysis of specific brain regions.] Each array ID (see table below) includes a three letter code; the first letter usually denotes sex of the case (note that we have made a few corrections and there are therefore several sex-discordant IDs), the second letter denotes the hemisphere (R or L), and the third letter is the mouse number within each cell. The F2 mice were experimentally naive, born within a 3-day period from second litters of each dam, and housed at weaning (20- to 24-days-of-age) in like-sex groups of 3 to 4 mice for females and 2 to 3 mice for males in standard mouse shoebox cages within Thoren racks. All 56 F2 mice were killed at 77 to 79 days-of-age by cervical dislocation on December 17, 2003. The brains were immediately split at the midline and then quickly frozen on dry ice. The brains were stored for about two weeks at -80 degrees C until further use.
-
-The F2 was derived as follows: C57BL/6J (B6) and DBA/2J (D2) breeders were obtained from The Jackson Laboratory, and two generations later their progeny were crossed to produce B6D2F1 and D2B6F1 hybrid at the Portland VA Veterinary Medical Unit (AAALAC approved). The reciprocal F1s were mated to create an F2 population with both progenitor X and Y chromosomes about equally represented.
diff --git a/general/datasets/SA_M2_0905_R/notes.rtf b/general/datasets/SA_M2_0905_R/notes.rtf
deleted file mode 100644
index 7fafba3..0000000
--- a/general/datasets/SA_M2_0905_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file was originally generated by John Belknap, March 2004. Updated by RWW, October 31, 2004, EJC June 21, 2005.
-
diff --git a/general/datasets/SA_M2_0905_R/platform.rtf b/general/datasets/SA_M2_0905_R/platform.rtf
deleted file mode 100644
index f0ee528..0000000
--- a/general/datasets/SA_M2_0905_R/platform.rtf
+++ /dev/null
@@ -1,1154 +0,0 @@
-All 56 430A&B arrays used in this project were purchased at one time and had the same Affymetrix lot number. The table below lists the arrays by Case ID, Array ID, Side, Cage ID and Sex.
-
-
-
-
-
-
-
-
- |
- Order
- |
-
- CaseID
- |
-
- ArrayID
- |
-
- Side
- |
-
- CageID
- |
-
- Sex
- |
-
-
- |
- 1
- |
-
- 20
- |
-
- FL10
- |
-
- L
- |
-
- H1
- |
-
- F
- |
-
-
- |
- 2
- |
-
- 2
- |
-
- FL11
- |
-
- L
- |
-
- H2
- |
-
- F
- |
-
-
- |
- 3
- |
-
- 5
- |
-
- FL12
- |
-
- L
- |
-
- H3
- |
-
- F
- |
-
-
- |
- 4
- |
-
- 63
- |
-
- FL13
- |
-
- L
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-
- H4
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-
- F
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-
-
- |
- 5
- |
-
- 6
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- FL14
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- K2
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-
-
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- 6
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-
- 10
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- FL15
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-
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- 52
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- 8
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- 53
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- FL3
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- L
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-
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- 9
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- 42
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- FL4
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- E3
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- F
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-
-
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- 10
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- 31
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-
- FL5
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- L
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- E4
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- F
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-
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- 11
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-
- 14
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- FL6
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- L
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- F1
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-
- M
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-
-
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- 12
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- 48
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- FL7
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-
- L
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- F2
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-
- F
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-
-
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- 13
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-
- 60
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-
- FL8
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-
- L
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- F3
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-
- M
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-
-
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- 14
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-
- 54
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- FL9
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-
- L
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- F4
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- F
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-
-
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- 15
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-
- 35
- |
-
- FR10
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-
- R
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-
- K3
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- F
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-
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- 16
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-
- 11
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-
- FR11
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-
- R
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- O1
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-
- F
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-
-
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- 17
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-
- 21
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- FR12
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- R
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- O2
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-
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- 18
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- 23
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- FR13
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-
- R
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-
- Q1
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- F
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-
-
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- 19
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-
- 15
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- FR14
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- R
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- Q3
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-
-
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- 20
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-
- 4
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-
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- 21
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- 41
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- A2
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-
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- 22
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- 44
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- FR3
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- 23
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- 37
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- 8
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- 25
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- 19
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- FR6
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- 26
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- 27
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- 62
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- 29
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- 13
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- ML1
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- 30
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- 22
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- ML10
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- 31
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- 32
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- 33
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- 58
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- ML13
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- N2
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- 34
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- 7
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- 35
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- 30
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- ML15
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-
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- 36
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- 46
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- ML3
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- G1
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-
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- 37
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- 57
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- ML4
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-
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- 38
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- ML5
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- I1
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-
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- 39
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- 27
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- ML6
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- L
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- I2
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-
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- 40
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- 50
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- ML7
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-
- L
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-
- J2
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-
- M
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-
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- 41
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-
- 16
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-
- FL1
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-
- L
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- O2
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- M
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-
-
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- 42
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-
- 3
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-
- ML9
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-
-
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- 43
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- 47
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- MR10
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-
- R
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- R2
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-
- M
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-
-
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- 44
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-
- 56
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- MR11
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-
- R
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- S1
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-
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- 45
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-
- 1
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-
- MR12
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-
- R
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- S2
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-
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- 46
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- 55
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- MR13
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- T1
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- M
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-
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- 47
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-
- 34
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- MR14
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- 48
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- 25
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- MR15
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- U2
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-
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- 49
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- 59
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- MR2
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- 50
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-
- 32
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- MR3
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- 51
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- 24
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- MR4
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- M3
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-
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- 52
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-
- 12
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- MR5
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- 53
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- 9
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- MR6
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- N1
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-
- M
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-
-
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- 54
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-
- 36
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- MR7
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- 55
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- 28
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- MR8
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- R
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-
- P1
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-
- M
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-
-
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- 56
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-
- 33
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-
- MR9
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-
- R
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-
- P2
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-
- M
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-
-
-
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-
-
-
diff --git a/general/datasets/SA_M2_0905_R/processing.rtf b/general/datasets/SA_M2_0905_R/processing.rtf
deleted file mode 100644
index 8a23d84..0000000
--- a/general/datasets/SA_M2_0905_R/processing.rtf
+++ /dev/null
@@ -1,26 +0,0 @@
-Probe (cell) level data from the CEL file: These CEL values produced by GCOS are the 75% quantiles from a set of 91 pixel values per cell. Probe values were processed as follows:
-
- - Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
- - Step 2: We took the log base 2 of each probe signal.
- - Step 3: We computed the Z scores for each probe signal.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6a: The 430A and 430B arrays include a set of 100 shared probe sets (2200 probes) that have identical sequences. These probes provide a way to calibrate expression of the A and B arrays to a common scale. The absolute mean expression on the 430B array is almost invariably lower than that on the 430A array. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression corrections to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a very small offset. The result of this step is that the mean of the 430A GeneChip expression is fixed at a value of 8, whereas that of the 430B chip is typically 7. Thus average of A and B arrays is approximately 7.5.
- - Step 6b: We recenter the whole set of 430A and B transcripts to a mean of 8 and a standard deviation of 2. This involves reapplying Steps 3 through 5 above but now using the entire set of probes and probe sets from a merged 430A and B data set.
-
-
-Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
-
-
-About the marker set:
-
-
-The 56 mice were each genotyped at 309 MIT microsatellite markers distributed across the genome, including the Y chromosome. The genotyping error check routine (Lincoln and Lander, 1992) implemented within R/qtl (Broman et al., 2003) showed no likely errors at p <.01 probability. Initial genotypes were generated at OHSU. Approximately 200 genotypes were generated at UTHSC by Jing Gu and Shuhua Qi.
-
-
-About the chromosome and megabase position values:
-
-The chromosomal locations of M430A and M430B probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released. We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).
-
-
-
diff --git a/general/datasets/SA_M2_0905_R/summary.rtf b/general/datasets/SA_M2_0905_R/summary.rtf
deleted file mode 100644
index 6f477fe..0000000
--- a/general/datasets/SA_M2_0905_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This August 2005 data freeze provides estimate of mRNA expression in adult brains of F2 intercross mice (C57BL/6J x DBA/2J F2) measured using Affymetrix M430A and M430B microarray pairs. Data were generated at The Oregon Health Sciences University (OHSU) in Portland, Oregon, by John Belknap and Robert Hitzemann. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.
diff --git a/general/datasets/SA_M2_0905_R/tissue.rtf b/general/datasets/SA_M2_0905_R/tissue.rtf
deleted file mode 100644
index ef85488..0000000
--- a/general/datasets/SA_M2_0905_R/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain samples were from 31 male and 25 females and between 28 right and 28 left hemispheres distributed with good balance across the two sexes. The tissue arrayed included the forebrain, midbrain, one olfactory bulb, the cerebellum; and the rostral part of the medulla. The medulla was trimmed transversely at the caudal aspect of the cerebellum. The sagittal cut was made from a dorsal to ventral direction. (Note that several of the other brain transcriptome databases do not include olfactory bulb or cerebellum.) Total RNA was isolated with TRIZOL Reagent (Life Technologies Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer’s protocol. The extracted RNA was then purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for purity; only samples with an A260/280 ratio greater than 1.8 were used. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. Samples containing at least 10 micrograms of total RNA were sent to the OHSU Gene Microarray Shared Resource facility for analysis. The procedures used at the facility precisely follow the manufacturer’s specifications. Details can be found at http://www.ohsu.edu/gmsr/amc. Following labeling, all samples were hybridized to the GeneChip Test3 array for quality control. If target performance did not meet recommended thresholds, the sample would have been discarded. All labeled samples passed the threshold and were hybridized to the 430A and 430B array pairs.
diff --git a/general/datasets/SA_M2_1104_G/acknowledgment.rtf b/general/datasets/SA_M2_1104_G/acknowledgment.rtf
deleted file mode 100644
index 909ea42..0000000
--- a/general/datasets/SA_M2_1104_G/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_1104_G/cases.rtf b/general/datasets/SA_M2_1104_G/cases.rtf
deleted file mode 100644
index 63bba4c..0000000
--- a/general/datasets/SA_M2_1104_G/cases.rtf
+++ /dev/null
@@ -1,184 +0,0 @@
-
-This data set includes estimate of gene expression for 24 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), and 22 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period (see the WebQTL BXD Published Phenotypes database). A significant advantage of this RI set is that both parental strains (B6 and D2) have been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
-
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 to 4 mice.
-
-
-
-
-Select the strain name in the table above to review details about the specific cases and to view the array quality control image processed using the PerfectMatch program by Li Zhang.
-
diff --git a/general/datasets/SA_M2_1104_G/experiment-design.rtf b/general/datasets/SA_M2_1104_G/experiment-design.rtf
deleted file mode 100644
index 1b0f0b3..0000000
--- a/general/datasets/SA_M2_1104_G/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 5 to 10 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25-30 mg of tissue from 6 striata) of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Rought 90 to 95% of all cells in the striatum are medium spiny neurons (Gerfen, 1992, for a review of the structure and function of the neostriatum).
-
-mRNA processing: We used the Amersham Biosciences cRNA synthesis kit protocol.
-
diff --git a/general/datasets/SA_M2_1104_G/notes.rtf b/general/datasets/SA_M2_1104_G/notes.rtf
deleted file mode 100644
index e37761f..0000000
--- a/general/datasets/SA_M2_1104_G/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004.
-
diff --git a/general/datasets/SA_M2_1104_G/platform.rtf b/general/datasets/SA_M2_1104_G/platform.rtf
deleted file mode 100644
index bd1a9e0..0000000
--- a/general/datasets/SA_M2_1104_G/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are actually duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_1104_G/processing.rtf b/general/datasets/SA_M2_1104_G/processing.rtf
deleted file mode 100644
index 5473eda..0000000
--- a/general/datasets/SA_M2_1104_G/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix CEL files obtained from the BIDMC Genomics Core were processed as follows.
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We plotted these modified Z score probe level expression estimates in DataDesk. Male-female scatterplots of the probe signals were compared strain by strain to highlight poor array data sets. A total of 36 arrays passed this stringent quality control step.
- - Step 7: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: The expression values were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/SA_M2_1104_G/summary.rtf b/general/datasets/SA_M2_1104_G/summary.rtf
deleted file mode 100644
index 427768f..0000000
--- a/general/datasets/SA_M2_1104_G/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This November 2004 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of BXD recombinant inbred mice measured using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays. Data were generated at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 125 brain samples from 24 strains were used in this initial experiment. Data were processed using the Affymetrix Microarray Suite 5 (MAS 5) transform. To simplify comparison among Nov04 data sets, values of each array have been log2 transformed and adjusted to an average expression of 8 units.
diff --git a/general/datasets/SA_M2_1104_M/acknowledgment.rtf b/general/datasets/SA_M2_1104_M/acknowledgment.rtf
deleted file mode 100644
index 909ea42..0000000
--- a/general/datasets/SA_M2_1104_M/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_1104_M/cases.rtf b/general/datasets/SA_M2_1104_M/cases.rtf
deleted file mode 100644
index 63bba4c..0000000
--- a/general/datasets/SA_M2_1104_M/cases.rtf
+++ /dev/null
@@ -1,184 +0,0 @@
-
-This data set includes estimate of gene expression for 24 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), and 22 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period (see the WebQTL BXD Published Phenotypes database). A significant advantage of this RI set is that both parental strains (B6 and D2) have been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
-
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 to 4 mice.
-
-
-
-
-Select the strain name in the table above to review details about the specific cases and to view the array quality control image processed using the PerfectMatch program by Li Zhang.
-
diff --git a/general/datasets/SA_M2_1104_M/experiment-design.rtf b/general/datasets/SA_M2_1104_M/experiment-design.rtf
deleted file mode 100644
index 1b0f0b3..0000000
--- a/general/datasets/SA_M2_1104_M/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 5 to 10 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25-30 mg of tissue from 6 striata) of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Rought 90 to 95% of all cells in the striatum are medium spiny neurons (Gerfen, 1992, for a review of the structure and function of the neostriatum).
-
-mRNA processing: We used the Amersham Biosciences cRNA synthesis kit protocol.
-
diff --git a/general/datasets/SA_M2_1104_M/notes.rtf b/general/datasets/SA_M2_1104_M/notes.rtf
deleted file mode 100644
index e37761f..0000000
--- a/general/datasets/SA_M2_1104_M/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004.
-
diff --git a/general/datasets/SA_M2_1104_M/platform.rtf b/general/datasets/SA_M2_1104_M/platform.rtf
deleted file mode 100644
index bd1a9e0..0000000
--- a/general/datasets/SA_M2_1104_M/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are actually duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_1104_M/processing.rtf b/general/datasets/SA_M2_1104_M/processing.rtf
deleted file mode 100644
index 5473eda..0000000
--- a/general/datasets/SA_M2_1104_M/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix CEL files obtained from the BIDMC Genomics Core were processed as follows.
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We plotted these modified Z score probe level expression estimates in DataDesk. Male-female scatterplots of the probe signals were compared strain by strain to highlight poor array data sets. A total of 36 arrays passed this stringent quality control step.
- - Step 7: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: The expression values were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/SA_M2_1104_M/summary.rtf b/general/datasets/SA_M2_1104_M/summary.rtf
deleted file mode 100644
index 427768f..0000000
--- a/general/datasets/SA_M2_1104_M/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This November 2004 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of BXD recombinant inbred mice measured using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays. Data were generated at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 125 brain samples from 24 strains were used in this initial experiment. Data were processed using the Affymetrix Microarray Suite 5 (MAS 5) transform. To simplify comparison among Nov04 data sets, values of each array have been log2 transformed and adjusted to an average expression of 8 units.
diff --git a/general/datasets/SA_M2_1104_P/acknowledgment.rtf b/general/datasets/SA_M2_1104_P/acknowledgment.rtf
deleted file mode 100644
index 909ea42..0000000
--- a/general/datasets/SA_M2_1104_P/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_1104_P/cases.rtf b/general/datasets/SA_M2_1104_P/cases.rtf
deleted file mode 100644
index 63bba4c..0000000
--- a/general/datasets/SA_M2_1104_P/cases.rtf
+++ /dev/null
@@ -1,184 +0,0 @@
-
-This data set includes estimate of gene expression for 24 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), and 22 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period (see the WebQTL BXD Published Phenotypes database). A significant advantage of this RI set is that both parental strains (B6 and D2) have been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
-
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 to 4 mice.
-
-
-
-
-Select the strain name in the table above to review details about the specific cases and to view the array quality control image processed using the PerfectMatch program by Li Zhang.
-
diff --git a/general/datasets/SA_M2_1104_P/experiment-design.rtf b/general/datasets/SA_M2_1104_P/experiment-design.rtf
deleted file mode 100644
index 1b0f0b3..0000000
--- a/general/datasets/SA_M2_1104_P/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 5 to 10 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25-30 mg of tissue from 6 striata) of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Rought 90 to 95% of all cells in the striatum are medium spiny neurons (Gerfen, 1992, for a review of the structure and function of the neostriatum).
-
-mRNA processing: We used the Amersham Biosciences cRNA synthesis kit protocol.
-
diff --git a/general/datasets/SA_M2_1104_P/notes.rtf b/general/datasets/SA_M2_1104_P/notes.rtf
deleted file mode 100644
index e37761f..0000000
--- a/general/datasets/SA_M2_1104_P/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004.
-
diff --git a/general/datasets/SA_M2_1104_P/platform.rtf b/general/datasets/SA_M2_1104_P/platform.rtf
deleted file mode 100644
index bd1a9e0..0000000
--- a/general/datasets/SA_M2_1104_P/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are actually duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_1104_P/processing.rtf b/general/datasets/SA_M2_1104_P/processing.rtf
deleted file mode 100644
index 5473eda..0000000
--- a/general/datasets/SA_M2_1104_P/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix CEL files obtained from the BIDMC Genomics Core were processed as follows.
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We plotted these modified Z score probe level expression estimates in DataDesk. Male-female scatterplots of the probe signals were compared strain by strain to highlight poor array data sets. A total of 36 arrays passed this stringent quality control step.
- - Step 7: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: The expression values were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/SA_M2_1104_P/summary.rtf b/general/datasets/SA_M2_1104_P/summary.rtf
deleted file mode 100644
index 427768f..0000000
--- a/general/datasets/SA_M2_1104_P/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This November 2004 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of BXD recombinant inbred mice measured using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays. Data were generated at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 125 brain samples from 24 strains were used in this initial experiment. Data were processed using the Affymetrix Microarray Suite 5 (MAS 5) transform. To simplify comparison among Nov04 data sets, values of each array have been log2 transformed and adjusted to an average expression of 8 units.
diff --git a/general/datasets/SA_M2_1104_R/acknowledgment.rtf b/general/datasets/SA_M2_1104_R/acknowledgment.rtf
deleted file mode 100644
index 909ea42..0000000
--- a/general/datasets/SA_M2_1104_R/acknowledgment.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Data were generated with funds to Glenn Rosen from P20 MH62009 (see below for specifics). Samples and arrays were processed by the Genomics Core at Beth Israel Deaconess Medical Center by Towia Libermann and colleagues.
-
diff --git a/general/datasets/SA_M2_1104_R/cases.rtf b/general/datasets/SA_M2_1104_R/cases.rtf
deleted file mode 100644
index 63bba4c..0000000
--- a/general/datasets/SA_M2_1104_R/cases.rtf
+++ /dev/null
@@ -1,184 +0,0 @@
-
-This data set includes estimate of gene expression for 24 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), and 22 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period (see the WebQTL BXD Published Phenotypes database). A significant advantage of this RI set is that both parental strains (B6 and D2) have been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.
-
-BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine.
-
-
-The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 to 4 mice.
-
-
-
-
-Select the strain name in the table above to review details about the specific cases and to view the array quality control image processed using the PerfectMatch program by Li Zhang.
-
diff --git a/general/datasets/SA_M2_1104_R/experiment-design.rtf b/general/datasets/SA_M2_1104_R/experiment-design.rtf
deleted file mode 100644
index 1b0f0b3..0000000
--- a/general/datasets/SA_M2_1104_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Animals were obtained from The Jackson Laboratory and housed for several weeks at BIDMC until they reached ~2 months of age (range from 55 to 62 days). Mice were killed by cervical dislocation and brains were removed and placed in RNAlater for 5 to 10 minutes prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both striata were dissected using a medial approach by Rosen that typically yields 5 to 7 mg of tissue per side. The purity of this dissection has been validated by an analysis of acetylcholinestase activity. A pool of dissected tissue from 3 or 4 adults (approximately 25-30 mg of tissue from 6 striata) of the same strain, sex, and age was collected in one session and used to generate cRNA samples. Rought 90 to 95% of all cells in the striatum are medium spiny neurons (Gerfen, 1992, for a review of the structure and function of the neostriatum).
-
-mRNA processing: We used the Amersham Biosciences cRNA synthesis kit protocol.
-
diff --git a/general/datasets/SA_M2_1104_R/notes.rtf b/general/datasets/SA_M2_1104_R/notes.rtf
deleted file mode 100644
index e37761f..0000000
--- a/general/datasets/SA_M2_1104_R/notes.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This text file originally generated by GDR, RWW, and YHQ Nov 2004. Updated by RWW Nov 17, 2004; GDR and RWW, Dec 23, 2004.
-
diff --git a/general/datasets/SA_M2_1104_R/platform.rtf b/general/datasets/SA_M2_1104_R/platform.rtf
deleted file mode 100644
index bd1a9e0..0000000
--- a/general/datasets/SA_M2_1104_R/platform.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are actually duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The array nominally contains the same probe sequence as the 430A and B series. However, we have found that roughy 75000 probes differ from those on A and B arrays.
-
diff --git a/general/datasets/SA_M2_1104_R/processing.rtf b/general/datasets/SA_M2_1104_R/processing.rtf
deleted file mode 100644
index 5473eda..0000000
--- a/general/datasets/SA_M2_1104_R/processing.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Affymetrix CEL files obtained from the BIDMC Genomics Core were processed as follows.
-
- - Step 1: We added an offset of 1 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
- - Step 2: We took the log base 2 of each cell.
- - Step 3: We computed the Z score for each cell.
- - Step 4: We multiplied all Z scores by 2.
- - Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
- - Step 6: We plotted these modified Z score probe level expression estimates in DataDesk. Male-female scatterplots of the probe signals were compared strain by strain to highlight poor array data sets. A total of 36 arrays passed this stringent quality control step.
- - Step 7: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file.
-
-Probe set data from the CHP file: The expression values were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.
diff --git a/general/datasets/SA_M2_1104_R/summary.rtf b/general/datasets/SA_M2_1104_R/summary.rtf
deleted file mode 100644
index 427768f..0000000
--- a/general/datasets/SA_M2_1104_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This November 2004 data freeze provides estimates of mRNA expression in the striatum (caudate nucleus of the forebrain) of BXD recombinant inbred mice measured using Affymetrix Mouse Genome 430 2.0 short oligomer microarrays. Data were generated at Beth Israel Deaconess Medical Center (BIDMC, Boston MA) by Glenn D. Rosen with the support of a Human Brain Project (HBP) grant. Approximately 125 brain samples from 24 strains were used in this initial experiment. Data were processed using the Affymetrix Microarray Suite 5 (MAS 5) transform. To simplify comparison among Nov04 data sets, values of each array have been log2 transformed and adjusted to an average expression of 8 units.
diff --git a/general/datasets/STSPL_1107_R/summary.rtf b/general/datasets/STSPL_1107_R/summary.rtf
deleted file mode 100644
index b74d6b2..0000000
--- a/general/datasets/STSPL_1107_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 43, Name: Stuart Spleen M430v2 (Nov07)
\ No newline at end of file
diff --git a/general/datasets/SUH_Liv_RMA_0611/processing.rtf b/general/datasets/SUH_Liv_RMA_0611/processing.rtf
deleted file mode 100644
index ca7e79b..0000000
--- a/general/datasets/SUH_Liv_RMA_0611/processing.rtf
+++ /dev/null
@@ -1,660 +0,0 @@
-QC Results: This data set consists of expression data for 33 strains. A total of 166 probe sets are associated with LOD scores above 10 and the highest linkage score of 22 for Rpl3 (probe set 10430669). Strain distribution patterns of eQTLs with a Mendelian expression pattern match those of their closest markers perfectly, verifying that there are no errors of strain assignment in this data set.
-
-Analysis of XIST probe set 1060617 confirms that most strains are purely female. However, only males were available for BXD1 and BXD6. BXD28 and BXD33 data are based on the average of two female samples and one male sample. All other strains are purely female.
-
-Data were analyzed by Rabea Hall and Dr. Frank Lammert at the Universitätsklinikum des Saarlandes in Homburg, Germany.
-
-Contacts: rabea.hall at uks.eu, Rabea.Hall at uniklinikum-saarland.de, and frank.lammert at uks.eu
-
-Table updated 7-19-2011
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Strain ID |
- Treatment |
-
-
- | 1 |
- 504 |
- B6D2F1 |
- CCl4 |
-
-
- | 2 |
- 506 |
- B6D2F1 |
- CCl4 |
-
-
- | 3 |
- 508 |
- B6D2F1 |
- CCl4 |
-
-
- | 4 |
- 414 |
- C57BL/6J |
- CCl4 |
-
-
- | 5 |
- 488 |
- C57BL/6J |
- CCl4 |
-
-
- | 6 |
- 489 |
- C57BL/6J |
- CCl4 |
-
-
- | 7 |
- B6J1 |
- C57BL/6J |
- untreated control |
-
-
- | 8 |
- B6J2 |
- C57BL/6J |
- untreated control |
-
-
- | 9 |
- B6J3 |
- C57BL/6J |
- untreated control |
-
-
- | 10 |
- 449 |
- DBA/2J |
- CCl4 |
-
-
- | 11 |
- 450 |
- DBA/2J |
- CCl4 |
-
-
- | 12 |
- 451 |
- DBA/2J |
- CCl4 |
-
-
- | 13 |
- 219.1 |
- DBA/2J |
- untreated control |
-
-
- | 14 |
- 219.2 |
- DBA/2J |
- untreated control |
-
-
- | 15 |
- 219.3 |
- DBA/2J |
- untreated control |
-
-
- | 16 |
- 276 |
- BXD1 |
- CCl4 |
-
-
- | 17 |
- 278 |
- BXD1 |
- CCl4 |
-
-
- | 18 |
- 279 |
- BXD1 |
- CCl4 |
-
-
- | 19 |
- 353 |
- BXD2 |
- CCl4 |
-
-
- | 20 |
- 357 |
- BXD2 |
- CCl4 |
-
-
- | 21 |
- 358 |
- BXD2 |
- CCl4 |
-
-
- | 22 |
- 272 |
- BXD6 |
- CCl4 |
-
-
- | 23 |
- 273 |
- BXD6 |
- CCl4 |
-
-
- | 24 |
- 274 |
- BXD6 |
- CCl4 |
-
-
- | 25 |
- 405 |
- BXD11 |
- CCl4 |
-
-
- | 26 |
- 406 |
- BXD11 |
- CCl4 |
-
-
- | 27 |
- 408 |
- BXD11 |
- CCl4 |
-
-
- | 28 |
- 239 |
- BXD12 |
- CCl4 |
-
-
- | 29 |
- 240 |
- BXD12 |
- CCl4 |
-
-
- | 30 |
- 241 |
- BXD12 |
- CCl4 |
-
-
- | 31 |
- 553 |
- BXD13 |
- CCl4 |
-
-
- | 32 |
- 554 |
- BXD13 |
- CCl4 |
-
-
- | 33 |
- 555 |
- BXD13 |
- CCl4 |
-
-
- | 34 |
- 249 |
- BXD14 |
- CCl4 |
-
-
- | 35 |
- 250 |
- BXD14 |
- CCl4 |
-
-
- | 36 |
- 288 |
- BXD14 |
- CCl4 |
-
-
- | 37 |
- 191 |
- BXD19 |
- CCl4 |
-
-
- | 38 |
- 644 |
- BXD19 |
- CCl4 |
-
-
- | 39 |
- 645 |
- BXD19 |
- CCl4 |
-
-
- | 40 |
- 442 |
- BXD24a |
- CCl4 |
-
-
- | 41 |
- 443 |
- BXD24a |
- CCl4 |
-
-
- | 42 |
- 444 |
- BXD24a |
- CCl4 |
-
-
- | 43 |
- 216 |
- BXD27 |
- CCl4 |
-
-
- | 44 |
- 218 |
- BXD27 |
- CCl4 |
-
-
- | 45 |
- 290 |
- BXD27 |
- CCl4 |
-
-
- | 46 |
- 28 |
- BXD28 |
- CCl4 |
-
-
- | 47 |
- 71 |
- BXD28 |
- CCl4 |
-
-
- | 48 |
- 129 |
- BXD28 |
- CCl4 |
-
-
- | 49 |
- 219 |
- BXD31 |
- CCl4 |
-
-
- | 50 |
- 220 |
- BXD31 |
- CCl4 |
-
-
- | 51 |
- 231 |
- BXD31 |
- CCl4 |
-
-
- | 52 |
- 549 |
- BXD32 |
- CCl4 |
-
-
- | 53 |
- 550 |
- BXD32 |
- CCl4 |
-
-
- | 54 |
- 551 |
- BXD32 |
- CCl4 |
-
-
- | 55 |
- 139 |
- BXD33 |
- CCl4 |
-
-
- | 56 |
- 140 |
- BXD33 |
- CCl4 |
-
-
- | 57 |
- 559 |
- BXD33 |
- CCl4 |
-
-
- | 58 |
- 132 |
- BXD34 |
- CCl4 |
-
-
- | 59 |
- 146 |
- BXD34 |
- CCl4 |
-
-
- | 60 |
- 147 |
- BXD34 |
- CCl4 |
-
-
- | 61 |
- 293 |
- BXD39 |
- CCl4 |
-
-
- | 62 |
- 597 |
- BXD39 |
- CCl4 |
-
-
- | 63 |
- 599 |
- BXD39 |
- CCl4 |
-
-
- | 64 |
- 154 |
- BXD40 |
- CCl4 |
-
-
- | 65 |
- 570 |
- BXD40 |
- CCl4 |
-
-
- | 66 |
- 572 |
- BXD40 |
- CCl4 |
-
-
- | 67 |
- 361 |
- BXD42 |
- CCl4 |
-
-
- | 68 |
- 362 |
- BXD42 |
- CCl4 |
-
-
- | 69 |
- 373 |
- BXD42 |
- CCl4 |
-
-
- | 70 |
- 428 |
- BXD43 |
- CCl4 |
-
-
- | 71 |
- 429 |
- BXD43 |
- CCl4 |
-
-
- | 72 |
- 556 |
- BXD43 |
- CCl4 |
-
-
- | 73 |
- 472 |
- BXD51 |
- CCl4 |
-
-
- | 74 |
- 473 |
- BXD51 |
- CCl4 |
-
-
- | 75 |
- 474 |
- BXD51 |
- CCl4 |
-
-
- | 76 |
- 533 |
- BXD55 |
- CCl4 |
-
-
- | 77 |
- 534 |
- BXD55 |
- CCl4 |
-
-
- | 78 |
- 535 |
- BXD55 |
- CCl4 |
-
-
- | 79 |
- 519 |
- BXD62 |
- CCl4 |
-
-
- | 80 |
- 520 |
- BXD62 |
- CCl4 |
-
-
- | 81 |
- 521 |
- BXD62 |
- CCl4 |
-
-
- | 82 |
- 463 |
- BXD65 |
- CCl4 |
-
-
- | 83 |
- 464 |
- BXD65 |
- CCl4 |
-
-
- | 84 |
- 465 |
- BXD65 |
- CCl4 |
-
-
- | 85 |
- 327 |
- BXD69 |
- CCl4 |
-
-
- | 86 |
- 346 |
- BXD69 |
- CCl4 |
-
-
- | 87 |
- 347 |
- BXD69 |
- CCl4 |
-
-
- | 88 |
- 614 |
- BXD73 |
- CCl4 |
-
-
- | 89 |
- 616 |
- BXD73 |
- CCl4 |
-
-
- | 90 |
- 619 |
- BXD73 |
- CCl4 |
-
-
- | 91 |
- 395 |
- BXD75 |
- CCl4 |
-
-
- | 92 |
- 482 |
- BXD75 |
- CCl4 |
-
-
- | 93 |
- 483 |
- BXD75 |
- CCl4 |
-
-
- | 94 |
- 317 |
- BXD87 |
- CCl4 |
-
-
- | 95 |
- 319 |
- BXD87 |
- CCl4 |
-
-
- | 96 |
- 322 |
- BXD87 |
- CCl4 |
-
-
- | 97 |
- 374 |
- BXD90 |
- CCl4 |
-
-
- | 98 |
- 388 |
- BXD90 |
- CCl4 |
-
-
- | 99 |
- 389 |
- BXD90 |
- CCl4 |
-
-
- | 100 |
- 402 |
- BXD96 |
- CCl4 |
-
-
- | 101 |
- 403 |
- BXD96 |
- CCl4 |
-
-
- | 102 |
- 404 |
- BXD96 |
- CCl4 |
-
-
- | 103 |
- 584 |
- BXD98 |
- CCl4 |
-
-
- | 104 |
- 585 |
- BXD98 |
- CCl4 |
-
-
- | 105 |
- 607 |
- BXD98 |
- CCl4 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/SUH_Liv_RMA_0611/summary.rtf b/general/datasets/SUH_Liv_RMA_0611/summary.rtf
deleted file mode 100644
index 2684b46..0000000
--- a/general/datasets/SUH_Liv_RMA_0611/summary.rtf
+++ /dev/null
@@ -1,22 +0,0 @@
-Saarland University Homburg (SUH) Carbon Tetrachloride-Treated BXD Mouse Affymetrix Mouse Gene 1.0 ST Array data set
-
-This experimental liver gene expression data set (~100 Affymetrix exon-type arrays), was generated by Frank Lammert, Sonja Hillebrandt, Rabea Hall, and colleagues at the Saarland University Medical Center in Homburg, Germany. This work is part of the German Network for Systems Genetics (GeNeSys).
-
-Expression data after carbon tetrachloride treatment (CCl4, also known as Halon, Freon, carbon tet, or tetrachloromethane) were generated using RNA sample from 30 BXD strains, both parental strains (C57BL/6J, DBA/2J), and B6D2 F1 hybrids. The great majority of cases were females and were treated with carbon tetrachloride injections over a six week period. Three arrays were run for each strain using independent liver samples.
-
-PURPOSE: The overall goal of the project is to understand the etiology of liver fibrogenesis using carbon tetracholoride as a toxin and inducer of liver disease. Liver fibrogenesis, or scarring of the liver, is the common end-stage of chronic liver diseases, in particular after chronic viral infections. In Germany along complications associated with liver fibrosis cause approximately 10,000 deaths per year. In the past decade key molecular pathomechanisms of hepatic fibrogenesis due to chronic viral infections have been identified. Activated hepatic stellate cells (HSCs) drive the process of de novo deposition of abnormal extracellular matrix, which is modulated by complex interactions between cytokines, receptors, and matrix components.
-
-Several studies have demonstrated that the course and progression of the fibrogenic response to chronic liver injury is highly variability among individuals. This marked variabilityhas been attributed to etiology, age, gender, and environmental factors. In humans these genetic disease fibrosis predisposition factors have not yet to be studied systematically.
-
-Our group recently identified a gene variant that contributes to liver fibrogenesis by using QTL mapping in an experimental crosses between fibrosis-susceptible and resistant strains of mice (Hillebrandt et al., 2005). We demonstrated that sequence differences in the HC gene that encodes complement factor C5 (also known as hemolytic complement), are responsible for this strain difference. Common haplotype-tagging polymorphisms of the human HC gene were shown to be associated with advanced fibrosis in chronic hepatitis C virus infection. Thus, the mouse analysis led to the identification of an unknown gene underlying human susceptibility to liver fibrosis, supporting the idea that HC has a causal role in chronic inflammatory disorders and organ fibrogenesis across species.
-
-As part of the GeNeSys program we have studied liver fibrogenesis in the BXD family of strains as a model for chronic liver injury. This expression data set is used to map complex genetic traits that modulate gene expression and determine gene networks during liver fibrogenesis in GRPs.
-
-The following assays are complete or are in progress:
-
-
- - Liver fibrosis studies: Phenotyping protocols include standard histology, morphometry, biochemical quantification of hepatic collagen contents, serum surrogate markers of fibrosis, immunohistochemistry, and expression profiling of proinflammatory and profibrogenic genes by qRT-PCR and Affymetrix microarrays (this data set).
- - Characterization of liver cells: Liver immune cell fractions will be isolated and sorted according to SOPs developed in the Lammert laboratory. In addition, in cooperation with the technology platforms of the HepatoSys Network of Excellence, we will characterize primary HSCs that play critical roles in liver fibrogenesis with respect to proinflammatory responses during chronic liver inflammation.
-
-
-PROTOCOL for carbon tetrachloride (CCl4) treatment (parental strains, F1, and BXD lines). Animals were injected with CCl4 (12 x 0.7 mg/kg ip) over a 6-week period on days 1 and 4 of each week. Intraperitoneal injections were begun between the ages of 6-8 weeks. Animals were sacrificed after 6 weeks of treatment at 12 to 14 weeks of age. Untreated control mice from only the two parental strains were also sacrificed at 12-14 weeks of age
diff --git a/general/datasets/SUH_Liv_RMA_0611/tissue.rtf b/general/datasets/SUH_Liv_RMA_0611/tissue.rtf
deleted file mode 100644
index 05a7607..0000000
--- a/general/datasets/SUH_Liv_RMA_0611/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Tissue: Livers were snap frozen in liquid nitrogen immediately after harvesting. RNA was extracted and submitted to the UTHSC Molecular Resource Core for expression profiling. Expression data were generated by Lorne Rose, William Taylor and colleagues. Data were entered into GeneNetwork by Arthur Centeno, June 17, 2011. Data were quality controlled by R. W. Williams.
diff --git a/general/datasets/SXMPublish/summary.rtf b/general/datasets/SXMPublish/summary.rtf
deleted file mode 100644
index 941152c..0000000
--- a/general/datasets/SXMPublish/summary.rtf
+++ /dev/null
@@ -1,482 +0,0 @@
-Barley Phenotype Database
-
-Steptoe x Morex (SxM):
-North American Barley Genome Project (NABGP) dataset
-Hayes, P. M., B. H. Liu, S. J. Knapp, F. Chen, B. Jones, T. Blake, J. Franckowiak, D Rasmusson, M. Sorrells, S. E. Ullrich, D. Wesenberg and A. Kleinhofs. 1993. Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor. Appl. Genet. 87: 392-401. The data set is available at the http://wheat.pw.usda.gov/ggpages/SxM/phenotypes.html
-
-It comprises the following agronomic and malting quality traits:
-
-
- - Grain yield (MT/ha)
- - Lodging (%)
- - Height (cm)
- - Heading date (days after January 1)
- - Grain protein (%)
- - Alpha amylase (20 Deg units)
- - Diastatic power (Deg)
- - Malt extract (%)
-
-
-Agronomic and malting quality traits were measured in 16 and 9 environments, respectively. The phenotype data files are coded for each environment as follows:
-Environment # Location Year Cooperator
-
-
- - Crookston, Minnesota 1992 D. Rasmusson (rasmu002@maroon.tc.umn.edu)
- - Ithaca, New York 1992 M. Sorrells (mes12@cornell.edu)
- - Guelph, Ontario 1992 D. Falk (dfalk@crop.uoguelph.ca)
- - Pullman, Washington 1992 S. Ullrich (ullrich@wsu.edu)
- - Brandon, Manitoba 1992 W. Legge (legge@mbrsbr.agr.ca)
- - Outlook, Saskatchewan 1992 R. Irvine
- - Goodale, Saskatchewan 1992 B. Rossnagel (rossnagel@sask.uask.ca)
- - Saskatoon, Saskatchewan 1992 B. Rossnagel (rossnagel@sask.uask.ca)
- - Tetonia, Idaho D. Wesenberg (fax: 208-397-4165) 1992
- - Bozeman, Montana (irrigated) 1992 T. Blake (blake@hordeum.oscs.montana.edu)
- - Bozeman, Montana (dryland) 1992 T. Blake (blake@hordeum.oscs.montana.edu)
- - Aberdeen, Idaho 1991 D. Wesenberg (fax: 208-397-4165)
- - Klamath Falls, Oregon 1991 P. Hayes (hayesp@css.orst.edu)
- - Pullman, Washington 1991 S. Ullrich (ullrich@wsu.edu)
- - Bozeman, Montana (irrigated) 1991 T. Blake (blake@hordeum.oscs.montana.edu)
- - Bozeman, Montana (dryland) 1991 T. Blake (blake@hordeum.oscs.montana.edu)
-
-
-Other data sets
-ENSAT-INP: Ecole Nationale Supérieure Agronomique de Toulouse, Institut National Polytechnique (ENSAT-INP), France
-UM: University of Minnesota, USA
-JLU: Justus Liebig University, Germany
-UW: University of Wageningen, Netherlands
-SCRI: Scottish Crop Research Institute, UK
-WSU: Washington State University, USA
-
-α-amylase (NABGP)
-(see description of the NABGP dataset)
-
-Diastatic power (NABGP)
-(see description of the NABGP dataset)
-
-Disease resistance, bacterial streak, Xanthomonas campestris (ENSAT-INP)
-El Attari H., Rebai A., Hayes P. M.; Barrault G.; Dechamp-Guillaume G.; Sarrafi A. Potential of doubled-haploid lines and localization of quantitative trait loci (QTL) for partial resistance to bacterial leaf streak (Xanthomonas campestris pv. hordei) in barley. Theoretical and Applied Genetics 1998, vol. 96, no1, pp. 95-100.
-
-Two experiments were undertaken in a randomized complete block design with three replicates, in a controlled growth chamber. Twenty seeds per replicate were planted in plastic containers (60 x 40 x 8 cm) containing moistened vermiculite. At the two-leaf stage seedlings were inoculated with an Iranian strain of the pathogen.
-
-Disease resistance, head blight, Fusarium graminearum (UM) or FHB data set
-Prom, L. K., B. J. Steffenson, B. Salas, T. G. Fetch Jr., and H. H. Casper. 1997. Barley accessions resistant to Fusarium head blight and the accumulation of deoxyvalenol. Cereal Res. Comm. 25:807-808.
-
-Prom, L.K., Horsley, R.D., Steffenson, B.J., and Schwarz, P.B. 1999. Development of Fusarium head blight and accumulation of deoxynivalenol in barley sampled at different growth stages. J. Am. Soc. Brew. Chem. 57:60-63.
-
-Steffenson, B. J. 2003. Fusarium head blight of barley: Impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. Pages 241-295: In: K. J. Leonard and W.R. Bushnell, eds. 2003. Fusarium Head Blight of Wheat and Barley. APS Press. St. Paul. 512 pp.
-
-Tacke, B. K., and H. H. Casper. 1996. Determination of deoxyvalenol in wheat, barley, and malt by column cleanup and gas chromatography with electron capture detection. J. Assoc. Off. Anal. Chem. 79:472-475.
-
-FHB and DON assays
-Parents and DH progeny from the Steptoe/Morex were assessed for FHB severity (in %) and DON accumulation (in ppm) at three different environments in 1994 and 1995: Fargo, ND in both 1994 and 1995 and Langdon, ND in 1995. A randomized complete block design was used in the three environments and included a single replicate. Progeny and parents were planted in short rows (10-20 seeds) spaced 0.33 cm apart in two adjacent rows. Planting, maintenance of plots, and inoculation protocols were as described by (Prom et al. 1997). Disease assessments were made when the parents and DH progeny were at the mid-dough stage of development (growth stage 84-86) (Zadoks et al. 1974). The percent severity of FHB was determined by counting the number of infected kernels (those with greater than one-fourth of their surface area showing disease symptoms) and dividing that quantity by the total number of kernels in that spike multiplied by 100 (Prom et al. 1997). These assessments were made on 10-20 randomly selected spikes per plot as described by Prom et al. (1997). When the plants were mature, all spikes from each plot were harvested, dried, and threshed. DON assays were made using the method developed by Tacke and Casper (Tacke and Casper 1996). For this assay, a random six-gram sample of seed was used from each parent and DH line (Prom et al. 1999).
-
-File names in the dataset:
-DON94F.TXT final
-amount of vomitoxin in samples vom ppm
-
-DONP195F.TXT final
-DON levels in ppm planting date 1 (Fargo 1995)
-
-DONP295F.TXT final
-DON levels in ppm planting date 2 (Fargo 1995)
-
-DONP295L.TXT final
-DON levels in ppm planting date 2 (Langdon 1995)
-
-DON94F.TXT final
-amount of vomitoxin vom ppm
-
-FGINC04.94
-incidence of Fusarium graminearum isolated from seed in all severity classes.
-
-FGINC14.94
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 1, 2, 3, or 4.
-
-FGINC24.94
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 2, 3, or 4.
-
-FGINC34.94
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 3 or 4.
-
-FHB1494F.TXT
-incidence of Fusarium head blight (visual rating) with a severity rating of 1, 2, 3, or 4.
-
-FHB1494F.TXT final
-incidence of Fusarium head blight (visual rating) with a severity rating of 1, 2, 3, or 4.
-
-FHB2494F.TXT
-no heading
-
-FHB2494F.TXT final
-no heading
-
-FHB3494F.TXT
-incidence of Fusarium head blight (visual rating) when severity categories 3 or 4 only are considered blighted.
-
-FHB3494F.TXT final
-incidence of Fusarium head blight (visual rating) when severity categories 3 or 4 only are considered blighted.
-
-FHBINC14.94
-incidence of Fusarium head blight (visual rating) with a severity rating of 1, 2, 3, or 4.
-
-FHBINC34.94
-incidence of Fusarium head blight (visual rating) when severity categories 3 or 4 only are considered blighted.
-
-FHBSE94F.TXT
-severity of Fusarium head blight
-
-FHBSE94F.TXT final
-severity of Fusarium head blight
-
-FHBSEV.94
-severity of Fusarium head blight
-
-FPPLTT95.TXT final
-Fusarium Poae Isolations from seed 1995 (Fargo PD1, Fargo PD2, and Langdon PD2)
-
-FSPD195F.TXT final
-Percentage of FHB infection in S/M lines from the first planting date at Fargo 1995
-
-FSPD295F.TXT final
-Percentage of FHB infection in S/M lines from the second planting date at Fargo 1995
-
-FSPD295L.TXT final
-Percentage of FHB infection in S/M lines from the second planting date at Langdon 1995
-
-GRSTG94F.TXT
-developmental stages of the Steptoe/Morex population
-The first column is the SM line,
-the second is Zadok's Growth Stage,
-the third estimated days to mid-milk and
-the 4th days to heading (St. Paul).
-
-GRSTG94F.TXT final
-developmental stages of the Steptoe/Morex population
-The first column is the SM line,
-the second is Zadok's Growth Stage,
-the third estimated days to mid-milk and
-the 4th days to heading (St. Paul).
-
-GRTHSTGE.94
-developmental stages of the Steptoe/Morex population
-The first column is the SM line,
-the second is Zadok's Growth Stage,
-the third estimated days to mid-milk and the 4th days to heading (St. Paul).
-
-GZP0494F.TXT
-incidence of Fusarium graminearum isolated from seed in all severity classes.
-
-GZP0494F.TXT final
-incidence of Fusarium graminearum isolated from seed in all severity classes.
-
-GZP1494F.TXT
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 1, 2, 3, or 4.
-
-GZP1494F.TXT final
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 1, 2, 3, or 4.
-
-GZP2494F.TXT
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 2, 3, or 4.
-
-GZP2494F.TXT final
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 2, 3, or 4.
-ND94
-
-GZP3494F.TXT
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 3 or 4.
-
-GZP3494F.TXT final
-incidence of Fusarium graminearum isolated from seeds with a severity rating of 3 or 4.
-
-GZPLT95.TXT final
-no heading
-
-HDPD295L.TXT final
-1995 LANGDON - number of days until heading (planted June 9)
-
-SEVPD1F95.TXT
-Percentage of FHB infection in S/M lines from the first planting date at Fargo 1995
-
-SEVPD2F95.TXT
-Percentage of FHB infection in S/M lines
-from the second planting date at Fargo 1995
-
-SEVPD2L95.TXT
-Percentage of FHB infection in S/M lines from the second planting date at Langdon 1995
-
-SMDNSITY.95 (Converted)
-head density ratings (field 1995)spikelets/cm
-
-SMFHB1.95F
-1st planting date Fargo
-
-SMFHB2.95F
-2nd planting date Fargo
-
-SMFHB2.95L
-2nd planting date Langdon
-
-SPDEN95F.TXT final
-spikelet density ratings (Fargo 1995)
-
-SPDEN95L.TXT final
-spikelet density ratings (Langdon 1995) spikelets/cm
-
-SPIKELET DENSITY FARGO 95
-spikelet density ratings (Fargo 1995) spikelets/cm
-
-SPIKELET DENSITY LANGDON 95
-spikelet density ratings (Langdon 1995) spikelets/cm
-
-SPKDENF95.TXT
-spikelet density ratings (Fargo 1995) spikelets/cm
-
-SPKDENL95.TXT
-spikelet density ratings (Langdon 1995) spikelets/cm
-
-VOMPPM.94
-No headings
-
-Disease resistance, leaf scald, Rhynchosporium secalis (JLU)
-Schweizer GF, Herz M, Mikolajewski S, Brenner M, Hartl L, Baumer M (2004) Genetic mapping of a novel scald resistance gene Rrs15CI8288 in barley. 9th International Barley Genetics Symposium, Brno, Czech Republic, 20-26 June 2004. Proceedings:258-265).
-
-Jackson LF, Webster RK (1976) Race differentiation, distribution and frequency of Rhynchosporium secalis in California. Phytopathology 66:719-725.
-
-Schweizer G, Baumer M, Daniel G, Rugel H, Röder MS (1995) RFLP-markers linked to scald (Rhynchosporium secalis) resistance gene Rh2 in barley. Theor Appl Genet 90:920-924.
-
-Disease resistance assay R. secalis
-
-General description
-Disease severity was assessed at seedling stage in a greenhouse chamber. Therefore, the plants were sown and grown at a temperature of 16-18°C in 9x9 cm plastic pots whereas each line was represented by four individuals. The plants were inoculated at the three-leaves stage, approximately 20 days after sowing. The parents as well as some differential genotypes (resistant: Atlas; susceptible: Alexis, Hendrix, Steffi) were included as internal controls.
-The single-spore isolate 271 (Straßmoos, Bavaria) of R. secalis, provided by Dr. Sachs, BBA Kleinmachnow, was grown for approximately 20 days on Lima bean agar (Difco, Detroit, USA) in Petri-dishes at 16°C in the dark. The spores were harvested after addition of water by gently rubbing of the mycel with a glass rod. The advanced spore suspension was decanted, filtrated and adjusted to 2-300.000 spores/ml. One inoculum preparation was used for the inoculation of all seedlings. by covering the inoculated plants with black plastic hoods for 48 hours high humidity and darkness were maintained to provide optimal infection conditions. 10-14 days after infection plants were assessed visually for scald symptoms on the lamina of the second leaf approximately according to the scale described by Jackson & Webster (1976). The third leaf was later consult to verify the infection. The final score of scald severity per DH line was achieved by averaging the scoring results of the four included plants.
-
-Detailed description
-The Steptoe/Morex DH mapping population and reference cultivars were tested for reaction to Rhynchosporium secalis according to Schweizer et al. 1995 with some modifications. The single-spore isolate “271” (Straßmoos, LfL-Bavaria, Germany) of R. secalis, provided by Dr. Sachs was grown for approximately 20 days on 2.3% (w/v) Lima bean agar (Difco Laboratories) in Petri-dishes at 16°C in the dark. For inoculation a conidial suspension was prepared by rinsing the plates with water and filtering the mycel through gauze. The spore concentration was adjusted to 200.000 spores/ml-1. One inoculum preparation was used for all seedlings in a given experiment.
-Seedlings at the 2- to 3-leaf stage (3 weeks after sowing) were sprayed uniformly with inoculum (approximately 0.25 ml per plant) and left for 20 min to dry. Inoculated plants were then lightly sprayed with water and kept for 48h in a dark moist chamber at 18°C. DH lines (four independent plants/DH line) were assessed 10-14 days after inoculation visually for scald symptoms on the lamina of the second leaf (the third leaf was used as further control) according to the scale described by Jackson & Webster (1976). Differential genotypes ´Atlas´ (res) and ´Steffi´ (susc) and the parents Steptoe and Morex were used as reference cultivars.
-
-Disease resistance, net blotch, Pyrenophora teres (UM)
-Steffenson, B.J., Hayes, P.M., and Kleinhofs, A. 1996. Genetics of seedling and adult plant resistance to net blotch (Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) in barley. Theor. Appl. Genet. 92:552-558.
-
-Burleigh JR, Loubane, M (1984) Plot size effects on disease progress and yield of wheat infected by Mycosphaerella graminicola and barley infected by Pyrenophora teres. Phytopathology 74:545--549
-
-Fetch, T.G., Jr., and Steffenson, B.J. 1999. Rating scales for assessing infection responses of barley infected with Cochliobolus sativus. Plant Dis. 83:213-217.
-
-James WC (1971) A manual of disease assessment keys for plant diseases. Can Dep Agric Publ 1458
-
-Tekauz, A (1985) A numerical scale to classify reactions of barley to Pyrenophora teres. Can J Plant Pathol 7:181—183
-
-Fetch, T. G., Jr., and Steffenson, B. J. 1999. Rating scales for assessing infection responses of
-barley infected with Cochliobolus sativus. Plant Dis. 83:213-217.
-
-Seedling evaluations
-For seedling evaluations, four to six seeds of parents and DH lines were sown in plastic cones (3.8 cm diameter and 21 cm length) filled with a peat moss:perlite (3:1) potting mix and grown at 22-26C in a greenhouse. Fertilization was provided at planting with water soluble (15-0-15, N-P-K) and controlled release (14-14-14, N-P-K) formulations. When the second leaves of plants were fully expanded (14 days after planting), inoculations were made with conidial suspensions of the individual pathogens using an atomizer pressured by an air pump at 414 kPa. Inoculations with isolate ND89-19 of P. t. f. teres and ND85F of C. sativus were made using a concentration of 5,000 and 8,000 conidia/ml, respectively. The volume of the inoculum suspension applied to each plant was approximately 0.15 ml. To facilitate even distribution and adherence of conidia, 10 ul of Tween® 20 (polyoxyethylene-20-sorbitan monolaurate) was added for every 100 ml of the inoculum suspension. Plants were allowed to dry slightly after inoculation before being placed in chambers maintained near saturation by periodic mistings from ultrasonic humidifiers. After a 16 hour infection period in complete darkness, the plants were allowed to dry slowly for approximately four hours before being returned to the greenhouse. Assessments of the infection response (IR) were made 9--11 days post-inoculation using the rating scale of Tekauz (1985) for net blotch and Fetch and Steffenson (1999) for spot blotch. The experiment was conducted in a randomized complete block design with two replicates and was repeated twice.
-
-Adult plant evaluations
-Parents and DH lines were also evaluated to the net and spot blotch pathogens in the field at Langdon and Fargo, North Dakota, respectively. The host entries were sown in hill plots (8--15 seeds/hill) spaced 0.3 m apart in paired rows. Susceptible barley genotypes (cultivar Hector for net blotch and line ND 5883 for spot blotch) were planted around the paired rows of hill plots to increase disease development in the nurseries. When most of the DH lines were at the mid-tillering stage of development, the susceptible spreader plants were inoculated with barley straw infected with either isolate ND89-19 of P. t. f. teres or ND85F of C. sativus. This infected barley straw was taken from the previous season's crop at the respective locations. Assessments of disease severity (percentage of leaf area affected by disease) were made at the mid-dough stage of development using standard disease area diagrams (Burleigh and Loubane [1984] for net blotch and James [1971] for spot blotch). The experimental design was a randomized complete block with three replications. Evaluations for net blotch reaction were made in 1991 only and for spot blotch both in 1991 and 1992.
-
-Disease resistance, leaf rust, Puccinia hordei (UW)
-Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJ, Graner A, Niks RE: A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor.Appl.Genet. 2007, 114:487-500.
-
-Disease evaluations at seedling plant stage
-The standard barley leaf rust isolate 1.2.1 (P. hordei Otth) was used to evaluate the level of partial resistance of the 150 DH lines of StMx at seedling stage in a greenhouse compartment. The disease experiments were conducted in six replications in time and within each replication one seedling of each DH line was inoculated. The seeds were sown in trays of 37 x 39 cm, each of them containing two rows of 10–15 seeds. In each tray one seed of each parental line, Steptoe and Morex and of the control lines, L94 and Vada, were sown. The inoculation was performed with about 200 spores per cm2. The latency period (LP) on each seedling was evaluated and the relative latency period (RLP50S) was calculated, relative to the LP on L94.
-
-Disease resistance, spot blotch, Cochliobolus sativus (UM)
-See the net blotch description
-
-Disease resistance, stem rust, Puccinia graminis (UM)
-Stakman EC, Stewart DM, Loegering WQ (1962) Identification of physiologic races of Puccinia graminis var. tritici. USDA Agricultural Research Service Bulletin 617.
-
-Miller JD, J.W.Lambert (1965) Variability and inheritance of reaction of barley to race
-32 l5B of stem rust. Aqron J 47:373-377.
-
-Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D.F., Steffenson, B.J., Close, T.J., Wise, R.P., Kleinhofs, A., Williams, R.W., Kearsey, M.J. and Waugh, R. 2008. Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley. Theoretical and Applied Genetics. 117(2):261-72
-
-Stem rust infection phenotyping
-Each of the St/Mx DH lines was challenged with the stem rust fungus race Pgt-MCC in 5 replications over 2 years (1990 and 1991). Phenotypic scores were made 12 to 14 days after inoculation according to the infection type (IT) scale of Stakman et al. (1962) as modified by Miller and Lambert (Miller and Lambert 1965). Under the Stakman system, IT 0 indicates no visible infection; only a necrotic “fleck” (i.e. hypersensitive response) with no sporulation; IT 1 designates a minute uredinium (i.e. sporulating pustule) surrounded by necrosis; IT 2 designates a small uredinium often surrounded by chlorosis; IT 3 designates a moderate sized uredinium sometimes surrounded by chlorosis; and IT 4 designates a large uredinium. Since barley exhibits chlorosis in association with most ITs (excluding IT 0, and IT 1), Miller and Lambert modified the Stakman system and classified ITs 2, 3, and 4 on the basis of uredinium size alone. Barley often exhibits a mixture of different ITs on a single plant—the “mesothetic” reaction described by Stakman et al (1962). ITs on the St/Mx DH lines were recorded according to prevalence. In most cases, the one or two most common ITs comprised over 75% of the total observed and were used to assign the general binary classes of resistant and susceptible. ITs 0, 1 and 2 were
-3 considered indicative of host resistance (i.e. a low infection type), whereas IT 3 and 4
-4 were indicative of host susceptibility (a high infection type). The classic “diamond
-5 shaped” uredinium of IT 4 was not observed on plants in the St/Mx population.
-
-Emergence of the second leaf (SCRI)
-Seeds of all 150 recombinant lines from the Steptoe x Morex DH population and the parents, Steptoe and Morex were planted in the 24 x 30 cm pots filled with the ‘Cereal Mix’ and placed on the automatically irrigated glasshouse benches (cubicle AO59). Three sterilized seeds per line were sown in each of four replicate pots. Placement of the pots was randomized across the glasshouse space. Temperature in the cubicle was set at 20° with 16-hr light/15° 8-hr dark periods. Intensity of the supplementary light was 400 µE m–1 sec–1.
-
-Single leaf frequency
-After 20 days, seedlings were counted based on number of emerged visible leaves (either single or two). Frequency of the single leaf across all four replicates within the recombinant line was used for QTL mapping.
-
-Ratio
-The lengths of the leaf blades were measured for the seedlings that have two visible leaves. Ratio of the length of both blades was used for QTL mapping.
-
-Endosperm modification (SCRI)
-Jorgensen (1988) Carlsberg Res. Commun. 53:277
-
-ImageJ is a public domain Java image processing program.
-Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, http://rsb.info.nih.gov/ij/, 1997-2008.
-
-Abramoff, M.D., Magelhaes, P.J., Ram, S.J. "Image Processing with ImageJ". Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.
-
-Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D., Waugh, R. 2006. An atlas of gene expression from seed to seed through barley development. Functional Integrative Genomics 6, 202-211.
-
-Plant material was generated essentially as described previously (Druka et al 2006) but with some modifications specific to these studies. To obtain embryo-derived tissue from the germinating grain, 30–50 sterilized seeds per line of the trial set were germinated on a petri plate between three layers of wet 3-mm filter paper in the dark, for 16 hr at 17° and 8 hr at 12°, for 96 hr total. 6-10 similarly looking or ‘average’ seeds were cut in half longitudally, and stained with calcuflor.
-
-Calcufluor staining
-1) 30 sec - 1min 0.1% calcufluor (H2O);
-2) 10 sec 70% EtOH;
-3) Dry shortly;
-4) 30-60 sec 0.1% fast green H2O;
-5) blot off residual stain, put under the UV microscope at 400 nm to take photographs.
-Photographs were taken by using Leica DM IL Inverted contrasting microscope Leica Microsystems. Image analysis was by using ImageJ software.
-
-Fermentability (SCRI)
-Fermentability is the proportion of fermentable material in a malt extract. It is measured using a standard yeast strain following 48 hrs fermentation according to the IoB Recommended Methods for Analysis (1992) buut modified for small aliquots as described by Swanson & Thomas (1996)
-
-Fermentable malt extract (SCRI)
-Fermentable malt extract is the total amount of fermentable material in a sample of barley grain and is the product of hot water extract and ferementability
-
-Flecking of leaves (SCRI)
-Leaf flecking is a visual score of the degree of flag and flag leaf-1 coverage by dark brown leasions that are not attributable to known foliar pathogens or pests. It is scored on a 1-8 scale with 1 = 0 and 9=100% coverage
-
-Germination (WSU)
-See Dormancy and Pre-harvest sprouting
-
-Grain length F0-F9 (SCRI)
-Number of seeds from a sample of approx 100 cleaned grain that have passed over a 2.5mm sieve and are between 2.5 and 3 mm in width as determined by MARVIN 4.0 analysis of a digital image (www.gta-sensorik.com)
-
-Grain length, average (SCRI)
-Grain length is the average length of a sample of approx 100 cleaned sseds that have passed over a 2.5mm sieve. Seed length is determined by analysis of digital images using the Marvin 4.0 system (www.gta-sensorik.com).
-
-Grain nitrogen (SCRI)
-Grain nitrogen is the estimated % nitrogen content of a sample of cleaned grain that has passed over a 2.5mm sieve. It was measured by a FOSS 1251 Near Infra Red Transmittance grain analyser (www.foss.dk)
-
-Grain protein (NABGP)
-(see description of the NABGP dataset).
-
-Grain shape (width/length) (SCRI)
-Grain shape is the average grain width divided by the average grain length.
-
-Grain surface area (SCRI)
-Grain surface area is the average area 2D area of a sample of approx 100 leaned barley grain that have passed over a 2.5mm sieve. Surface area is determined by analysis of digital images using the Marvin 4.0 system (www.gta-sensorik.com).
-
-Grain width (average) (SCRI)
-Grain width is the average width of a sample of approx 100 cleaned seeds that have passed over a 2.5mm sieve. Seed width is determined by analysis of digital images using the Marvin 4.0 system (www.gta-sensorik.com).
-
-Grain width F0-F9 (SCRI)
-Number of seeds from a sample of approx 100 cleaned grain that have passed over a 2.5mm sieve and are between 2.5 and 3 mm in width as determined by MARVIN 4.0 analysis of a digital image (www.gta-sensorik.com).
-
-Head length (SCRI)
-Length (cm) of ear from collar to base of awn of last spikelet measured on a random sample from a field grown barley plot.
-
-Heading date - glasshouse (SCRI)
-Seeds of all 150 recombinant lines from the Steptoe x Morex DH population and the parents, Steptoe and Morex were planted in the 24 x 30 cm pots filled with the ‘Cereal Mix’ and placed on the automatically irrigated glasshouse benches (cubicle AO59). Three sterilized seeds per line were sown in each of four replicate pots. Placement of the pots was randomized across the glasshouse space. Temperature in the cubicle was set at 20° with 16-hr light/15° 8-hr dark periods. Intensity of the supplementary light was 400 µE m–1 sec–1.
-
-Heading date was measured as number of days to anthesis. Anthesis was determined by observing the colour and the response of anthers to the mechanical disturbance. Anthers should be yellow and a slight mechanical disturbance should cause shedding of the pollen meaning that anthesis is about to happen.
-
-Heading date (NABGP)
-(see description of the NABGP dataset)
-
-Heading date (SCRI)
-Days after May31st on which 50% of the plot first reached DGS53
-
-Heading date (UM)
-Steffenson, B. J. 2003. Fusarium head blight of barley: Impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. Pages 241-295: In: K. J. Leonard and W.R. Bushnell, eds. 2003. Fusarium Head Blight of Wheat and Barley. APS Press. St. Paul. 512 pp.
-
-Zadoks, J. C., T. T. Chang, and C. F. Konzak. 1974. A decimal code for the growth stages of cereals. Weed. Res. 14:415-421.
-
-Morphological and agronomic trait assessment
-Various morphological (especially spike characters) and agronomic traits may affect the development of FHB on lines in the field (Steffenson 2003). To determine the possible contribution of such factors on FHB severity, assessments were made on heading date, plant height, spike, and the number of nodes per cm of rachis in the spike (kernel density). Heading date was defined as the number of days from planting to when 50% of the plants in a plot had emerged spikes. Plant height was the number of cm from the ground to the tip of the spike, excluding the awns. Spike angle was rated at maturity on a scale of 1 to 3 where spikes bending less than 45 degrees from vertical were scored as 1; those bending from 45-120 degrees from vertical were scored as 2, and those bending greater than 120 degrees from vertical were scored as 3. The number of nodes per cm of rachis was measured on four randomly selected spikes for each parent and DH line.
-
-Hot water extract (SCRI)
-Amount of material extracted by hot water from a clean 25g sample of barley grain that has passed over a 2.5mm sieve following micro-malting under standard conditions of steeping and air rests. Hot water extract is measured by refractometry and expressed as Lintner degrees per kg. NB, this is equivalent to malt extract but the micro-malting protocol will be different.
-
-Lodging (NABGP)
-(see description of the NABGP dataset)
-
-Lodging (SCRI)
-Lodging is the proportion of the plot that is less than 45 degrees from horizontal. It is measured on a 1-9 scale with 1=0 and 9=100%.
-
-Malt extract (NABGP)
-(see description of the NABGP dataset)
-
-Malt extract (SCRI)
-See HWE
-
-Maturity (SCRI)
-Maturity is a visual estimate of the relative physiological maturity of a plot with 1=early and 9=late.
-
-Milling energy (SCRI)
-Milling energy is the amount of energy required to mill a weighed sample of clean grain that has passed over a 2.5mm sieve. It is expressed as Joules per 5g grain ane measured using the Comparamill.
-
-Moisture content in the grain (SCRI)
-Estimate of moisture in sample by NIT after drying and storage!
-
-Necrotic spotting doughy stage (SCRI)
-Spotting at the doughy stage is a visual score of the degree of flag and flag leaf-1 coverage by dark brown lesions that are considered to be due to infection by Ramularia collo-cygni. It is scored on a 1-9 scale with 1 = 0 and 9=100% covereage
-
-Normalised difference vegetation index (SCRI)
-NDVI is ((ref660nm-ref770nm)/(ref660nm+ref770nm)) as measured by the Greenseeker (www.ntechindustries.com) at GS61
-
-Normalised difference vegetation index @GS43 (SCRI)
-NDVI is ((ref660nm-ref770nm)/(ref660nm+ref770nm)) as measured by the Greenseeker (www.ntechindustries.com) at GS43
-
-Plant height (NABGP)
-(see description of the NABGP dataset)
-
-Plant height (SCRI)
-Height is the height(cm) of a plot from the ground to the collar at GS71+
-
-Dormancy and pre-harvest sprouting (WSU)
-AOSA (1988) Association of Official Seed Analysis rules for testing seeds. J Seed Technol 12 (3).
-Ullrich, S.E., J.A. Clancy, I.A. del Blanco, H. Lee, V.A. Jitkov, F. Han, A. Kleinhofs, and K. Matsui. 2007. Genetic analysis of preharvest sprouting in a six-row barley cross. Molecular Breeding. Submitted.
-
-Hayes, P. M., B. H. Liu, S. J. Knapp, F. Chen, B. Jones, T. Blake, J. Franckowiak, D Rasmusson, M. Sorrells, S. E. Ullrich, D. Wesenberg and A. Kleinhofs. 1993. Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor. Appl. Genet. 87: 392-401.
-
-Han, F., and S.E. Ullrich. 1994. Mapping of quantitative trait loci for malting quality traits in barley. Barley Genetics Newsletter 23:84-97.
-
-Ullrich, S. E., P. M. Hayes, W. E. Dyer, T. K. Blake, and J. A. Clancy. 1993. Quantitative trait locus analysis of seed dormancy in "Steptoe" barley. p. 136-145. In: M. K. Walker-Simmons and J. L. Reid (eds.) Preharvest sprouting in cereals 1992. Amer.Assoc. Cereal Chemist, St. Paul.
-
-Oberthur, L., T.K. Blake, W.E. Dyer, and S.E. Ullrich. 1995. Genetic analysis of seed dormancy in barley (Hordeum vulgare L.). J. Quant. Trait Loci (on line), available: http://probe.nalusda.gov. 8000/other docs/jqtl/jqtl 1995-05/ dormancy.html.
-
-Han, F., S.E. Ullrich, S. Chirat, S. Menteur, L. Jestin, A. Sarrafi, P.M. Hayes, B.L. Jones, T.K. Blake, D.M. Wesenberg, A. Kleinhofs, and A. Kilian. 1995. Mapping of b-glucan content and b-glucanase activity loci in barley grain and malt. Theor. Appl. Genet. 91:921-927.
-
-Clancy, J.A., F. Han, and S.E. Ullrich. 2003. Comparative mapping of b-amylase activity QTLs among three barley crosses. Crop Sci.43:1043-1052.
-
-Ullrich, S.E., J.A. Clancy, I.A. del Blanco, H. Lee, V.A. Jitkov, F. Han, A. Kleinhofs, and K. Matsui. 2007. Genetic analysis of preharvest sprouting in a six-row barley cross. Molecular Breeding. Submitted.
-
-Dormancy as measured by germination tests
-Dormancy defined as the failure of viable mature seed to germinate under favorable conditions was measured indirectly by measuring germination percentage, as there is no known direct test for dormancy. Two different after-ripening periods (0 and 14 days) were included in the study to measure the state of and change in dormancy over time. Genetic sub-traits for dormancy based on physiological activity/state could include the development of dormancy as seeds mature, the state of dormancy at maturity, and the dissipation of dormancy with time following maturity. The latter two situations were considered in this study. Germination percentage has also been used to measure susceptibility/resistance to preharvest sprouting (PHS) as well, but it is also a very indirect measure, which assumes that dormancy is the opposite of PHS, which may or may not be entirely true.
-
-Seeds were harvested at physiological maturity (as determined when green color was lost from the spike). Heads were collected and stored in a -20°C freezer prior to germination tests of the seeds to arrest physiological activity. Germination tests were carried out after two different post-harvest after-ripening periods at room temperature; 0 d and 14 d for materials grown in field and glasshouse environments. For each after-ripening period, two replications of 100 seeds were germinated at 20°C on moist filter paper in a petri dish. Standard germination tests were performed (AOSA 1988). After 7 d the number of germinated seeds were counted and expressed as a percentage of the total.
-
-Pre-harvest Sprouting (PHS) experiment in the greenhouse.
-Trait scores:
-0 = no visible roots
-1 = roots <or = 3/ no shoots
-2 = roots < or = 5/ shoots < or = 3
-3 = roots < or = 8/ shoots < or = 5
-4 = roots and shoots over 25% but < 50% of head
-5 roots and shoots over 50% of head
-
-Predicted spirit yield (SCRI)
-PSY is fermentable extract multiplied vy a constant to give the yield of spirit(l) per tonne of malt (Dolan, 1982).
-
-Soluble nitrogen content of wort (SCRI)
-Soluble nitrogen content is the amount of nirogen that has been solubilised in a hot water extract follwing micro-malting under standard conditions (see Hot Water Extract, HWE). It is measure by UV spectrophotometry (Haselmore & Gill, 1995).
-
-Spike density (UM)
-Steffenson, B. J. 2003. Fusarium head blight of barley: Impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. Pages 241-295: In: K. J. Leonard and W.R. Bushnell, eds. 2003. Fusarium Head Blight of Wheat and Barley. APS Press. St. Paul. 512 pp.
-
-Zadoks, J. C., T. T. Chang, and C. F. Konzak. 1974. A decimal code for the growth stages of cereals. Weed. Res. 14:415-421.
-
-Morphological and agronomic trait assessment
-Various morphological (especially spike characters) and agronomic traits may affect the development of Fusarium Head Blight (FHB) on lines in the field (Steffenson 2003). To determine the possible contribution of such factors on FHB severity, assessments were made on heading date, plant height, spike, and the number of nodes per cm of rachis in the spike (kernel density). Heading date was defined as the number of days from planting to when 50% of the plants in a plot had emerged spikes. Plant height was the number of cm from the ground to the tip of the spike, excluding the awns. Spike angle was rated at maturity on a scale of 1 to 3 where spikes bending less than 45 degrees from vertical were scored as 1; those bending from 45-120 degrees from vertical were scored as 2, and those bending greater than 120 degrees from vertical were scored as 3. The number of nodes per cm of rachis was measured on four randomly selected spikes for each parent and DH line.
-
-Thousand grain weight (SCRI)
-Thousand grain weight is measured by counting and weighing a clean sample of grain that has passed over a 2.5 mm sieve using MARVIN 4.0 (www.gta-sensorik.com)
-
-Vegetation index (SCRI)
-This is Infra Red Vegetation Index, IRVI (ref660nm/ref770nm) as measured by the Greenseeker (www.ntechindustries.com) at GS61.
-
-Vegetation index @ GS43 (SCRI)
-This is Infra Red Vegetation Index, IRVI (ref660nm/ref770nm) as measured by the Greenseeker (www.ntechindustries.com) at GS43.
-
-Yield (MT/ha) (NABGP)
-(see description of the NABGP dataset).
diff --git a/general/datasets/Stj_pln_0912/experiment-type.rtf b/general/datasets/Stj_pln_0912/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Stj_pln_0912/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Striatum_Exon_0209/cases.rtf b/general/datasets/Striatum_Exon_0209/cases.rtf
deleted file mode 100644
index e4db26e..0000000
--- a/general/datasets/Striatum_Exon_0209/cases.rtf
+++ /dev/null
@@ -1,947 +0,0 @@
-A movie of the dissection of the brain, including the striatum, by Dr. Glenn Rosen.
-
-About the strains used to generate this set of data
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tube No. |
- Tissue |
- Strain |
- Age |
- Sex |
-
-
- | 1 |
- R3025SA |
- 1705 |
- Striatum |
- 129S1/SvImJ |
- 60 |
- F |
-
-
- | 2 |
- R3026SA |
- 1375 |
- Striatum |
- 129S1/SvImJ |
- 59 |
- M |
-
-
- | 3 |
- R3027SA |
- 1435 |
- Striatum |
- A/J |
- 59 |
- F |
-
-
- | 4 |
- R3028SA |
- 1455 |
- Striatum |
- A/J |
- 59 |
- M |
-
-
- | 5 |
- R3029SA |
- 1395 |
- Striatum |
- AKR/J |
- 59 |
- F |
-
-
- | 6 |
- R3030SA |
- 1415 |
- Striatum |
- AKR/J |
- 59 |
- M |
-
-
- | 7 |
- R3031SA |
- 1227 |
- Striatum |
- B6D2F1 |
- 59 |
- F |
-
-
- | 8 |
- R3032SA |
- 1225 |
- Striatum |
- B6D2F1 |
- 59 |
- M |
-
-
- | 9 |
- R3033SA |
- 1495 |
- Striatum |
- BALB/cByJ |
- 59 |
- F |
-
-
- | 10 |
- R3034SA |
- 1475 |
- Striatum |
- BALB/cByJ |
- 59 |
- M |
-
-
- | 11 |
- R3035SA |
- 1665 |
- Striatum |
- BTBRT<+>tf/J |
- 59 |
- F |
-
-
- | 12 |
- R3036SA |
- 1615 |
- Striatum |
- BTBRT<+>tf/J |
- 60 |
- M |
-
-
- | 13 |
- R3037SA |
- 457 |
- Striatum |
- BXD1 |
- 59 |
- F |
-
-
- | 14 |
- R3038SA |
- 927 |
- Striatum |
- BXD1 |
- 59 |
- M |
-
-
- | 15 |
- R3055SA |
- 487 |
- Striatum |
- BXD2 |
- 61 |
- F |
-
-
- | 16 |
- R3056SA |
- 477 |
- Striatum |
- BXD2 |
- 61 |
- M |
-
-
- | 17 |
- R3089SA |
- 977 |
- Striatum |
- BXD5 |
- 58 |
- F |
-
-
- | 18 |
- R3090SA |
- 967 |
- Striatum |
- BXD5 |
- 58 |
- M |
-
-
- | 19 |
- R3091SA |
- 557 |
- Striatum |
- BXD6 |
- 59 |
- F |
-
-
- | 20 |
- R3092SA |
- 547 |
- Striatum |
- BXD6 |
- 59 |
- M |
-
-
- | 21 |
- R3093SA |
- 717 |
- Striatum |
- BXD8 |
- 61 |
- F |
-
-
- | 22 |
- R3094SA |
- 707 |
- Striatum |
- BXD8 |
- 61 |
- M |
-
-
- | 23 |
- R3095SA |
- 647 |
- Striatum |
- BXD9 |
- 60 |
- F |
-
-
- | 24 |
- R3096SA |
- 637 |
- Striatum |
- BXD9 |
- 60 |
- M |
-
-
- | 25 |
- R3039SA |
- 517 |
- Striatum |
- BXD11 |
- 59 |
- F |
-
-
- | 26 |
- R3040SA |
- 787 |
- Striatum |
- BXD11 |
- 59 |
- M |
-
-
- | 27 |
- R3041SA |
- 817 |
- Striatum |
- BXD12 |
- 62 |
- F |
-
-
- | 28 |
- R3042SA |
- 807 |
- Striatum |
- BXD12 |
- 59 |
- M |
-
-
- | 29 |
- R3043SA |
- 877 |
- Striatum |
- BXD13 |
- 60 |
- F |
-
-
- | 30 |
- R3044SA |
- 867 |
- Striatum |
- BXD13 |
- 60 |
- M |
-
-
- | 31 |
- R3045SA |
- 1067 |
- Striatum |
- BXD14 |
- 59 |
- F |
-
-
- | 32 |
- R3144SA |
- 1077 |
- Striatum |
- BXD14 |
- 59 |
- M |
-
-
- | 33 |
- R3047SA |
- 1057 |
- Striatum |
- BXD15 |
- 60 |
- F |
-
-
- | 34 |
- R3048SA |
- 1047 |
- Striatum |
- BXD15 |
- 60 |
- M |
-
-
- | 35 |
- R3049SA |
- 767 |
- Striatum |
- BXD16 |
- 61 |
- F |
-
-
- | 36 |
- R3050SA |
- 777 |
- Striatum |
- BXD16 |
- 61 |
- M |
-
-
- | 37 |
- R3051SA |
- 1177 |
- Striatum |
- BXD18 |
- 59 |
- F |
-
-
- | 38 |
- R3052SA |
- 1167 |
- Striatum |
- BXD18 |
- 59 |
- M |
-
-
- | 39 |
- R3053SA |
- 957 |
- Striatum |
- BXD19 |
- 60 |
- F |
-
-
- | 40 |
- R3054SA |
- 947 |
- Striatum |
- BXD19 |
- 60 |
- M |
-
-
- | 41 |
- R3057SA |
- 1255 |
- Striatum |
- BXD20 |
- 60 |
- F |
-
-
- | 42 |
- R3058SA |
- 1245 |
- Striatum |
- BXD20 |
- 60 |
- M |
-
-
- | 43 |
- R3059SA |
- 1197 |
- Striatum |
- BXD21 |
- 48 |
- F |
-
-
- | 44 |
- R3060SA |
- 1187 |
- Striatum |
- BXD21 |
- 48 |
- M |
-
-
- | 45 |
- R3061SA |
- 1235 |
- Striatum |
- BXD22 |
- 58 |
- F |
-
-
- | 46 |
- R3062SA |
- 1275 |
- Striatum |
- BXD22 |
- 60 |
- M |
-
-
- | 47 |
- R3063SA |
- 1137 |
- Striatum |
- BXD23 |
- 60 |
- F |
-
-
- | 48 |
- R3064SA |
- 1127 |
- Striatum |
- BXD23 |
- 60 |
- M |
-
-
- | 49 |
- R3065SA |
- 437 |
- Striatum |
- BXD24 |
- 59 |
- F |
-
-
- | 50 |
- R3066SA |
- 587 |
- Striatum |
- BXD24 |
- 60 |
- M |
-
-
- | 51 |
- R3067SA |
- 1107 |
- Striatum |
- BXD27 |
- 60 |
- F |
-
-
- | 52 |
- R3068SA |
- 1117 |
- Striatum |
- BXD27 |
- 60 |
- M |
-
-
- | 53 |
- R3069SA |
- 1027 |
- Striatum |
- BXD28 |
- 60 |
- F |
-
-
- | 54 |
- R3070SA |
- 1037 |
- Striatum |
- BXD28 |
- 60 |
- M |
-
-
- | 55 |
- R3071SA |
- 1007 |
- Striatum |
- BXD29 |
- 58 |
- F |
-
-
- | 56 |
- R3072SA |
- 1017 |
- Striatum |
- BXD29 |
- 58 |
- M |
-
-
- | 57 |
- R3073SA |
- 997 |
- Striatum |
- BxD31 |
- 60 |
- F |
-
-
- | 58 |
- R3074SA |
- 987 |
- Striatum |
- BxD31 |
- 60 |
- M |
-
-
- | 59 |
- R3075SA |
- 917 |
- Striatum |
- BXD32 |
- 57 |
- F |
-
-
- | 60 |
- R3076SA |
- 907 |
- Striatum |
- BXD32 |
- 57 |
- M |
-
-
- | 61 |
- R3077SA |
- 897 |
- Striatum |
- BXD33 |
- 59 |
- F |
-
-
- | 62 |
- R3078SA |
- 887 |
- Striatum |
- BXD33 |
- 59 |
- M |
-
-
- | 63 |
- R3079SA |
- 837 |
- Striatum |
- BXD34 |
- 60 |
- F |
-
-
- | 64 |
- R3080SA |
- 827 |
- Striatum |
- BXD34 |
- 60 |
- M |
-
-
- | 65 |
- R3081SA |
- 857 |
- Striatum |
- BXD36 |
- 57 |
- F |
-
-
- | 66 |
- R3082SA |
- 847 |
- Striatum |
- BXD36 |
- 57 |
- M |
-
-
- | 67 |
- R3083SA |
- 697 |
- Striatum |
- BXD38 |
- 60 |
- F |
-
-
- | 68 |
- R3084SA |
- 687 |
- Striatum |
- BXD38 |
- 60 |
- M |
-
-
- | 69 |
- R3085SA |
- 677 |
- Striatum |
- BXD40 |
- 60 |
- F |
-
-
- | 70 |
- R3086SA |
- 667 |
- Striatum |
- BXD40 |
- 60 |
- M |
-
-
- | 71 |
- R3087SA |
- 577 |
- Striatum |
- BXD42 |
- 58 |
- F |
-
-
- | 72 |
- R3088SA |
- 567 |
- Striatum |
- BXD42 |
- 58 |
- M |
-
-
- | 73 |
- R3097SA |
- 1975 |
- Striatum |
- BXSB/MpJ |
- 61 |
- F |
-
-
- | 74 |
- R3098SA |
- 1945 |
- Striatum |
- BXSB/MpJ |
- 61 |
- M |
-
-
- | 75 |
- R3099SA |
- 1575 |
- Striatum |
- C3H/HeJ |
- 60 |
- F |
-
-
- | 76 |
- R3100SA |
- 1595 |
- Striatum |
- C3H/HeJ |
- 60 |
- M |
-
-
- | 77 |
- R3101SA |
- 1228 |
- Striatum |
- C57BL/6J |
- 58 |
- F |
-
-
- | 78 |
- R3102SA |
- 343 |
- Striatum |
- C57BL/6J |
- 59 |
- M |
-
-
- | 79 |
- R3103SA (sample removed) |
- 2305 |
- Striatum |
- CAST/Ei |
- 61 |
- F |
-
-
- | 80 |
- R3104SA (sample removed) |
- 2285 |
- Striatum |
- CAST/Ei |
- 59 |
- M |
-
-
- | 81 |
- R3105SA |
- 1223 |
- Striatum |
- DBA/2J |
- 58 |
- F |
-
-
- | 82 |
- R3106SA |
- 344 |
- Striatum |
- DBA/2J |
- 59 |
- M |
-
-
- | 83 |
- R3107SA |
- 1535 |
- Striatum |
- FVB/NJ |
- 60 |
- F |
-
-
- | 84 |
- R3108SA |
- 1555 |
- Striatum |
- FVB/NJ |
- 60 |
- M |
-
-
- | 85 |
- R3109SA |
- 1845 |
- Striatum |
- KK/HlJ |
- 61 |
- F |
-
-
- | 86 |
- R3110SA |
- 1835 |
- Striatum |
- KK/HlJ |
- 61 |
- M |
-
-
- | 87 |
- R3111SA |
- 1865 |
- Striatum |
- MOLF/EiJ |
- 60 |
- F |
-
-
- | 88 |
- R3112SA |
- 1855 |
- Striatum |
- MOLF/EiJ |
- 60 |
- M |
-
-
- | 89 |
- R3113SA |
- 1295 |
- Striatum |
- NOD/LtJ |
- 58 |
- F |
-
-
- | 90 |
- R3114SA |
- 1315 |
- Striatum |
- NOD/LtJ |
- 58 |
- M |
-
-
- | 91 |
- R3115SA |
- 2075 |
- Striatum |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 92 |
- R3116SA |
- 1515 |
- Striatum |
- NZB/BlNJ |
- 58 |
- M |
-
-
- | 93 |
- R3117SA |
- 1745 |
- Striatum |
- NZO/HlLtJ |
- 61 |
- F |
-
-
- | 94 |
- R3118SA |
- 1725 |
- Striatum |
- NZO/HlLtJ |
- 61 |
- M |
-
-
- | 95 |
- R3119SA |
- 1805 |
- Striatum |
- NZW/LacJ |
- 65 |
- F |
-
-
- | 96 |
- R3120SA |
- 1685 |
- Striatum |
- NZW/LacJ |
- 70 |
- M |
-
-
- | 97 |
- R3121SA |
- 1875 |
- Striatum |
- PWD/PhJ |
- 70 |
- F |
-
-
- | 98 |
- R3122SA |
- 1885 |
- Striatum |
- PWD/PhJ |
- 70 |
- M |
-
-
- | 99 |
- R3123SA |
- 1765 |
- Striatum |
- PWK/PhJ |
- 59 |
- F |
-
-
- | 100 |
- R3124SA |
- 1785 |
- Striatum |
- PWK/PhJ |
- 60 |
- M |
-
-
- | 101 |
- R3125SA |
- 1825 |
- Striatum |
- WSB/EiJ |
- 71 |
- F |
-
-
- | 102 |
- R3126SA |
- 1655 |
- Striatum |
- WSB/EiJ |
- 71 |
- M |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/Striatum_Exon_0209/notes.rtf b/general/datasets/Striatum_Exon_0209/notes.rtf
deleted file mode 100644
index 677a1bd..0000000
--- a/general/datasets/Striatum_Exon_0209/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Final and fully corrected Exon 1.0 ST array data. Entered by Arthur Centeno. Data error-checking by Manjunatha N. Jagalur . Tissue collected by Glenn Rosen. Array processing by Weikuan Gu.
diff --git a/general/datasets/Striatum_Exon_1212/cases.rtf b/general/datasets/Striatum_Exon_1212/cases.rtf
deleted file mode 100644
index e4db26e..0000000
--- a/general/datasets/Striatum_Exon_1212/cases.rtf
+++ /dev/null
@@ -1,947 +0,0 @@
-A movie of the dissection of the brain, including the striatum, by Dr. Glenn Rosen.
-
-About the strains used to generate this set of data
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Tube No. |
- Tissue |
- Strain |
- Age |
- Sex |
-
-
- | 1 |
- R3025SA |
- 1705 |
- Striatum |
- 129S1/SvImJ |
- 60 |
- F |
-
-
- | 2 |
- R3026SA |
- 1375 |
- Striatum |
- 129S1/SvImJ |
- 59 |
- M |
-
-
- | 3 |
- R3027SA |
- 1435 |
- Striatum |
- A/J |
- 59 |
- F |
-
-
- | 4 |
- R3028SA |
- 1455 |
- Striatum |
- A/J |
- 59 |
- M |
-
-
- | 5 |
- R3029SA |
- 1395 |
- Striatum |
- AKR/J |
- 59 |
- F |
-
-
- | 6 |
- R3030SA |
- 1415 |
- Striatum |
- AKR/J |
- 59 |
- M |
-
-
- | 7 |
- R3031SA |
- 1227 |
- Striatum |
- B6D2F1 |
- 59 |
- F |
-
-
- | 8 |
- R3032SA |
- 1225 |
- Striatum |
- B6D2F1 |
- 59 |
- M |
-
-
- | 9 |
- R3033SA |
- 1495 |
- Striatum |
- BALB/cByJ |
- 59 |
- F |
-
-
- | 10 |
- R3034SA |
- 1475 |
- Striatum |
- BALB/cByJ |
- 59 |
- M |
-
-
- | 11 |
- R3035SA |
- 1665 |
- Striatum |
- BTBRT<+>tf/J |
- 59 |
- F |
-
-
- | 12 |
- R3036SA |
- 1615 |
- Striatum |
- BTBRT<+>tf/J |
- 60 |
- M |
-
-
- | 13 |
- R3037SA |
- 457 |
- Striatum |
- BXD1 |
- 59 |
- F |
-
-
- | 14 |
- R3038SA |
- 927 |
- Striatum |
- BXD1 |
- 59 |
- M |
-
-
- | 15 |
- R3055SA |
- 487 |
- Striatum |
- BXD2 |
- 61 |
- F |
-
-
- | 16 |
- R3056SA |
- 477 |
- Striatum |
- BXD2 |
- 61 |
- M |
-
-
- | 17 |
- R3089SA |
- 977 |
- Striatum |
- BXD5 |
- 58 |
- F |
-
-
- | 18 |
- R3090SA |
- 967 |
- Striatum |
- BXD5 |
- 58 |
- M |
-
-
- | 19 |
- R3091SA |
- 557 |
- Striatum |
- BXD6 |
- 59 |
- F |
-
-
- | 20 |
- R3092SA |
- 547 |
- Striatum |
- BXD6 |
- 59 |
- M |
-
-
- | 21 |
- R3093SA |
- 717 |
- Striatum |
- BXD8 |
- 61 |
- F |
-
-
- | 22 |
- R3094SA |
- 707 |
- Striatum |
- BXD8 |
- 61 |
- M |
-
-
- | 23 |
- R3095SA |
- 647 |
- Striatum |
- BXD9 |
- 60 |
- F |
-
-
- | 24 |
- R3096SA |
- 637 |
- Striatum |
- BXD9 |
- 60 |
- M |
-
-
- | 25 |
- R3039SA |
- 517 |
- Striatum |
- BXD11 |
- 59 |
- F |
-
-
- | 26 |
- R3040SA |
- 787 |
- Striatum |
- BXD11 |
- 59 |
- M |
-
-
- | 27 |
- R3041SA |
- 817 |
- Striatum |
- BXD12 |
- 62 |
- F |
-
-
- | 28 |
- R3042SA |
- 807 |
- Striatum |
- BXD12 |
- 59 |
- M |
-
-
- | 29 |
- R3043SA |
- 877 |
- Striatum |
- BXD13 |
- 60 |
- F |
-
-
- | 30 |
- R3044SA |
- 867 |
- Striatum |
- BXD13 |
- 60 |
- M |
-
-
- | 31 |
- R3045SA |
- 1067 |
- Striatum |
- BXD14 |
- 59 |
- F |
-
-
- | 32 |
- R3144SA |
- 1077 |
- Striatum |
- BXD14 |
- 59 |
- M |
-
-
- | 33 |
- R3047SA |
- 1057 |
- Striatum |
- BXD15 |
- 60 |
- F |
-
-
- | 34 |
- R3048SA |
- 1047 |
- Striatum |
- BXD15 |
- 60 |
- M |
-
-
- | 35 |
- R3049SA |
- 767 |
- Striatum |
- BXD16 |
- 61 |
- F |
-
-
- | 36 |
- R3050SA |
- 777 |
- Striatum |
- BXD16 |
- 61 |
- M |
-
-
- | 37 |
- R3051SA |
- 1177 |
- Striatum |
- BXD18 |
- 59 |
- F |
-
-
- | 38 |
- R3052SA |
- 1167 |
- Striatum |
- BXD18 |
- 59 |
- M |
-
-
- | 39 |
- R3053SA |
- 957 |
- Striatum |
- BXD19 |
- 60 |
- F |
-
-
- | 40 |
- R3054SA |
- 947 |
- Striatum |
- BXD19 |
- 60 |
- M |
-
-
- | 41 |
- R3057SA |
- 1255 |
- Striatum |
- BXD20 |
- 60 |
- F |
-
-
- | 42 |
- R3058SA |
- 1245 |
- Striatum |
- BXD20 |
- 60 |
- M |
-
-
- | 43 |
- R3059SA |
- 1197 |
- Striatum |
- BXD21 |
- 48 |
- F |
-
-
- | 44 |
- R3060SA |
- 1187 |
- Striatum |
- BXD21 |
- 48 |
- M |
-
-
- | 45 |
- R3061SA |
- 1235 |
- Striatum |
- BXD22 |
- 58 |
- F |
-
-
- | 46 |
- R3062SA |
- 1275 |
- Striatum |
- BXD22 |
- 60 |
- M |
-
-
- | 47 |
- R3063SA |
- 1137 |
- Striatum |
- BXD23 |
- 60 |
- F |
-
-
- | 48 |
- R3064SA |
- 1127 |
- Striatum |
- BXD23 |
- 60 |
- M |
-
-
- | 49 |
- R3065SA |
- 437 |
- Striatum |
- BXD24 |
- 59 |
- F |
-
-
- | 50 |
- R3066SA |
- 587 |
- Striatum |
- BXD24 |
- 60 |
- M |
-
-
- | 51 |
- R3067SA |
- 1107 |
- Striatum |
- BXD27 |
- 60 |
- F |
-
-
- | 52 |
- R3068SA |
- 1117 |
- Striatum |
- BXD27 |
- 60 |
- M |
-
-
- | 53 |
- R3069SA |
- 1027 |
- Striatum |
- BXD28 |
- 60 |
- F |
-
-
- | 54 |
- R3070SA |
- 1037 |
- Striatum |
- BXD28 |
- 60 |
- M |
-
-
- | 55 |
- R3071SA |
- 1007 |
- Striatum |
- BXD29 |
- 58 |
- F |
-
-
- | 56 |
- R3072SA |
- 1017 |
- Striatum |
- BXD29 |
- 58 |
- M |
-
-
- | 57 |
- R3073SA |
- 997 |
- Striatum |
- BxD31 |
- 60 |
- F |
-
-
- | 58 |
- R3074SA |
- 987 |
- Striatum |
- BxD31 |
- 60 |
- M |
-
-
- | 59 |
- R3075SA |
- 917 |
- Striatum |
- BXD32 |
- 57 |
- F |
-
-
- | 60 |
- R3076SA |
- 907 |
- Striatum |
- BXD32 |
- 57 |
- M |
-
-
- | 61 |
- R3077SA |
- 897 |
- Striatum |
- BXD33 |
- 59 |
- F |
-
-
- | 62 |
- R3078SA |
- 887 |
- Striatum |
- BXD33 |
- 59 |
- M |
-
-
- | 63 |
- R3079SA |
- 837 |
- Striatum |
- BXD34 |
- 60 |
- F |
-
-
- | 64 |
- R3080SA |
- 827 |
- Striatum |
- BXD34 |
- 60 |
- M |
-
-
- | 65 |
- R3081SA |
- 857 |
- Striatum |
- BXD36 |
- 57 |
- F |
-
-
- | 66 |
- R3082SA |
- 847 |
- Striatum |
- BXD36 |
- 57 |
- M |
-
-
- | 67 |
- R3083SA |
- 697 |
- Striatum |
- BXD38 |
- 60 |
- F |
-
-
- | 68 |
- R3084SA |
- 687 |
- Striatum |
- BXD38 |
- 60 |
- M |
-
-
- | 69 |
- R3085SA |
- 677 |
- Striatum |
- BXD40 |
- 60 |
- F |
-
-
- | 70 |
- R3086SA |
- 667 |
- Striatum |
- BXD40 |
- 60 |
- M |
-
-
- | 71 |
- R3087SA |
- 577 |
- Striatum |
- BXD42 |
- 58 |
- F |
-
-
- | 72 |
- R3088SA |
- 567 |
- Striatum |
- BXD42 |
- 58 |
- M |
-
-
- | 73 |
- R3097SA |
- 1975 |
- Striatum |
- BXSB/MpJ |
- 61 |
- F |
-
-
- | 74 |
- R3098SA |
- 1945 |
- Striatum |
- BXSB/MpJ |
- 61 |
- M |
-
-
- | 75 |
- R3099SA |
- 1575 |
- Striatum |
- C3H/HeJ |
- 60 |
- F |
-
-
- | 76 |
- R3100SA |
- 1595 |
- Striatum |
- C3H/HeJ |
- 60 |
- M |
-
-
- | 77 |
- R3101SA |
- 1228 |
- Striatum |
- C57BL/6J |
- 58 |
- F |
-
-
- | 78 |
- R3102SA |
- 343 |
- Striatum |
- C57BL/6J |
- 59 |
- M |
-
-
- | 79 |
- R3103SA (sample removed) |
- 2305 |
- Striatum |
- CAST/Ei |
- 61 |
- F |
-
-
- | 80 |
- R3104SA (sample removed) |
- 2285 |
- Striatum |
- CAST/Ei |
- 59 |
- M |
-
-
- | 81 |
- R3105SA |
- 1223 |
- Striatum |
- DBA/2J |
- 58 |
- F |
-
-
- | 82 |
- R3106SA |
- 344 |
- Striatum |
- DBA/2J |
- 59 |
- M |
-
-
- | 83 |
- R3107SA |
- 1535 |
- Striatum |
- FVB/NJ |
- 60 |
- F |
-
-
- | 84 |
- R3108SA |
- 1555 |
- Striatum |
- FVB/NJ |
- 60 |
- M |
-
-
- | 85 |
- R3109SA |
- 1845 |
- Striatum |
- KK/HlJ |
- 61 |
- F |
-
-
- | 86 |
- R3110SA |
- 1835 |
- Striatum |
- KK/HlJ |
- 61 |
- M |
-
-
- | 87 |
- R3111SA |
- 1865 |
- Striatum |
- MOLF/EiJ |
- 60 |
- F |
-
-
- | 88 |
- R3112SA |
- 1855 |
- Striatum |
- MOLF/EiJ |
- 60 |
- M |
-
-
- | 89 |
- R3113SA |
- 1295 |
- Striatum |
- NOD/LtJ |
- 58 |
- F |
-
-
- | 90 |
- R3114SA |
- 1315 |
- Striatum |
- NOD/LtJ |
- 58 |
- M |
-
-
- | 91 |
- R3115SA |
- 2075 |
- Striatum |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 92 |
- R3116SA |
- 1515 |
- Striatum |
- NZB/BlNJ |
- 58 |
- M |
-
-
- | 93 |
- R3117SA |
- 1745 |
- Striatum |
- NZO/HlLtJ |
- 61 |
- F |
-
-
- | 94 |
- R3118SA |
- 1725 |
- Striatum |
- NZO/HlLtJ |
- 61 |
- M |
-
-
- | 95 |
- R3119SA |
- 1805 |
- Striatum |
- NZW/LacJ |
- 65 |
- F |
-
-
- | 96 |
- R3120SA |
- 1685 |
- Striatum |
- NZW/LacJ |
- 70 |
- M |
-
-
- | 97 |
- R3121SA |
- 1875 |
- Striatum |
- PWD/PhJ |
- 70 |
- F |
-
-
- | 98 |
- R3122SA |
- 1885 |
- Striatum |
- PWD/PhJ |
- 70 |
- M |
-
-
- | 99 |
- R3123SA |
- 1765 |
- Striatum |
- PWK/PhJ |
- 59 |
- F |
-
-
- | 100 |
- R3124SA |
- 1785 |
- Striatum |
- PWK/PhJ |
- 60 |
- M |
-
-
- | 101 |
- R3125SA |
- 1825 |
- Striatum |
- WSB/EiJ |
- 71 |
- F |
-
-
- | 102 |
- R3126SA |
- 1655 |
- Striatum |
- WSB/EiJ |
- 71 |
- M |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/Striatum_Exon_1212/notes.rtf b/general/datasets/Striatum_Exon_1212/notes.rtf
deleted file mode 100644
index 677a1bd..0000000
--- a/general/datasets/Striatum_Exon_1212/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Final and fully corrected Exon 1.0 ST array data. Entered by Arthur Centeno. Data error-checking by Manjunatha N. Jagalur . Tissue collected by Glenn Rosen. Array processing by Weikuan Gu.
diff --git a/general/datasets/TSRI-DRG-AffyMOE430_0113-MDP/summary.rtf b/general/datasets/TSRI-DRG-AffyMOE430_0113-MDP/summary.rtf
deleted file mode 100644
index 643b371..0000000
--- a/general/datasets/TSRI-DRG-AffyMOE430_0113-MDP/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 159, Name: TSRI DRG Affy Mouse Genome 430 2.0 (Jan13) RMA MDP **
\ No newline at end of file
diff --git a/general/datasets/UAB_DrosWB_LC_RMA_1009/platform.rtf b/general/datasets/UAB_DrosWB_LC_RMA_1009/platform.rtf
deleted file mode 100644
index 2a01b87..0000000
--- a/general/datasets/UAB_DrosWB_LC_RMA_1009/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Drosophila Genome 2.0 Array GEO_GPL1322
diff --git a/general/datasets/UAB_DrosWB_LC_RMA_1009/summary.rtf b/general/datasets/UAB_DrosWB_LC_RMA_1009/summary.rtf
deleted file mode 100644
index ef884bc..0000000
--- a/general/datasets/UAB_DrosWB_LC_RMA_1009/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The genetics of gene expression in recombinant inbred lines (RILs) can be mapped as expression quantitative trait loci (eQTLs). So-called "genetical genomics" studies have identified locally acting eQTLs (cis-eQTLs) for genes that show differences in steady-state RNA levels. These studies have also identified distantly acting master-modulatory trans-eQTLs that regulate tens or hundreds of transcripts (hotspots or transbands). We expand on these studies by performing genetical genomics experiments in two environments in order to identify trans-eQTL thatmight be regulated by developmental exposure to the neurotoxin lead. Flies from each of 75 RIL were raised from eggs to adults on either control food (made with 250 mM sodium acetate), or lead-treated food (made with 250 mM lead acetate, PbAc). RNA expression analyses of whole adult male flies (5–10 days old) were performed with Affymetrix DrosII whole genome arrays (18,952 probesets). Among the 1389 genes with cis-eQTL, there were 405 genes unique to control flies and 544 genes unique to lead-treated ones (440 genes had the same cis-eQTLs in both samples). There are 2396 genes with trans-eQTL which mapped to 12major transbands with greater than 95 genes. Permutation analyses of the strain labels but not the expression data suggests that the total number of eQTL and the number of transbands are more important criteria for validation than the size of the transband. Two transbands, one located on the 2nd chromosome and one on the 3rd chromosome, co-regulate 33 lead-induced genes, many of which are involved in neurodevelopmental processes. For these 33 genes, rather than allelic variation at one locus exerting differential effects in two environments, we found that variation at two different loci are required for optimal effects on lead-induced expression.
diff --git a/general/datasets/UAB_DrosWB_LE_RMA_1009/platform.rtf b/general/datasets/UAB_DrosWB_LE_RMA_1009/platform.rtf
deleted file mode 100644
index 2a01b87..0000000
--- a/general/datasets/UAB_DrosWB_LE_RMA_1009/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Affymetrix Drosophila Genome 2.0 Array GEO_GPL1322
diff --git a/general/datasets/UAB_DrosWB_LE_RMA_1009/summary.rtf b/general/datasets/UAB_DrosWB_LE_RMA_1009/summary.rtf
deleted file mode 100644
index ef884bc..0000000
--- a/general/datasets/UAB_DrosWB_LE_RMA_1009/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The genetics of gene expression in recombinant inbred lines (RILs) can be mapped as expression quantitative trait loci (eQTLs). So-called "genetical genomics" studies have identified locally acting eQTLs (cis-eQTLs) for genes that show differences in steady-state RNA levels. These studies have also identified distantly acting master-modulatory trans-eQTLs that regulate tens or hundreds of transcripts (hotspots or transbands). We expand on these studies by performing genetical genomics experiments in two environments in order to identify trans-eQTL thatmight be regulated by developmental exposure to the neurotoxin lead. Flies from each of 75 RIL were raised from eggs to adults on either control food (made with 250 mM sodium acetate), or lead-treated food (made with 250 mM lead acetate, PbAc). RNA expression analyses of whole adult male flies (5–10 days old) were performed with Affymetrix DrosII whole genome arrays (18,952 probesets). Among the 1389 genes with cis-eQTL, there were 405 genes unique to control flies and 544 genes unique to lead-treated ones (440 genes had the same cis-eQTLs in both samples). There are 2396 genes with trans-eQTL which mapped to 12major transbands with greater than 95 genes. Permutation analyses of the strain labels but not the expression data suggests that the total number of eQTL and the number of transbands are more important criteria for validation than the size of the transband. Two transbands, one located on the 2nd chromosome and one on the 3rd chromosome, co-regulate 33 lead-induced genes, many of which are involved in neurodevelopmental processes. For these 33 genes, rather than allelic variation at one locus exerting differential effects in two environments, we found that variation at two different loci are required for optimal effects on lead-induced expression.
diff --git a/general/datasets/UCLA_BDF2_LIVER_1999/experiment-design.rtf b/general/datasets/UCLA_BDF2_LIVER_1999/experiment-design.rtf
deleted file mode 100644
index 592d9aa..0000000
--- a/general/datasets/UCLA_BDF2_LIVER_1999/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers from 311 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BDF2_LIVER_1999/summary.rtf b/general/datasets/UCLA_BDF2_LIVER_1999/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BDF2_LIVER_1999/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_0605/experiment-design.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_0605/experiment-design.rtf
deleted file mode 100644
index 54a15e7..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_0605/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Adipose from 295 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_0605/summary.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_0605/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_0605/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/experiment-design.rtf
deleted file mode 100644
index 54a15e7..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Adipose from 295 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/specifics.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/summary.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_MALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_MALE/experiment-design.rtf
deleted file mode 100644
index 54a15e7..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Adipose from 295 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_MALE/specifics.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHF2_ADIPOSE_MALE/summary.rtf b/general/datasets/UCLA_BHF2_ADIPOSE_MALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_ADIPOSE_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_BRAIN_0605/experiment-design.rtf b/general/datasets/UCLA_BHF2_BRAIN_0605/experiment-design.rtf
deleted file mode 100644
index 171d4d8..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_0605/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain from 249 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_BRAIN_0605/summary.rtf b/general/datasets/UCLA_BHF2_BRAIN_0605/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_0605/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_BRAIN_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_BRAIN_FEMALE/experiment-design.rtf
deleted file mode 100644
index 171d4d8..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain from 249 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_BRAIN_FEMALE/specifics.rtf b/general/datasets/UCLA_BHF2_BRAIN_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHF2_BRAIN_FEMALE/summary.rtf b/general/datasets/UCLA_BHF2_BRAIN_FEMALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_BRAIN_MALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_BRAIN_MALE/experiment-design.rtf
deleted file mode 100644
index 171d4d8..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain from 249 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_BRAIN_MALE/specifics.rtf b/general/datasets/UCLA_BHF2_BRAIN_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHF2_BRAIN_MALE/summary.rtf b/general/datasets/UCLA_BHF2_BRAIN_MALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_BRAIN_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_LIVER_0605/experiment-design.rtf b/general/datasets/UCLA_BHF2_LIVER_0605/experiment-design.rtf
deleted file mode 100644
index 592d9aa..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_0605/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers from 311 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_LIVER_0605/summary.rtf b/general/datasets/UCLA_BHF2_LIVER_0605/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_0605/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_LIVER_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_LIVER_FEMALE/experiment-design.rtf
deleted file mode 100644
index 592d9aa..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers from 311 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_LIVER_FEMALE/specifics.rtf b/general/datasets/UCLA_BHF2_LIVER_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHF2_LIVER_FEMALE/summary.rtf b/general/datasets/UCLA_BHF2_LIVER_FEMALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_LIVER_MALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_LIVER_MALE/experiment-design.rtf
deleted file mode 100644
index 592d9aa..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Livers from 311 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_LIVER_MALE/specifics.rtf b/general/datasets/UCLA_BHF2_LIVER_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHF2_LIVER_MALE/summary.rtf b/general/datasets/UCLA_BHF2_LIVER_MALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_LIVER_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_0605/experiment-design.rtf b/general/datasets/UCLA_BHF2_MUSCLE_0605/experiment-design.rtf
deleted file mode 100644
index fda46c2..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_0605/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Muscle from 319 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_0605/summary.rtf b/general/datasets/UCLA_BHF2_MUSCLE_0605/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_0605/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/experiment-design.rtf
deleted file mode 100644
index fda46c2..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Muscle from 319 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/specifics.rtf b/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/summary.rtf b/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_MALE/experiment-design.rtf b/general/datasets/UCLA_BHF2_MUSCLE_MALE/experiment-design.rtf
deleted file mode 100644
index fda46c2..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Muscle from 319 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) derived from C57BL/6J and C3H/HeJ parental strains with both on ApoE null backgrounds. All samples were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=Genetics of Gene Expression Keywords=C57BL/6J Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_MALE/specifics.rtf b/general/datasets/UCLA_BHF2_MUSCLE_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHF2_MUSCLE_MALE/summary.rtf b/general/datasets/UCLA_BHF2_MUSCLE_MALE/summary.rtf
deleted file mode 100644
index c5cf6bd..0000000
--- a/general/datasets/UCLA_BHF2_MUSCLE_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The (C57BL/6J X C3H/HeJ)F2 intercross consists of 334 animals of both sexes. All are ApoE null and received a high fat Western diet from 8-24 weeks of age.
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_2005/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_2005/experiment-design.rtf
deleted file mode 100644
index 6df1de9..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_2005/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Adipose from 295 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast adipose tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_2005/summary.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_2005/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/experiment-design.rtf
deleted file mode 100644
index 6df1de9..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Adipose from 295 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast adipose tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/summary.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/experiment-design.rtf
deleted file mode 100644
index 6df1de9..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Adipose from 295 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast adipose tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/summary.rtf b/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_ADIPOSE_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_2005/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_2005/experiment-design.rtf
deleted file mode 100644
index b1ce841..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_2005/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain from 292 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15%cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Brain tissues were dissected and flash frozen in LN2 and stored at -80°C.
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_2005/summary.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_2005/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/experiment-design.rtf
deleted file mode 100644
index b1ce841..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain from 292 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15%cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Brain tissues were dissected and flash frozen in LN2 and stored at -80°C.
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/summary.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_MALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_MALE/experiment-design.rtf
deleted file mode 100644
index b1ce841..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Brain from 292 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15%cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Brain tissues were dissected and flash frozen in LN2 and stored at -80°C.
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_MALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHHBF2_BRAIN_MALE/summary.rtf b/general/datasets/UCLA_BHHBF2_BRAIN_MALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_BRAIN_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_2005/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_LIVER_2005/experiment-design.rtf
deleted file mode 100644
index dad76ff..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_2005/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver from 302 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast liver tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_2005/summary.rtf b/general/datasets/UCLA_BHHBF2_LIVER_2005/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/experiment-design.rtf
deleted file mode 100644
index dad76ff..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver from 302 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast liver tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/summary.rtf b/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_MALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_LIVER_MALE/experiment-design.rtf
deleted file mode 100644
index dad76ff..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Liver from 302 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast liver tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_MALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_LIVER_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHHBF2_LIVER_MALE/summary.rtf b/general/datasets/UCLA_BHHBF2_LIVER_MALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_LIVER_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_2005/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_2005/experiment-design.rtf
deleted file mode 100644
index fa6a257..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_2005/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Muscle from 285 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Muscle tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_2005/summary.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_2005/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/experiment-design.rtf
deleted file mode 100644
index fa6a257..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Muscle from 285 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Muscle tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/specifics.rtf
deleted file mode 100644
index 3a8cf6f..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Females only
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/summary.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/experiment-design.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/experiment-design.rtf
deleted file mode 100644
index fa6a257..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Muscle from 285 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Muscle tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/specifics.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/specifics.rtf
deleted file mode 100644
index 6b7200b..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Males only
diff --git a/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/summary.rtf b/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/summary.rtf
deleted file mode 100644
index e7144bf..0000000
--- a/general/datasets/UCLA_BHHBF2_MUSCLE_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).
diff --git a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/acknowledgment.rtf b/general/datasets/UCLA_BXD-on_Femur_0113_RSN/acknowledgment.rtf
deleted file mode 100644
index 841713a..0000000
--- a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Calabrese G, Bennett BJ, Orozco L, Kang HM, Eskin E, Dombret C, De Backer O, Lusis AJ, Farber CR.
diff --git a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/experiment-design.rtf b/general/datasets/UCLA_BXD-on_Femur_0113_RSN/experiment-design.rtf
deleted file mode 100644
index 6a72392..0000000
--- a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-RNA from cortical bone (femoral diaphysis free of marrow) were profiled from 99 Hybrid Mouse Diversity Panel strains were profiled. Sixteen-week old male mice were used in this study. A total of 1-3 mice per strain were arrayed.
diff --git a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/platform.rtf b/general/datasets/UCLA_BXD-on_Femur_0113_RSN/platform.rtf
deleted file mode 100644
index 578985c..0000000
--- a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina mouse-6 v1.1 expression beadchip
diff --git a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/processing.rtf b/general/datasets/UCLA_BXD-on_Femur_0113_RSN/processing.rtf
deleted file mode 100644
index 9f66d05..0000000
--- a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The expression values were transformed using the Variance Stabilizing Transformation (VST), and normalized with the Robust Spline Normalization (RSN) algorithm using the LumiR R package. After normalization, the ComBat software was used to adjust for batch effects using an empirical Bayes method.
diff --git a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/summary.rtf b/general/datasets/UCLA_BXD-on_Femur_0113_RSN/summary.rtf
deleted file mode 100644
index df75fa6..0000000
--- a/general/datasets/UCLA_BXD-on_Femur_0113_RSN/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Significant advances have been made in the discovery of genes affecting bone mineral density (BMD); however, our understanding of its genetic basis remains incomplete. In the current study, genome-wide association (GWA) and co-expression network analysis was used in the recently described Hybrid Mouse Diversity Panel (HMDP) to identify and functionally characterize novel BMD genes. In the HMDP, a GWA of total body, spinal and femoral BMD revealed four significant associations (-log10P > 5.39) affecting at least one BMD trait on chromosomes (Chrs.) 7, 11, 12 and 17. The associations implicated a total of 163 genes with each association harboring between 14 and 112 genes. This list was reduced to 26 functional candidates by identifying those genes that were regulated by local eQTL in bone or harbored potentially functional non-synonymous (NS) SNPs. This analysis revealed that the most significant BMD SNP on Chr. 12 was a NS SNP in the additional sex combs like-2 (Asxl2) gene that was predicted to be functional. The involvement of Asxl2 in the regulation of bone mass was confirmed by the observation that Asxl2 knockout mice had reduced BMD. To begin to unravel the mechanism though which Asxl2 influenced BMD, a gene co-expression network was created using cortical bone gene expression microarray data from the HMDP strains. Asxl2 was identified as a member of a co-expression gene module enriched for genes involved in the differentiation of myeloid cells. In bone, osteoclasts are bone-resorbing cell of myeloid origin, suggesting that Asxl2 may play a role in osteoclast differentiation. In agreement, the knockdown of Asxl2 in bone marrow macrophages impaired their ability to form osteoclasts. This study identifies a new regulator of BMD and osteoclastogenesis and highlights the power of GWA and systems genetics in the mouse for dissecting complex genetic traits.
diff --git a/general/datasets/UCLA_BXDBXH_CARTILAGE/experiment-design.rtf b/general/datasets/UCLA_BXDBXH_CARTILAGE/experiment-design.rtf
deleted file mode 100644
index 93735b8..0000000
--- a/general/datasets/UCLA_BXDBXH_CARTILAGE/experiment-design.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
- -
- -
-
diff --git a/general/datasets/UCLA_BXDBXH_CARTILAGE/summary.rtf b/general/datasets/UCLA_BXDBXH_CARTILAGE/summary.rtf
deleted file mode 100644
index fbd364b..0000000
--- a/general/datasets/UCLA_BXDBXH_CARTILAGE/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Summary of DatasetId 59, Name: UCLA BXD and BXH Cartilage
-
-​J Bone Miner Res. 2011 Apr;26(4):747-60. doi: 10.1002/jbmr.271.
-
-Systems genetics analysis of mouse chondrocyte differentiation.
-
-Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ
-
-One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development.
-
-PMID:20954177, PMCID:PMC3179327, DOI:10.1002/jbmr.271
diff --git a/general/datasets/UCLA_BXDBXH_CARTILAGE_V2/experiment-design.rtf b/general/datasets/UCLA_BXDBXH_CARTILAGE_V2/experiment-design.rtf
deleted file mode 100644
index 93735b8..0000000
--- a/general/datasets/UCLA_BXDBXH_CARTILAGE_V2/experiment-design.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
- -
- -
-
diff --git a/general/datasets/UCLA_BXDBXH_CARTILAGE_V2/summary.rtf b/general/datasets/UCLA_BXDBXH_CARTILAGE_V2/summary.rtf
deleted file mode 100644
index fbd364b..0000000
--- a/general/datasets/UCLA_BXDBXH_CARTILAGE_V2/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Summary of DatasetId 59, Name: UCLA BXD and BXH Cartilage
-
-​J Bone Miner Res. 2011 Apr;26(4):747-60. doi: 10.1002/jbmr.271.
-
-Systems genetics analysis of mouse chondrocyte differentiation.
-
-Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ
-
-One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development.
-
-PMID:20954177, PMCID:PMC3179327, DOI:10.1002/jbmr.271
diff --git a/general/datasets/UCLA_BXD_CARTILAGE/experiment-design.rtf b/general/datasets/UCLA_BXD_CARTILAGE/experiment-design.rtf
deleted file mode 100644
index 93735b8..0000000
--- a/general/datasets/UCLA_BXD_CARTILAGE/experiment-design.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
- -
- -
-
diff --git a/general/datasets/UCLA_BXD_CARTILAGE/summary.rtf b/general/datasets/UCLA_BXD_CARTILAGE/summary.rtf
deleted file mode 100644
index fbd364b..0000000
--- a/general/datasets/UCLA_BXD_CARTILAGE/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Summary of DatasetId 59, Name: UCLA BXD and BXH Cartilage
-
-​J Bone Miner Res. 2011 Apr;26(4):747-60. doi: 10.1002/jbmr.271.
-
-Systems genetics analysis of mouse chondrocyte differentiation.
-
-Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ
-
-One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development.
-
-PMID:20954177, PMCID:PMC3179327, DOI:10.1002/jbmr.271
diff --git a/general/datasets/UCLA_BXD_Femur_0113_RSN/acknowledgment.rtf b/general/datasets/UCLA_BXD_Femur_0113_RSN/acknowledgment.rtf
deleted file mode 100644
index 841713a..0000000
--- a/general/datasets/UCLA_BXD_Femur_0113_RSN/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Calabrese G, Bennett BJ, Orozco L, Kang HM, Eskin E, Dombret C, De Backer O, Lusis AJ, Farber CR.
diff --git a/general/datasets/UCLA_BXD_Femur_0113_RSN/experiment-design.rtf b/general/datasets/UCLA_BXD_Femur_0113_RSN/experiment-design.rtf
deleted file mode 100644
index 6a72392..0000000
--- a/general/datasets/UCLA_BXD_Femur_0113_RSN/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-RNA from cortical bone (femoral diaphysis free of marrow) were profiled from 99 Hybrid Mouse Diversity Panel strains were profiled. Sixteen-week old male mice were used in this study. A total of 1-3 mice per strain were arrayed.
diff --git a/general/datasets/UCLA_BXD_Femur_0113_RSN/platform.rtf b/general/datasets/UCLA_BXD_Femur_0113_RSN/platform.rtf
deleted file mode 100644
index 578985c..0000000
--- a/general/datasets/UCLA_BXD_Femur_0113_RSN/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina mouse-6 v1.1 expression beadchip
diff --git a/general/datasets/UCLA_BXD_Femur_0113_RSN/processing.rtf b/general/datasets/UCLA_BXD_Femur_0113_RSN/processing.rtf
deleted file mode 100644
index 9f66d05..0000000
--- a/general/datasets/UCLA_BXD_Femur_0113_RSN/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The expression values were transformed using the Variance Stabilizing Transformation (VST), and normalized with the Robust Spline Normalization (RSN) algorithm using the LumiR R package. After normalization, the ComBat software was used to adjust for batch effects using an empirical Bayes method.
diff --git a/general/datasets/UCLA_BXD_Femur_0113_RSN/summary.rtf b/general/datasets/UCLA_BXD_Femur_0113_RSN/summary.rtf
deleted file mode 100644
index df75fa6..0000000
--- a/general/datasets/UCLA_BXD_Femur_0113_RSN/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Significant advances have been made in the discovery of genes affecting bone mineral density (BMD); however, our understanding of its genetic basis remains incomplete. In the current study, genome-wide association (GWA) and co-expression network analysis was used in the recently described Hybrid Mouse Diversity Panel (HMDP) to identify and functionally characterize novel BMD genes. In the HMDP, a GWA of total body, spinal and femoral BMD revealed four significant associations (-log10P > 5.39) affecting at least one BMD trait on chromosomes (Chrs.) 7, 11, 12 and 17. The associations implicated a total of 163 genes with each association harboring between 14 and 112 genes. This list was reduced to 26 functional candidates by identifying those genes that were regulated by local eQTL in bone or harbored potentially functional non-synonymous (NS) SNPs. This analysis revealed that the most significant BMD SNP on Chr. 12 was a NS SNP in the additional sex combs like-2 (Asxl2) gene that was predicted to be functional. The involvement of Asxl2 in the regulation of bone mass was confirmed by the observation that Asxl2 knockout mice had reduced BMD. To begin to unravel the mechanism though which Asxl2 influenced BMD, a gene co-expression network was created using cortical bone gene expression microarray data from the HMDP strains. Asxl2 was identified as a member of a co-expression gene module enriched for genes involved in the differentiation of myeloid cells. In bone, osteoclasts are bone-resorbing cell of myeloid origin, suggesting that Asxl2 may play a role in osteoclast differentiation. In agreement, the knockdown of Asxl2 in bone marrow macrophages impaired their ability to form osteoclasts. This study identifies a new regulator of BMD and osteoclastogenesis and highlights the power of GWA and systems genetics in the mouse for dissecting complex genetic traits.
diff --git a/general/datasets/UCLA_BXHBXD_CARTILAGE/experiment-design.rtf b/general/datasets/UCLA_BXHBXD_CARTILAGE/experiment-design.rtf
deleted file mode 100644
index 93735b8..0000000
--- a/general/datasets/UCLA_BXHBXD_CARTILAGE/experiment-design.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
- -
- -
-
diff --git a/general/datasets/UCLA_BXHBXD_CARTILAGE/summary.rtf b/general/datasets/UCLA_BXHBXD_CARTILAGE/summary.rtf
deleted file mode 100644
index fbd364b..0000000
--- a/general/datasets/UCLA_BXHBXD_CARTILAGE/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Summary of DatasetId 59, Name: UCLA BXD and BXH Cartilage
-
-​J Bone Miner Res. 2011 Apr;26(4):747-60. doi: 10.1002/jbmr.271.
-
-Systems genetics analysis of mouse chondrocyte differentiation.
-
-Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ
-
-One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development.
-
-PMID:20954177, PMCID:PMC3179327, DOI:10.1002/jbmr.271
diff --git a/general/datasets/UCLA_BXHBXD_CARTILAGE_V2/experiment-design.rtf b/general/datasets/UCLA_BXHBXD_CARTILAGE_V2/experiment-design.rtf
deleted file mode 100644
index 93735b8..0000000
--- a/general/datasets/UCLA_BXHBXD_CARTILAGE_V2/experiment-design.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
- -
- -
-
diff --git a/general/datasets/UCLA_BXHBXD_CARTILAGE_V2/summary.rtf b/general/datasets/UCLA_BXHBXD_CARTILAGE_V2/summary.rtf
deleted file mode 100644
index fbd364b..0000000
--- a/general/datasets/UCLA_BXHBXD_CARTILAGE_V2/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Summary of DatasetId 59, Name: UCLA BXD and BXH Cartilage
-
-​J Bone Miner Res. 2011 Apr;26(4):747-60. doi: 10.1002/jbmr.271.
-
-Systems genetics analysis of mouse chondrocyte differentiation.
-
-Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ
-
-One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development.
-
-PMID:20954177, PMCID:PMC3179327, DOI:10.1002/jbmr.271
diff --git a/general/datasets/UCLA_BXH_CARTILAGE/experiment-design.rtf b/general/datasets/UCLA_BXH_CARTILAGE/experiment-design.rtf
deleted file mode 100644
index 93735b8..0000000
--- a/general/datasets/UCLA_BXH_CARTILAGE/experiment-design.rtf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
- -
- -
-
diff --git a/general/datasets/UCLA_BXH_CARTILAGE/summary.rtf b/general/datasets/UCLA_BXH_CARTILAGE/summary.rtf
deleted file mode 100644
index fbd364b..0000000
--- a/general/datasets/UCLA_BXH_CARTILAGE/summary.rtf
+++ /dev/null
@@ -1,11 +0,0 @@
-Summary of DatasetId 59, Name: UCLA BXD and BXH Cartilage
-
-​J Bone Miner Res. 2011 Apr;26(4):747-60. doi: 10.1002/jbmr.271.
-
-Systems genetics analysis of mouse chondrocyte differentiation.
-
-Suwanwela J, Farber CR, Haung BL, Song B, Pan C, Lyons KM, Lusis AJ
-
-One of the goals of systems genetics is the reconstruction of gene networks that underlie key processes in development and disease. To identify cartilage gene networks that play an important role in bone development, we used a systems genetics approach that integrated microarray gene expression profiles from cartilage and bone phenotypic data from two sets of recombinant inbred strains. Microarray profiles generated from isolated chondrocytes were used to generate weighted gene coexpression networks. This analysis resulted in the identification of subnetworks (modules) of coexpressed genes that then were examined for relationships with bone geometry and density. One module exhibited significant correlation with femur length (r = 0.416), anteroposterior diameter (r = 0.418), mediolateral diameter (r = 0.576), and bone mineral density (r = 0.475). Highly connected genes (n = 28) from this and other modules were tested in vitro using prechondrocyte ATDC5 cells and RNA interference. Five of the 28 genes were found to play a role in chondrocyte differentiation. Two of these, Hspd1 and Cdkn1a, were known previously to function in chondrocyte development, whereas the other three, Bhlhb9, Cugbp1, and Spcs3, are novel genes. Our integrative analysis provided a systems-level view of cartilage development and identified genes that may be involved in bone development.
-
-PMID:20954177, PMCID:PMC3179327, DOI:10.1002/jbmr.271
diff --git a/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_2005/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_2005/summary.rtf
deleted file mode 100644
index 5cbfe56..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 51, Name: UCLA CTB6B6CTF2 Adipose mlratio
diff --git a/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_FEMALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_FEMALE/summary.rtf
deleted file mode 100644
index 5cbfe56..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 51, Name: UCLA CTB6B6CTF2 Adipose mlratio
diff --git a/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_MALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_MALE/summary.rtf
deleted file mode 100644
index 5cbfe56..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_ADIPOSE_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 51, Name: UCLA CTB6B6CTF2 Adipose mlratio
diff --git a/general/datasets/UCLA_CTB6B6CTF2_BRAIN_2005/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_BRAIN_2005/summary.rtf
deleted file mode 100644
index 9d8eb19..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_BRAIN_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 52, Name: UCLA CTB6/B6CTF2 Brain (2005) mlratio
\ No newline at end of file
diff --git a/general/datasets/UCLA_CTB6B6CTF2_BRAIN_FEMALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_BRAIN_FEMALE/summary.rtf
deleted file mode 100644
index 9d8eb19..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_BRAIN_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 52, Name: UCLA CTB6/B6CTF2 Brain (2005) mlratio
\ No newline at end of file
diff --git a/general/datasets/UCLA_CTB6B6CTF2_BRAIN_MALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_BRAIN_MALE/summary.rtf
deleted file mode 100644
index 9d8eb19..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_BRAIN_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 52, Name: UCLA CTB6/B6CTF2 Brain (2005) mlratio
\ No newline at end of file
diff --git a/general/datasets/UCLA_CTB6B6CTF2_LIVER_2005/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_LIVER_2005/summary.rtf
deleted file mode 100644
index fdd0e9f..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_LIVER_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 53, Name: UCLA CTB6B6CTF2 Liver Female mlratio **
\ No newline at end of file
diff --git a/general/datasets/UCLA_CTB6B6CTF2_LIVER_FEMALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_LIVER_FEMALE/summary.rtf
deleted file mode 100644
index fdd0e9f..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_LIVER_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 53, Name: UCLA CTB6B6CTF2 Liver Female mlratio **
\ No newline at end of file
diff --git a/general/datasets/UCLA_CTB6B6CTF2_LIVER_MALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_LIVER_MALE/summary.rtf
deleted file mode 100644
index fdd0e9f..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_LIVER_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 53, Name: UCLA CTB6B6CTF2 Liver Female mlratio **
\ No newline at end of file
diff --git a/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_2005/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_2005/summary.rtf
deleted file mode 100644
index f1e6b81..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_2005/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 54, Name: UCLA CTB6B6CTF2 Muscle Female mlratio **
diff --git a/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_FEMALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_FEMALE/summary.rtf
deleted file mode 100644
index f1e6b81..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_FEMALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 54, Name: UCLA CTB6B6CTF2 Muscle Female mlratio **
diff --git a/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_MALE/summary.rtf b/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_MALE/summary.rtf
deleted file mode 100644
index f1e6b81..0000000
--- a/general/datasets/UCLA_CTB6B6CTF2_MUSCLE_MALE/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 54, Name: UCLA CTB6B6CTF2 Muscle Female mlratio **
diff --git a/general/datasets/UIOWA_Eye_RMA_0906/summary.rtf b/general/datasets/UIOWA_Eye_RMA_0906/summary.rtf
deleted file mode 100644
index 7815ecc..0000000
--- a/general/datasets/UIOWA_Eye_RMA_0906/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 73, Name: UIOWA Eye mRNA RAE230v2 (Sep06)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_Eryth/summary.rtf b/general/datasets/UMCG_0907_Eryth/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_Eryth/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_Eryth_ori/summary.rtf b/general/datasets/UMCG_0907_Eryth_ori/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_Eryth_ori/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_HemaStem/summary.rtf b/general/datasets/UMCG_0907_HemaStem/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_HemaStem/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_HemaStem_ori/summary.rtf b/general/datasets/UMCG_0907_HemaStem_ori/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_HemaStem_ori/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_Myeloid/summary.rtf b/general/datasets/UMCG_0907_Myeloid/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_Myeloid/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_Myeloid_ori/summary.rtf b/general/datasets/UMCG_0907_Myeloid_ori/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_Myeloid_ori/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_Pro/summary.rtf b/general/datasets/UMCG_0907_Pro/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_Pro/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMCG_0907_Pro_ori/summary.rtf b/general/datasets/UMCG_0907_Pro_ori/summary.rtf
deleted file mode 100644
index 9afd234..0000000
--- a/general/datasets/UMCG_0907_Pro_ori/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 38, Name: UMCG Myeloid Cells ILM6v1.1 (Apr09)
\ No newline at end of file
diff --git a/general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf b/general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf
deleted file mode 100644
index 9f0655d..0000000
--- a/general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-We thank Affymetrix Inc. for their generous support of this project and array data set.
diff --git a/general/datasets/UMUTAffyExon_0209_RMA/cases.rtf b/general/datasets/UMUTAffyExon_0209_RMA/cases.rtf
deleted file mode 100644
index 35ae421..0000000
--- a/general/datasets/UMUTAffyExon_0209_RMA/cases.rtf
+++ /dev/null
@@ -1,1182 +0,0 @@
-
-
-
-
-
-
-
- | Index |
- Original CEL |
- Tube ID |
- Strain |
- Age |
- Sex |
- Source |
-
-
- | 1 |
- JR3551H.CEL |
- jr3551h |
- C57BL/6J |
- 60 |
- F |
- UTM RW |
-
-
- | 2 |
- JR3552H.CEL |
- jr3552hre |
- C57BL/6J |
- 60 |
- F |
- UTM RW |
-
-
- | 3 |
- R0572H.CEL |
- r0572h |
- C57BL/6J |
- 69 |
- F |
- |
-
-
- | 4 |
- R2137H.CEL |
- r2137h |
- C57BL/6J |
- 55 |
- F |
- JAX |
-
-
- | 5 |
- R3552H.CEL |
- r3552h |
- C57BL/6J |
- 60 |
- F |
- Glenn |
-
-
- | 6 |
- JR3549H.CEL |
- jr3549h |
- C57BL/6J |
- 60 |
- M |
- UTM RW |
-
-
- | 7 |
- JR3550H.CEL |
- jr3550hre |
- C57BL/6J |
- 60 |
- M |
- UTM RW |
-
-
- | 8 |
- R0574H.CEL |
- r0574h |
- C57BL/6J |
- 69 |
- M |
- |
-
-
- | 9 |
- R2136H.CEL |
- r2136h |
- C57BL/6J |
- 55 |
- M |
- JAX |
-
-
- | 10 |
- R3549H.CEL |
- r3549h |
- C57BL/6J |
- 60 |
- M |
- Glenn |
-
-
- | 11 |
- JR3557H.CEL |
- jr3557h |
- DBA/2J |
- 60 |
- F |
- UTM RW |
-
-
- | 12 |
- JR3558H.CEL |
- jr3558hre |
- DBA/2J |
- 60 |
- F |
- UTM RW |
-
-
- | 13 |
- R3558H.CEL |
- r3558h |
- DBA/2J |
- 60 |
- F |
- Glenn |
-
-
- | 14 |
- JR3555H.CEL |
- jr3555h |
- DBA/2J |
- 60 |
- M |
- UTM RW |
-
-
- | 15 |
- JR3556H.CEL |
- jr3556h |
- DBA/2J |
- 60 |
- M |
- UTM RW |
-
-
- | 16 |
- R3555H.CEL |
- r3555h |
- DBA/2J |
- 60 |
- M |
- Glenn |
-
-
- | 17 |
- R3497H.CEL |
- r3497h |
- B6D2F1 |
- 58 |
- F |
- Glenn |
-
-
- | 18 |
- R3500H.CEL |
- r3500h |
- B6D2F1 |
- 58 |
- M |
- Glenn |
-
-
- | 19 |
- R1374H.CEL |
- r1374h |
- D2B6F1 |
- 58 |
- F |
- UTM RW |
-
-
- | 20 |
- R1382H.CEL |
- r1382h |
- D2B6F1 |
- 59 |
- M |
- UTM RW |
-
-
- | 21 |
- R3532H.CEL |
- r3532h |
- 129S1/SvImJ |
- 60 |
- F |
- Glenn |
-
-
- | 22 |
- R3512H.CEL |
- r3512h |
- 129S1/SvImJ |
- 59 |
- M |
- Glenn |
-
-
- | 23 |
- R3520H.CEL |
- r3520h |
- A/J |
- 59 |
- F |
- Glenn |
-
-
- | 24 |
- R3523H.CEL |
- r3523h |
- A/J |
- 59 |
- M |
- Glenn |
-
-
- | 25 |
- R3514H.CEL |
- r3514h |
- AKR/J |
- 59 |
- F |
- Glenn |
-
-
- | 26 |
- R3515H.CEL |
- r3515h |
- AKR/J |
- 59 |
- M |
- Glenn |
-
-
- | 27 |
- R3508H.CEL |
- r3508h |
- BALB/cByJ |
- 59 |
- F |
- Glenn |
-
-
- | 28 |
- R3505H.CEL |
- r3505h |
- BALB/cByJ |
- 59 |
- M |
- Glenn |
-
-
- | 29 |
- R3524H.CEL |
- r3524h |
- BTBR T+ tf/J |
- 60 |
- F |
- Glenn |
-
-
- | 30 |
- R3509H.CEL |
- r3509h |
- BTBR T+ tf/J |
- 60 |
- M |
- Glenn |
-
-
- | 31 |
- R1542H.CEL |
- r1542h |
- BXD1 |
- 59 |
- F |
- Glenn |
-
-
- | 32 |
- R1520H.CEL |
- r1520h |
- BXD2 |
- 56 |
- F |
- Glenn |
-
-
- | 33 |
- R1694H.CEL |
- r1694h |
- BXD5 |
- 58 |
- M |
- Glenn |
-
-
- | 34 |
- R3454H.CEL |
- r3454h |
- BXD6 |
- 58 |
- M |
- Glenn |
-
-
- | 35 |
- R3457H.CEL |
- r3457h |
- BXD8 |
- 61 |
- F |
- Glenn |
-
-
- | 36 |
- R3455H.CEL |
- r3455h |
- BXD9 |
- 60 |
- M |
- Glenn |
-
-
- | 37 |
- R3462H.CEL |
- r3462h |
- BXD11 |
- 59 |
- M |
- Glenn |
-
-
- | 38 |
- R3464H.CEL |
- r3464h |
- BXD12 |
- 59 |
- F |
- Glenn |
-
-
- | 39 |
- R2315H.CEL |
- r2315h |
- BXD13 |
- 84 |
- M |
- UTM RW |
-
-
- | 40 |
- R3480H.CEL |
- r3480h |
- BXD14 |
- 60 |
- F |
- Glenn |
-
-
- | 41 |
- R3478H.CEL |
- r3478h |
- BXD15 |
- 60 |
- M |
- Glenn |
-
-
- | 42 |
- R3482H.CEL |
- r3482h |
- BXD16 |
- 59 |
- F |
- Glenn |
-
-
- | 43 |
- R3488H.CEL |
- r3488h |
- BXD18 |
- 59 |
- M |
- Glenn |
-
-
- | 44 |
- R3471H.CEL |
- r3471h |
- BXD19 |
- 60 |
- M |
- Glenn |
-
-
- | 45 |
- R2506H.CEL |
- r2506h |
- BXD20 |
- 60 |
- M |
- Glenn |
-
-
- | 46 |
- R3490H.CEL |
- r3490h |
- BXD21 |
- 60 |
- F |
- Glenn |
-
-
- | 47 |
- R3492H.CEL |
- r3492h |
- BXD22 |
- 60 |
- F |
- Glenn |
-
-
- | 48 |
- R3486H.CEL |
- r3486h |
- BXD23 |
- 60 |
- F |
- Glenn |
-
-
- | 49 |
- R1547H.CEL |
- r1547h |
- BXD24 |
- 59 |
- M |
- Glenn |
-
-
- | 50 |
- R2892H.CEL |
- r2892h |
- BXD25 |
- 67 |
- F |
- UTM RW |
-
-
- | 51 |
- R3485H.CEL |
- r3485h |
- BXD27 |
- 60 |
- M |
- Glenn |
-
-
- | 52 |
- R3477H.CEL |
- r3477h |
- BXD28 |
- 60 |
- F |
- Glenn |
-
-
- | 53 |
- R3475H.CEL |
- r3475h |
- BXD29 |
- 60 |
- F |
- Glenn |
-
-
- | 54 |
- R3456H.CEL |
- r3456h |
- BXD31 |
- 60 |
- M |
- Glenn |
-
-
- | 55 |
- R3570H.CEL |
- r3570h |
- BXD32 |
- 66 |
- F |
- |
-
-
- | 56 |
- R3571H.CEL |
- r3571h |
- BXD32 |
- 58 |
- M |
- |
-
-
- | 57 |
- R3467H.CEL |
- r3467h |
- BXD33 |
- 59 |
- M |
- Glenn |
-
-
- | 58 |
- R3466H.CEL |
- r3466h |
- BXD34 |
- 60 |
- F |
- Glenn |
-
-
- | 59 |
- R3463H.CEL |
- r3463h |
- BXD36 |
- 61 |
- F |
- Glenn |
-
-
- | 60 |
- R3458H.CEL |
- r3458h |
- BXD38 |
- 55 |
- M |
- Glenn |
-
-
- | 61 |
- JR4433H.CEL |
- jr4433sa |
- BXD39 |
- 63 |
- F |
- UTM RW |
-
-
- | 62 |
- R1535H.CEL |
- r1535h |
- BXD39 |
- 60 |
- F |
- Glenn |
-
-
- | 63 |
- R3459H.CEL |
- r3459h |
- BXD40 |
- 60 |
- M |
- Glenn |
-
-
- | 64 |
- R1541H.CEL |
- r1541h |
- BXD42 |
- 58 |
- F |
- Glenn |
-
-
- | 65 |
- R1279H.CEL |
- r1279h |
- BXD43 |
- 57 |
- M |
- UTM RW |
-
-
- | 66 |
- R1472H.CEL |
- r1472h |
- BXD45 |
- 65 |
- M |
- UTM RW |
-
-
- | 67 |
- R1586H.CEL |
- r1586h |
- BXD48 |
- 59 |
- F |
- UTM RW |
-
-
- | 68 |
- R2936H.CEL |
- r2936h |
- BXD50 |
- 61 |
- F |
- UTM RW |
-
-
- | 69 |
- R1313H.CEL |
- r1313h |
- BXD51 |
- 62 |
- M |
- UTM RW |
-
-
- | 70 |
- JR2680H.CEL |
- jr2680h |
- BXD55 |
- 65 |
- M |
- UTM RW |
-
-
- | 71 |
- R1340H.CEL |
- r1340h |
- BXD60 |
- 64 |
- F |
- UTM RW |
-
-
- | 72 |
- R1856H.CEL |
- r1856h |
- BXD61 |
- 94 |
- M |
- UTM RW |
-
-
- | 73 |
- R1317H.CEL |
- r1317h |
- BXD62 |
- 59 |
- F |
- UTM RW |
-
-
- | 74 |
- R1945H.CEL |
- r1945h |
- BXD63 |
- 107 |
- F |
- UTM RW |
-
-
- | 75 |
- R2615H.CEL |
- r2615h |
- BXD64 |
- 68 |
- F |
- UTM RW |
-
-
- | 76 |
- R3567H.CEL |
- r3567h |
- BXD65 |
- 60 |
- F |
- UTRW |
-
-
- | 77 |
- R1949H.CEL |
- r1949h |
- BXD66 |
- 96 |
- M |
- UTM RW |
-
-
- | 78 |
- R2060H.CEL |
- r2060h |
- BXD67 |
- 54 |
- F |
- UTM RW |
-
-
- | 79 |
- R2902H.CEL |
- r2902h |
- BXD68 |
- 57 |
- M |
- UTM RW |
-
-
- | 80 |
- R1466H.CEL |
- r1466h |
- BXD69 |
- 59 |
- F |
- UTM RW |
-
-
- | 81 |
- R2063H.CEL |
- r2063h |
- BXD70 |
- 55 |
- M |
- UTM RW |
-
-
- | 82 |
- R1269H.CEL |
- r1269h |
- BXD73 |
- 72 |
- M |
- UTM RW |
-
-
- | 83 |
- JR2316H.CEL |
- jr2316hre |
- BXD74 |
- 193 |
- M |
- UTM RW |
-
-
- | 84 |
- R1871H.CEL |
- r1871h |
- BXD75 |
- 61 |
- F |
- UTM RW |
-
-
- | 85 |
- JR1948H.CEL |
- jr1948h |
- BXD76 |
- 81 |
- F |
- UTM RW |
-
-
- | 86 |
- R1427H.CEL |
- r1427h |
- BXD77 |
- 61 |
- M |
- UTM RW |
-
-
- | 87 |
- JR4434H.CEL |
- jr4434sare |
- BXD79 |
- 63 |
- F |
- UTM RW |
-
-
- | 88 |
- R3568H.CEL |
- r3568h |
- BXD80 |
- 66 |
- M |
- UTRW |
-
-
- | 89 |
- R2959H.CEL |
- r2959h |
- BXD83 |
- 58 |
- F |
- UTM RW |
-
-
- | 90 |
- R2898H.CEL |
- r2898h |
- BXD84 |
- 67 |
- M |
- UTM RW |
-
-
- | 91 |
- R3566H.CEL |
- r3566h |
- BXD85 |
- 65 |
- M |
- UTRW |
-
-
- | 92 |
- R1556H.CEL |
- r1556h |
- BXD86 |
- 57 |
- F |
- UTM RW |
-
-
- | 93 |
- R1710H.CEL |
- r1710h |
- BXD87 |
- 84 |
- M |
- UTM RW |
-
-
- | 94 |
- JR4079H.CEL |
- jr4079hre |
- BXD89 |
- 63 |
- M |
- UTM RW |
-
-
- | 95 |
- R2058H.CEL |
- r2058h |
- BXD90 |
- 61 |
- F |
- UTM RW |
-
-
- | 96 |
- R1284H.CEL |
- r1284h |
- BXD92 |
- 58 |
- M |
- UTM RW |
-
-
- | 97 |
- JR2057H.CEL |
- jr2057h |
- BXD93 |
- 92 |
- F |
- UTM RW |
-
-
- | 98 |
- JR2313H.CEL |
- jr2313h-re |
- BXD94 |
- 59 |
- F |
- UTM RW |
-
-
- | 99 |
- R1915H.CEL |
- r1915h |
- BXD96 |
- 65 |
- F |
- UTM RW |
-
-
- | 100 |
- R2648H.CEL |
- r2648h |
- BXD97 |
- 74 |
- F |
- UTM RW |
-
-
- | 101 |
- R1942H.CEL |
- r1942h |
- BXD98 |
- 62 |
- F |
- UTM RW |
-
-
- | 102 |
- R1369H.CEL |
- r1369h |
- BXD99 |
- 76 |
- M |
- UMemphis |
-
-
- | 103 |
- R2889H.CEL |
- r2889h |
- BXSB/MpJ |
- 61 |
- F |
- Glenn |
-
-
- | 104 |
- R2887H.CEL |
- r2887h |
- BXSB/MpJ |
- 61 |
- M |
- Glenn |
-
-
- | 105 |
- R3501H.CEL |
- r3501h |
- C3H/HeJ |
- 60 |
- F |
- Glenn |
-
-
- | 106 |
- R3504H.CEL |
- r3504h |
- C3H/HeJ |
- 60 |
- M |
- Glenn |
-
-
- | 107 |
- R3564H.CEL |
- r3564h |
- CAST/EiJ |
- 57 |
- F |
- Glenn |
-
-
- | 108 |
- R3565H.CEL |
- r3565h |
- CAST/EiJ |
- 61 |
- M |
- Glenn |
-
-
- | 109 |
- R3493H.CEL |
- r3493h |
- FVB/NJ |
- 60 |
- F |
- Glenn |
-
-
- | 110 |
- R3496H.CEL |
- r3496h |
- FVB/NJ |
- 60 |
- M |
- Glenn |
-
-
- | 111 |
- JR1683H.CEL |
- jr1683h |
- KK/HlJ |
- 72 |
- F |
- UTM RW |
-
-
- | 112 |
- JR3542H.CEL |
- jr3542hre |
- KK/HlJ |
- 61 |
- M |
- UTM RW |
-
-
- | 113 |
- JR2046H.CEL |
- jr2046hre |
- LG/J |
- 63 |
- F |
- UTM RW |
-
-
- | 114 |
- JR2047H.CEL |
- jr2047h |
- LG/J |
- 63 |
- M |
- UTM RW |
-
-
- | 115 |
- R3541H.CEL |
- r3541h |
- MOLF/EiJ |
- 60 |
- F |
- Glenn |
-
-
- | 116 |
- R3553H.CEL |
- r3553h |
- MOLF/EiJ |
- 60 |
- M |
- Glenn |
-
-
- | 117 |
- R3516H.CEL |
- r3516h |
- NOD/LtJ |
- 58 |
- F |
- Glenn |
-
-
- | 118 |
- R3519H.CEL |
- r3519h |
- NOD/LtJ |
- 58 |
- M |
- Glenn |
-
-
- | 119 |
- R3554H.CEL |
- r3554h |
- NZB/BlNJ |
- 61 |
- F |
- Glenn |
-
-
- | 120 |
- R3513H.CEL |
- r3513h |
- NZB/BlNJ |
- 58 |
- M |
- Glenn |
-
-
- | 121 |
- R3539H.CEL |
- r3539h |
- NZO/HlLtJ |
- 60 |
- F |
- Glenn |
-
-
- | 122 |
- R3536H.CEL |
- r3536h |
- NZO/HlLtJ |
- 60 |
- M |
- Glenn |
-
-
- | 123 |
- R3540H.CEL |
- r3540h |
- NZW/LacJ |
- 65 |
- F |
- Glenn |
-
-
- | 124 |
- R3535H.CEL |
- r3535h |
- NZW/LacJ |
- 60 |
- M |
- Glenn |
-
-
- | 125 |
- R3527H.CEL |
- r3527h |
- PWD/PhJ |
- 60 |
- F |
- Glenn |
-
-
- | 126 |
- R3526H.CEL |
- r3526h |
- PWD/PhJ |
- 60 |
- M |
- Glenn |
-
-
- | 127 |
- R3531H.CEL |
- r3531h |
- PWK/PhJ |
- 60 |
- M |
- Glenn |
-
-
- | 128 |
- R3561H.CEL |
- r3561h |
- WSB/EiJ |
- 60 |
- F |
- Glenn |
-
-
- | 129 |
- R3525H.CEL |
- r3525h |
- WSB/EiJ |
- 60 |
- M |
- Glenn |
-
-
-
- |
-
-
-
diff --git a/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf b/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf
deleted file mode 100644
index 6e4dc8e..0000000
--- a/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf
+++ /dev/null
@@ -1,9 +0,0 @@
-The following steps were applied to refine the data by M. Jagalur in RWW lab:
-
-
- - Strain correction: In this step the strong probe level cis-QTLs were identified and using an expectation maximization (EM)-like method, the genotypes of each marker was re-assigned. This set of reassigned markers was compared to existing list genotypes of BXD strains and the maximal match was identified as the correct strain.
- - Sex correction: In this step probes that are highly correlated to sex were identified and using an EM-like method we detected and corrected the sex of single array data sets.
- - Data exclusion criteria: In this step individual arrays were evaluated. Arrays were systematically excluded from the data set (drop one out) and the number of cis-QTLs was recomputed. If excluding an array resulted in s significantly higher number of cis-QTLs then that array was considered to be of poor quality and was excluded from the final data set This step was repeated across all arrays in multiple cycles until there was no improvement in number of cis-QTLs.
- - Tissue correction: In this step probes that are highly correlated to tissue type were identified and EM-like method was used to identify correct tissue.
- - Noise Removal: A noise component was calculated using the expression of "unhybridized"probes (those with the lowest signal) and was removed from the data.
-
diff --git a/general/datasets/UMUTAffyExon_0209_RMA/summary.rtf b/general/datasets/UMUTAffyExon_0209_RMA/summary.rtf
deleted file mode 100644
index a1fe16a..0000000
--- a/general/datasets/UMUTAffyExon_0209_RMA/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Data generated by RW Williams, Lu Lu, Manjunatha Jagalur, and David Kulp. All arrays run at the VA Medical Center, Memphis, by Yan Jiao.
-
-Data entered by Arthur Centeno and Manju Jagalur, Feb 27, 2009. This data set modified data for two BXD strains. Data were added for BXD79 that had been incorrectly included as a striatum sample (this data set was therefore deleted from the Exon 1.0ST striatum data set). We also changed data for BXD39. As expected, this addition and correction improved QTL mapping values. For example, for Kcnj9 probe set 4519178 the LRS values increased from 103.3 in the Aug08 data to 115.7 for these Feb09 data. Rob is concerned about the high error term of BXD39.
diff --git a/general/datasets/UMUTAffyExon_0209_RMA_MDP/summary.rtf b/general/datasets/UMUTAffyExon_0209_RMA_MDP/summary.rtf
deleted file mode 100644
index afe9391..0000000
--- a/general/datasets/UMUTAffyExon_0209_RMA_MDP/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 98, Name: UMUTAffy Hippocampus Exon (Feb09)
\ No newline at end of file
diff --git a/general/datasets/UTHSC_1107_RankInv/summary.rtf b/general/datasets/UTHSC_1107_RankInv/summary.rtf
deleted file mode 100644
index cc6ac0f..0000000
--- a/general/datasets/UTHSC_1107_RankInv/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 42, Name: HQF BXD Striatum ILM6.1 (Dec10)
\ No newline at end of file
diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf
deleted file mode 100644
index 2b37c95..0000000
--- a/general/datasets/UTHSC_BXD_HArev3_0912/cases.rtf
+++ /dev/null
@@ -1,1258 +0,0 @@
-The study includes 137 mice (11~25 months old) from 73 strains (B6, D2, DBF1, and 70 BXD strains). All procedures were approved by the UTHSC Institutional Animal Care and Use Committee.
-
-The table of samples that are finally used for this study:
-
-
-
-
-
-
-
-
-
-
-
-
- | Index |
- Strain |
- Sex |
- RNA ID |
- Age |
- Phase |
- Tissue |
-
-
- | 1 |
- BXD1 |
- F |
- R7281H |
- 448 |
- II |
- Hippocampus |
-
-
- | 2 |
- BXD1 |
- M |
- R7276H |
- 323 |
- II |
- Hippocampus |
-
-
- | 3 |
- BXD2 |
- M |
- R7261H |
- 394 |
- I |
- Hippocampus |
-
-
- | 4 |
- BXD2 |
- F |
- R7256H |
- 456 |
- I |
- Hippocampus |
-
-
- | 5 |
- BXD6 |
- M |
- R7223H |
- 526 |
- I |
- Hippocampus |
-
-
- | 6 |
- BXD8 |
- M |
- R7203H |
- 471 |
- I |
- Hippocampus |
-
-
- | 7 |
- BXD8 |
- F |
- R7200H |
- 460 |
- I |
- Hippocampus |
-
-
- | 8 |
- BXD8 |
- F |
- R7198H |
- 433 |
- I |
- Hippocampus |
-
-
- | 9 |
- BXD9 |
- F |
- R7294H |
- 456 |
- II |
- Hippocampus |
-
-
- | 10 |
- BXD11 |
- M |
- R7300H |
- 457 |
- II |
- Hippocampus |
-
-
- | 11 |
- BXD11 |
- F |
- R7227H |
- 536 |
- I |
- Hippocampus |
-
-
- | 12 |
- BXD12 |
- F |
- R7183H |
- 506 |
- I |
- Hippocampus |
-
-
- | 13 |
- BXD12 |
- F |
- R7233H |
- 561 |
- I |
- Hippocampus |
-
-
- | 14 |
- BXD12 |
- M |
- R7234H |
- 606 |
- I |
- Hippocampus |
-
-
- | 15 |
- BXD14 |
- F |
- R7238H |
- 605 |
- I |
- Hippocampus |
-
-
- | 16 |
- BXD14 |
- M |
- R7235H |
- 605 |
- I |
- Hippocampus |
-
-
- | 17 |
- BXD16 |
- F |
- R7236H |
- 561 |
- I |
- Hippocampus |
-
-
- | 18 |
- BXD16 |
- M |
- R7239H |
- 475 |
- I |
- Hippocampus |
-
-
- | 19 |
- BXD18 |
- F |
- R7229H |
- 493 |
- I |
- Hippocampus |
-
-
- | 20 |
- BXD19 |
- F |
- R7267H |
- 551 |
- I |
- Hippocampus |
-
-
- | 21 |
- BXD19 |
- M |
- R7268H |
- 492 |
- I |
- Hippocampus |
-
-
- | 22 |
- BXD20 |
- M |
- R7232H |
- 506 |
- I |
- Hippocampus |
-
-
- | 23 |
- BXD20 |
- M |
- R7263H |
- 489 |
- I |
- Hippocampus |
-
-
- | 24 |
- BXD21 |
- F |
- R7230H |
- 537 |
- I |
- Hippocampus |
-
-
- | 25 |
- BXD22 |
- F |
- R7260H |
- 502 |
- I |
- Hippocampus |
-
-
- | 26 |
- BXD22 |
- M |
- R7262H |
- 596 |
- I |
- Hippocampus |
-
-
- | 27 |
- BXD23 |
- F |
- R7258H |
- 502 |
- I |
- Hippocampus |
-
-
- | 28 |
- BXD23 |
- M |
- R7257H |
- 462 |
- I |
- Hippocampus |
-
-
- | 29 |
- BXD24 |
- M |
- R7231H |
- 470 |
- I |
- Hippocampus |
-
-
- | 30 |
- BXD24 |
- F |
- R7228H |
- 415 |
- I |
- Hippocampus |
-
-
- | 31 |
- BXD24 |
- F |
- R7255H |
- 456 |
- I |
- Hippocampus |
-
-
- | 32 |
- BXD25 |
- F |
- R7252H |
- 454 |
- I |
- Hippocampus |
-
-
- | 33 |
- BXD27 |
- F |
- R7286H |
- 472 |
- II |
- Hippocampus |
-
-
- | 34 |
- BXD27 |
- F |
- R7170H |
- 472 |
- I |
- Hippocampus |
-
-
- | 35 |
- BXD28 |
- M |
- R7254H |
- 493 |
- I |
- Hippocampus |
-
-
- | 36 |
- BXD28 |
- F |
- R7251H |
- 543 |
- I |
- Hippocampus |
-
-
- | 37 |
- BXD29 |
- F |
- R7259H |
- 483 |
- I |
- Hippocampus |
-
-
- | 38 |
- BXD33 |
- M |
- R7253H |
- 464 |
- I |
- Hippocampus |
-
-
- | 39 |
- BXD33 |
- F |
- R7174H |
- 471 |
- I |
- Hippocampus |
-
-
- | 40 |
- BXD33 |
- F |
- R7244H |
- 448 |
- I |
- Hippocampus |
-
-
- | 41 |
- BXD33 |
- M |
- R7270H |
- 662 |
- I |
- Hippocampus |
-
-
- | 42 |
- BXD38 |
- F |
- R7242H |
- 464 |
- I |
- Hippocampus |
-
-
- | 43 |
- BXD38 |
- M |
- R7247H |
- 446 |
- I |
- Hippocampus |
-
-
- | 44 |
- BXD39 |
- M |
- R7250H |
- 536 |
- I |
- Hippocampus |
-
-
- | 45 |
- BXD39 |
- F |
- R7173H |
- 500 |
- I |
- Hippocampus |
-
-
- | 46 |
- BXD39 |
- M |
- R7175H |
- 500 |
- I |
- Hippocampus |
-
-
- | 47 |
- BXD40 |
- F |
- R7288H |
- 451 |
- II |
- Hippocampus |
-
-
- | 48 |
- BXD40 |
- M |
- R7210H |
- 470 |
- I |
- Hippocampus |
-
-
- | 49 |
- BXD40 |
- M |
- R7197H |
- 614 |
- I |
- Hippocampus |
-
-
- | 50 |
- BXD42 |
- F |
- R7280H |
- 518 |
- II |
- Hippocampus |
-
-
- | 51 |
- BXD42 |
- M |
- R7246H |
- 446 |
- I |
- Hippocampus |
-
-
- | 52 |
- BXD42 |
- F |
- R7266H |
- 486 |
- I |
- Hippocampus |
-
-
- | 53 |
- BXD43 |
- F |
- R7249H |
- 454 |
- I |
- Hippocampus |
-
-
- | 54 |
- BXD43 |
- M |
- R7248H |
- 462 |
- I |
- Hippocampus |
-
-
- | 55 |
- BXD44 |
- M |
- R7241H |
- 415 |
- I |
- Hippocampus |
-
-
- | 56 |
- BXD44 |
- M |
- R7279H |
- 419 |
- II |
- Hippocampus |
-
-
- | 57 |
- BXD44 |
- F |
- R7243H |
- 438 |
- I |
- Hippocampus |
-
-
- | 58 |
- BXD45 |
- F |
- R7176H |
- 451 |
- I |
- Hippocampus |
-
-
- | 59 |
- BXD48 |
- F |
- R7245H |
- 499 |
- I |
- Hippocampus |
-
-
- | 60 |
- BXD48 |
- M |
- R7220H |
- 526 |
- I |
- Hippocampus |
-
-
- | 61 |
- BXD48a |
- F |
- R7299H |
- 479 |
- II |
- Hippocampus |
-
-
- | 62 |
- BXD48a |
- M |
- R7297H |
- 479 |
- II |
- Hippocampus |
-
-
- | 63 |
- BXD50 |
- F |
- R7224H |
- 530 |
- I |
- Hippocampus |
-
-
- | 64 |
- BXD50 |
- M |
- R7221H |
- 530 |
- I |
- Hippocampus |
-
-
- | 65 |
- BXD51 |
- F |
- R7177H |
- 487 |
- I |
- Hippocampus |
-
-
- | 66 |
- BXD51 |
- M |
- R7290H |
- 407 |
- II |
- Hippocampus |
-
-
- | 67 |
- BXD55 |
- M |
- R7222H |
- 528 |
- I |
- Hippocampus |
-
-
- | 68 |
- BXD55 |
- F |
- R7225H |
- 587 |
- I |
- Hippocampus |
-
-
- | 69 |
- BXD56 |
- M |
- R7178H |
- 501 |
- I |
- Hippocampus |
-
-
- | 70 |
- BXD62 |
- M |
- R7291H |
- 439 |
- II |
- Hippocampus |
-
-
- | 71 |
- BXD63 |
- M |
- R7218H |
- 438 |
- I |
- Hippocampus |
-
-
- | 72 |
- BXD63 |
- F |
- R7215H |
- 475 |
- I |
- Hippocampus |
-
-
- | 73 |
- BXD64 |
- M |
- R7219H |
- 528 |
- I |
- Hippocampus |
-
-
- | 74 |
- BXD64 |
- F |
- R7216H |
- 587 |
- I |
- Hippocampus |
-
-
- | 75 |
- BXD65 |
- F |
- R7217H |
- 425 |
- I |
- Hippocampus |
-
-
- | 76 |
- BXD65a |
- F |
- R7273H |
- 389 |
- II |
- Hippocampus |
-
-
- | 77 |
- BXD65a |
- M |
- R7277H |
- 715 |
- II |
- Hippocampus |
-
-
- | 78 |
- BXD65b |
- M |
- R7271H |
- 483 |
- II |
- Hippocampus |
-
-
- | 79 |
- BXD66 |
- M |
- R7214H |
- 463 |
- I |
- Hippocampus |
-
-
- | 80 |
- BXD66 |
- F |
- R7302H |
- 446 |
- III |
- Hippocampus |
-
-
- | 81 |
- BXD67 |
- F |
- R7240H |
- 499 |
- I |
- Hippocampus |
-
-
- | 82 |
- BXD67 |
- M |
- R7213H |
- 425 |
- I |
- Hippocampus |
-
-
- | 83 |
- BXD67 |
- F |
- R7278H |
- 415 |
- II |
- Hippocampus |
-
-
- | 84 |
- BXD68 |
- M |
- R7212H |
- 421 |
- I |
- Hippocampus |
-
-
- | 85 |
- BXD68 |
- F |
- R7211H |
- 415 |
- I |
- Hippocampus |
-
-
- | 86 |
- BXD69 |
- F |
- R7305H |
- 504 |
- III |
- Hippocampus |
-
-
- | 87 |
- BXD70 |
- F |
- R7207H |
- 458 |
- I |
- Hippocampus |
-
-
- | 88 |
- BXD70 |
- M |
- R7204H |
- 460 |
- I |
- Hippocampus |
-
-
- | 89 |
- BXD71 |
- M |
- R7205H |
- 471 |
- I |
- Hippocampus |
-
-
- | 90 |
- BXD71 |
- F |
- R7208H |
- 474 |
- I |
- Hippocampus |
-
-
- | 91 |
- BXD73 |
- F |
- R7209H |
- 470 |
- I |
- Hippocampus |
-
-
- | 92 |
- BXD73 |
- M |
- R7206H |
- 464 |
- I |
- Hippocampus |
-
-
- | 93 |
- BXD73a |
- F |
- R7181H |
- 443 |
- I |
- Hippocampus |
-
-
- | 94 |
- BXD73a |
- M |
- R7182H |
- 614 |
- I |
- Hippocampus |
-
-
- | 95 |
- BXD76 |
- M |
- R7179H |
- 579 |
- I |
- Hippocampus |
-
-
- | 96 |
- BXD76 |
- F |
- R7188H |
- 408 |
- I |
- Hippocampus |
-
-
- | 97 |
- BXD76 |
- M |
- R7187H |
- 564 |
- I |
- Hippocampus |
-
-
- | 98 |
- BXD77 |
- M |
- R7292H |
- 347 |
- II |
- Hippocampus |
-
-
- | 99 |
- BXD77 |
- F |
- R7201H |
- 454 |
- I |
- Hippocampus |
-
-
- | 100 |
- BXD79 |
- M |
- R7202H |
- 485 |
- I |
- Hippocampus |
-
-
- | 101 |
- BXD79 |
- F |
- R7199H |
- 515 |
- I |
- Hippocampus |
-
-
- | 102 |
- BXD79 |
- M |
- R7298H |
- 704 |
- II |
- Hippocampus |
-
-
- | 103 |
- BXD81 |
- M |
- R7196H |
- 515 |
- I |
- Hippocampus |
-
-
- | 104 |
- BXD81 |
- F |
- R7190H |
- 458 |
- I |
- Hippocampus |
-
-
- | 105 |
- BXD83 |
- M |
- R7184H |
- 441 |
- I |
- Hippocampus |
-
-
- | 106 |
- BXD84 |
- M |
- R7195H |
- 474 |
- I |
- Hippocampus |
-
-
- | 107 |
- BXD84 |
- M |
- R7296H |
- 484 |
- II |
- Hippocampus |
-
-
- | 108 |
- BXD84 |
- F |
- R7192H |
- 522 |
- I |
- Hippocampus |
-
-
- | 109 |
- BXD85 |
- M |
- R7272H |
- 425 |
- II |
- Hippocampus |
-
-
- | 110 |
- BXD85 |
- F |
- R7193H |
- 506 |
- I |
- Hippocampus |
-
-
- | 111 |
- BXD86 |
- M |
- R7191H |
- 425 |
- I |
- Hippocampus |
-
-
- | 112 |
- BXD87 |
- F |
- R7194H |
- 425 |
- I |
- Hippocampus |
-
-
- | 113 |
- BXD87 |
- M |
- R7303H |
- 478 |
- III |
- Hippocampus |
-
-
- | 114 |
- BXD87 |
- M |
- R7186H |
- 442 |
- I |
- Hippocampus |
-
-
- | 115 |
- BXD89 |
- F |
- R7295H |
- 446 |
- II |
- Hippocampus |
-
-
- | 116 |
- BXD90 |
- M |
- R7287H |
- 434 |
- II |
- Hippocampus |
-
-
- | 117 |
- BXD90 |
- M |
- R7293H |
- 558 |
- II |
- Hippocampus |
-
-
- | 118 |
- BXD95 |
- F |
- R7180H |
- 467 |
- I |
- Hippocampus |
-
-
- | 119 |
- BXD95 |
- M |
- R7169H |
- 467 |
- I |
- Hippocampus |
-
-
- | 120 |
- BXD98 |
- M |
- R7237H |
- 605 |
- I |
- Hippocampus |
-
-
- | 121 |
- BXD98 |
- F |
- R7171H |
- 639 |
- I |
- Hippocampus |
-
-
- | 122 |
- BXD98 |
- F |
- R7275H |
- 488 |
- II |
- Hippocampus |
-
-
- | 123 |
- BXD99 |
- M |
- R7189H |
- 524 |
- I |
- Hippocampus |
-
-
- | 124 |
- BXD99 |
- F |
- R7172H |
- 471 |
- I |
- Hippocampus |
-
-
- | 125 |
- BXD100 |
- F |
- R7282H |
- 463 |
- II |
- Hippocampus |
-
-
- | 126 |
- BXD100 |
- M |
- R7283H |
- 507 |
- II |
- Hippocampus |
-
-
- | 127 |
- BXD100 |
- M |
- R7274H |
- 577 |
- II |
- Hippocampus |
-
-
- | 128 |
- BXD100 |
- F |
- R7226H |
- 464 |
- I |
- Hippocampus |
-
-
- | 129 |
- BXD101 |
- F |
- R7284H |
- 490 |
- II |
- Hippocampus |
-
-
- | 130 |
- BXD101 |
- M |
- R7285H |
- 408 |
- II |
- Hippocampus |
-
-
- | 131 |
- C57BL/6J |
- M |
- R7264H |
- 489 |
- I |
- Hippocampus |
-
-
- | 132 |
- C57BL/6J |
- M |
- R7289H |
- 756 |
- II |
- Hippocampus |
-
-
- | 133 |
- D2B6F1 |
- M |
- R7265H |
- 492 |
- I |
- Hippocampus |
-
-
- | 134 |
- D2B6F1 |
- F |
- R7304H |
- 495 |
- III |
- Hippocampus |
-
-
- | 135 |
- DBA/2J |
- F |
- R7185H |
- 433 |
- I |
- Hippocampus |
-
-
- | 136 |
- DBA/2J |
- M |
- R7269H |
- 367 |
- I |
- Hippocampus |
-
-
- | 137 |
- DBA/2J |
- F |
- R7301H |
- 566 |
- III |
- Hippocampus |
-
-
-
diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf
deleted file mode 100644
index d6b2d5b..0000000
--- a/general/datasets/UTHSC_BXD_HArev3_0912/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-RNA Extraction
-
-RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufactures’ procedure. 2100 BioAnalyzer (Agilent Technologies) was used to evaluate RNA integrity and quality. Samples with RNA Integrity Numbers (RIN values) > 8.0 were run on Affy MoGene1.0 ST at the UTHSC
diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf
deleted file mode 100644
index e951515..0000000
--- a/general/datasets/UTHSC_BXD_HArev3_0912/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About data processing:
-
-Raw microarray data were normalized using the Robust Multichip Array (RMA) method. The expression data were then re-normalized using a modified Z score.
diff --git a/general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf b/general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf
deleted file mode 100644
index 3166717..0000000
--- a/general/datasets/UTHSC_BXD_HArev3_0912/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Tissue Harvest
-
-The animals were sacrificed under saturated isoflurane. Hippocampus from the animals were dissected and stored at −80°C until RNA extraction.
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf b/general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf
deleted file mode 100644
index 2f0fdc0..0000000
--- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf
+++ /dev/null
@@ -1,245 +0,0 @@
-
-
-
-
-
-
-
-
- | Index |
- Original Strain |
- Corrected Strain |
- Sex |
- Age |
-
-
- | 1 |
- BXD13_batch2 |
- BXD18 |
- M |
- 67 |
-
-
- | 2 |
- BXD15_batch2 |
- BXD15 |
- F |
- 62 |
-
-
- | 3 |
- BXD18_batch2 |
- BXD19 |
- F |
- 65 |
-
-
- | 4 |
- BXD24_batch2 |
- BXD24 |
- F |
- 63 |
-
-
- | 5 |
- BXD36_batch2 |
- BXD45 removed |
- M |
- 67 |
-
-
- | 6 |
- BXD39_batch2 |
- BXD39 |
- F |
- 60 |
-
-
- | 7 |
- BXD42_batch2 |
- BXD43 |
- F |
- 67 |
-
-
- | 8 |
- BXD43_batch2 |
- BXD42 |
- F |
- 60 |
-
-
- | 9 |
- BXD45_batch2 |
- BXD45 |
- F |
- 60 |
-
-
- | 10 |
- BXD50_batch2 |
- BXD50 |
- F |
- 57 |
-
-
- | 11 |
- BXD51_batch2 |
- BXD55 |
- F |
- 59 |
-
-
- | 12 |
- BXD55_batch2 |
- BXD51 |
- F |
- 61 |
-
-
- | 13 |
- BXD56_batch2 |
- BXD56 |
- F |
- 67 |
-
-
- | 14 |
- BXD6_batch2 |
- BXD6 |
- F |
- 59 |
-
-
- | 15 |
- BXD8_batch2 |
- BXD9 |
- F |
- 62 |
-
-
- | 16 |
- BXD9_batch2 |
- BXD8 |
- M |
- 70 |
-
-
- | 17 |
- BXD14_batch3 |
- BXD40 |
- F |
- 76 |
-
-
- | 18 |
- BXD16_batch3 |
- BXD19 |
- M |
- 74 |
-
-
- | 19 |
- BXD32_batch3 |
- BXD32 |
- M |
- 54 |
-
-
- | 20 |
- BXD38_batch3 |
- BXD38 |
- F |
- 102 |
-
-
- | 21 |
- BXD40_batch3 |
- BXD14 |
- M |
- 81 |
-
-
- | 22 |
- BXD48_batch3 |
- BXD48 |
- M |
- 68 |
-
-
- | 23 |
- BXD60_batch3 |
- BXD60 |
- F |
- 64 |
-
-
- | 24 |
- BXD66_batch3 |
- BXD66 |
- M |
- 61 |
-
-
- | 25 |
- BXD69_batch3 |
- BXD69 |
- F |
- 66 |
-
-
- | 26 |
- BXD70_batch3 |
- BXD70 |
- M |
- 72 |
-
-
- | 27 |
- BXD29m_batch4 |
- BXD1 |
- F |
- 60 |
-
-
- | 28 |
- BXD29n_batch4 |
- BXD29 |
- F |
- 344 |
-
-
- | 29 |
- BXD34_batch4 |
- BXD34 |
- F |
- 108 |
-
-
- | 30 |
- BXD49_batch4 |
- BXD49 |
- M |
- 76 |
-
-
- | 31 |
- BXD65_batch4 |
- BXD29 |
- F |
- 58 |
-
-
- | 32 |
- BXD22_batch6 |
- BXD22 |
- F |
- 67 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeq1112/notes.rtf b/general/datasets/UTHSC_BXD_WB_RNASeq1112/notes.rtf
deleted file mode 100644
index c16bd50..0000000
--- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-RNA sequencing for BXD strains on SOLiD by David Li.
-All Bam files alignment done by Xusheng Wang
-Aligned files were uploaded to Partek Genomic Suite 6.5 (version 6.10.0810) and processed by K Mozhui
-Normalization: RPKM (reads per kilobase per million mapped reads)
-Batch effect due to low exonic reads for batch 2
-
-Revision 1.6 Untrimmed (current) LRS=(23 999) ->350 records
-Max LRS = 102.6 Record Id:uthsc_nr_015498, Gene Symbol:1500004A13Rik **Note: 1 sample BXD45 and BXD34 removed. BXD41 switched to BXD1 as a second posible candidate.
-
-Revision 1.5 Untrimmed LRS=(23 999) ->268 records
-Max LRS = 80.0 Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed. BXD41 switched to BXD1 as a second posible candidate.
-
-Revision 1.4 Untrimmed LRS=(23 999) ->246 records
-Max LRS = 80.0 Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed and keep BXD41
-
-Revision 1.3 Untrimmed LRS=(23 999) ->233 records
-Max LRS = 80.7 Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1
-
-Revision 1.2 Untrimmed LRS=(23 999) ->190 records
-Max LRS = 56.9 Record Id:uthsc_nr_003513, Gene Symbol:Neat1
-
-Revision 1 Untrimmed LRS=(23 999) ->126 records
-Max LRS = 35.3 Record Id:uthsc_nm_001113412, Gene Symbol:Fggy
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeq1112/specifics.rtf b/general/datasets/UTHSC_BXD_WB_RNASeq1112/specifics.rtf
deleted file mode 100644
index 8e3eb6f..0000000
--- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Note: March 2019: now actually 449 transcripts/genes with LRS > 23 and peak LRS is still 102.6.
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeq1112/summary.rtf b/general/datasets/UTHSC_BXD_WB_RNASeq1112/summary.rtf
deleted file mode 100644
index 82080d4..0000000
--- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/summary.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-
- - UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed
- - UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed dataset have been re-normalized by forcing values down to zero at level of individual mRNA seq assay.
-
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeqEx1112/specifics.rtf b/general/datasets/UTHSC_BXD_WB_RNASeqEx1112/specifics.rtf
deleted file mode 100644
index 7c1a914..0000000
--- a/general/datasets/UTHSC_BXD_WB_RNASeqEx1112/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Exon Level
\ No newline at end of file
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeqEx1112/summary.rtf b/general/datasets/UTHSC_BXD_WB_RNASeqEx1112/summary.rtf
deleted file mode 100644
index 0ffc063..0000000
--- a/general/datasets/UTHSC_BXD_WB_RNASeqEx1112/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM
diff --git a/general/datasets/UTHSC_SPL_RMA_1010/cases.rtf b/general/datasets/UTHSC_SPL_RMA_1010/cases.rtf
deleted file mode 100644
index 7fa108f..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1010/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 111 strains, including 81 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1), and 26 other common inbred strains were quantified. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by Lu Lu and colleagues. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. XX strains have matched male and female samples. XX strains have male only samples (BXDX, XX, XX, XXX and XXX). XX strains have only female samples (BXDXX, XX, and XX.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/UTHSC_SPL_RMA_1010/experiment-design.rtf b/general/datasets/UTHSC_SPL_RMA_1010/experiment-design.rtf
deleted file mode 100644
index a0aeba6..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1010/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-RNA Processing. Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-Array Processing: All arrays were processed by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. The spleen was dissected by both Dr. Lu Lu and colleagues and Dr. Abdeltawab and colleagues. All arrays were run together (interleaved) as a single large batch.
diff --git a/general/datasets/UTHSC_SPL_RMA_1010/notes.rtf b/general/datasets/UTHSC_SPL_RMA_1010/notes.rtf
deleted file mode 100644
index c7bb873..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1010/notes.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-Data Status and Use. This is a provisional release that will soon be replaced by a final corrected data set. In the interim this data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/UTHSC_SPL_RMA_1010/processing.rtf b/general/datasets/UTHSC_SPL_RMA_1010/processing.rtf
deleted file mode 100644
index deaf264..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1010/processing.rtf
+++ /dev/null
@@ -1,1932 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required some correction for batch effects and the data in this initial release incorporate any additional corrections. There are several additional confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest probe sets in this spleen data set accounts of XX% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the spleen data set can be mapped as a trait.
-
-
-Data Release. This data set was first uploaded into GeneNetwork by Arthur Centeno, October 11, 2010 and made accessible without a password to all users on November 1, 2010. The initial data release had numerous strain identification errors that have now largely been fixed. Based on an analysis of the top 20 Mendelian loci, the following 21 strains were likely to have been incorrectly identified or assigned in the current release:
-
-
- - BXD8, e.g., Probe set 10450161, 1036098. 10338684
- - BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
- - BXD21 (may be ok, only one probe set 10338684 is problematic)
- - BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
- - BXD36 (may be ok, only one probe set 10421128 is problematic)
- - BXD40, e.g., Probe set 10341070
- - BXD43, e.g., Probe set 10450161, 1036098, 10338684
- - BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
- - BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
- - BXD68 (may be ok, only one probe set 10338684 is problematic)
- - BXD69, e.g., Probe set 10450161
- - BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
- - BXD74, e.g., Probe set 10402390
- - BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
- - BXD83, e.g., Probe set 10450161, 10338684
- - BXD87 (may be ok, only one probe set 10421128 is problematic)
- - BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
- - BXD93, e.g., Probe set 10402390, 10357381
- - BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
- - LP/J, e.g., Probe set 10592493
- - DBA/2J, e.g., Probe set 10592493
-
-
-Data Evaluation Summary
-
-
- - Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
- - After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
- - Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 237.9
- - After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 278.1
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
Table 1 (please confirm that these assignments are after correction)
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Phase |
- Strain |
- Age |
- Sex |
-
-
- | 1 |
- R5583S |
- 1 |
- 129P3/J |
- 65 |
- F |
-
-
- | 2 |
- R5584S |
- 1 |
- 129P3/J |
- 66 |
- M |
-
-
- | 3 |
- R5585S |
- 1 |
- 129S1/SvImJ |
- 66 |
- F |
-
-
- | 4 |
- R5586S |
- 1 |
- 129S1/SvImJ |
- 66 |
- M |
-
-
- | 5 |
- R5587S |
- 1 |
- 129X1/SvJ |
- 65 |
- F |
-
-
- | 6 |
- R5588S |
- 1 |
- 129X1/SvJ |
- 66 |
- M |
-
-
- | 7 |
- R6348S |
- 3 |
- B6D2F1 |
- 67 |
- F |
-
-
- | 8 |
- R6347S |
- 3 |
- B6D2F1 |
- 62 |
- F |
-
-
- | 9 |
- R5590S |
- 1 |
- B6D2F1 |
- 79 |
- M |
-
-
- | 10 |
- R5662S |
- 1 |
- BALB/cByJ |
- 59 |
- F |
-
-
- | 11 |
- R5664S |
- 1 |
- BALB/cByJ |
- 59 |
- M |
-
-
- | 12 |
- R5591S |
- 1 |
- BALB/cJ |
- 51 |
- F |
-
-
- | 13 |
- R5592S |
- 1 |
- BALB/cJ |
- 51 |
- M |
-
-
- | 14 |
- R6154S |
- 2 |
- BTBR T+ tf/J |
- 60 |
- F |
-
-
- | 15 |
- R6516S |
- 3 |
- BXD1 |
- 82 |
- F |
-
-
- | 16 |
- R6584S |
- 3 |
- BXD1 |
- 95 |
- M |
-
-
- | 17 |
- R5759S |
- 1 |
- BXD2 |
- N/A |
- F |
-
-
- | 18 |
- R5837S |
- 1 |
- BXD2 |
- 106 |
- M |
-
-
- | 19 |
- R5874S |
- 2 |
- BXD5 |
- 86 |
- F |
-
-
- | 20 |
- R6554S |
- 3 |
- BXD5 |
- 60 |
- M |
-
-
- | 21 |
- R6359S |
- 3 |
- BXD6 |
- 72 |
- F |
-
-
- | 22 |
- R5777S |
- 1 |
- BXD6 |
- 149 |
- M |
-
-
- | 23 |
- R6364S |
- 3 |
- BXD8 |
- 76 |
- F |
-
-
- | 24 |
- R5637S |
- 1 |
- BXD8 |
- 71 |
- F |
-
-
- | 25 |
- R6365S |
- 3 |
- BXD8 |
- 76 |
- M |
-
-
- | 26 |
- R5746S |
- 1 |
- BXD9 |
- 70 |
- F |
-
-
- | 27 |
- R5981S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 28 |
- R5980S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 29 |
- R6182S |
- 2 |
- BXD11 |
- 84 |
- F |
-
-
- | 30 |
- R6486S |
- 3 |
- BXD11 |
- 58 |
- M |
-
-
- | 31 |
- R6711S2 |
- 4 |
- BXD12 |
- 71 |
- F |
-
-
- | 32 |
- R6608S |
- 3 |
- BXD12 |
- 48 |
- F |
-
-
- | 33 |
- R5885S |
- 2 |
- BXD12 |
- 44 |
- M |
-
-
- | 34 |
- R5755S |
- 1 |
- BXD13 |
- 160 |
- F |
-
-
- | 35 |
- R5887S |
- 2 |
- BXD13 |
- 53 |
- M |
-
-
- | 36 |
- R6180S |
- 2 |
- BXD14 |
- 70 |
- F |
-
-
- | 37 |
- R5669S |
- 1 |
- BXD14 |
- 91 |
- M |
-
-
- | 38 |
- R6456S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 39 |
- R6622S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 40 |
- R6626S |
- 3 |
- BXD15 |
- 60 |
- M |
-
-
- | 41 |
- R6181S |
- 2 |
- BXD16 |
- 74 |
- F |
-
-
- | 42 |
- R6515S |
- 3 |
- BXD16 |
- 64 |
- M |
-
-
- | 43 |
- R5673S |
- 1 |
- BXD18 |
- 80 |
- F |
-
-
- | 44 |
- R5674S |
- 1 |
- BXD18 |
- 65 |
- M |
-
-
- | 45 |
- R6553S |
- 3 |
- BXD19 |
- 158 |
- F |
-
-
- | 46 |
- R6551S |
- 3 |
- BXD19 |
- 60 |
- M |
-
-
- | 47 |
- R6643S4 |
- 4 |
- BXD20 |
- 59 |
- F |
-
-
- | 48 |
- R6595S |
- 3 |
- BXD20 |
- 60 |
- M |
-
-
- | 49 |
- R5735S |
- 1 |
- BXD21 |
- 64 |
- F |
-
-
- | 50 |
- R5892S |
- 2 |
- BXD21 |
- 99 |
- M |
-
-
- | 51 |
- R5896S |
- 2 |
- BXD22 |
- 60 |
- F |
-
-
- | 52 |
- R6414S |
- 3 |
- BXD22 |
- 73 |
- M |
-
-
- | 53 |
- R6550S |
- 3 |
- BXD23 |
- 74 |
- F |
-
-
- | 54 |
- R6586S |
- 3 |
- BXD23 |
- 102 |
- F |
-
-
- | 55 |
- R5630S |
- 1 |
- BXD24 |
- 71 |
- F |
-
-
- | 56 |
- R6356S |
- 3 |
- BXD24 |
- 57 |
- M |
-
-
- | 57 |
- R6162S |
- 2 |
- BXD25 |
- 67 |
- F |
-
-
- | 58 |
- R6625S |
- 3 |
- BXD25 |
- 67 |
- F |
-
-
- | 59 |
- R6642S4 |
- 4 |
- BXD25 |
- 58 |
- M |
-
-
- | 60 |
- R5761S |
- 1 |
- BXD27 |
- N/A |
- F |
-
-
- | 61 |
- R5763S |
- 1 |
- BXD27 |
- 90 |
- M |
-
-
- | 62 |
- R6621S |
- 3 |
- BXD28 |
- 113 |
- F |
-
-
- | 63 |
- R6548S |
- 3 |
- BXD28 |
- 60 |
- M |
-
-
- | 64 |
- R6547S |
- 3 |
- BXD29 |
- 60 |
- F |
-
-
- | 65 |
- R6453S |
- 3 |
- BXD31 |
- 48 |
- F |
-
-
- | 66 |
- R6452S |
- 3 |
- BXD31 |
- 48 |
- M |
-
-
- | 67 |
- R6583S |
- 3 |
- BXD32 |
- 60 |
- F |
-
-
- | 68 |
- R5765S |
- 1 |
- BXD32 |
- 71 |
- M |
-
-
- | 69 |
- R5689S |
- 1 |
- BXD33 |
- 65 |
- F |
-
-
- | 70 |
- R6450S |
- 3 |
- BXD33 |
- 55 |
- M |
-
-
- | 71 |
- R5767S |
- 1 |
- BXD34 |
- 72 |
- F |
-
-
- | 72 |
- R5900S |
- 2 |
- BXD34 |
- 70 |
- M |
-
-
- | 73 |
- R6588S |
- 3 |
- BXD36 |
- 61 |
- F |
-
-
- | 74 |
- R6490S |
- 3 |
- BXD36 |
- 63 |
- M |
-
-
- | 75 |
- R6417S |
- 3 |
- BXD38 |
- 64 |
- F |
-
-
- | 76 |
- R6439S |
- 3 |
- BXD38 |
- 72 |
- M |
-
-
- | 77 |
- R5769S |
- 1 |
- BXD39 |
- N/A |
- F |
-
-
- | 78 |
- R5771S |
- 1 |
- BXD39 |
- 74 |
- M |
-
-
- | 79 |
- R5773S |
- 1 |
- BXD40 |
- N/A |
- F |
-
-
- | 80 |
- R5775S |
- 1 |
- BXD40 |
- N/A |
- M |
-
-
- | 81 |
- R6494S |
- 3 |
- BXD41 |
- 72 |
- F |
-
-
- | 82 |
- R5910S |
- 2 |
- BXD42 |
- 79 |
- F |
-
-
- | 83 |
- R6493S |
- 3 |
- BXD42 |
- 69 |
- M |
-
-
- | 84 |
- R6341S |
- 3 |
- BXD43 |
- 59 |
- F |
-
-
- | 85 |
- R6401S |
- 3 |
- BXD43 |
- 99 |
- M |
-
-
- | 86 |
- R5916S |
- 2 |
- BXD43 |
- 79 |
- M |
-
-
- | 87 |
- R5839S |
- 1 |
- BXD44 |
- 141 |
- F |
-
-
- | 88 |
- R5779S |
- 1 |
- BXD44 |
- 124 |
- M |
-
-
- | 89 |
- R6405S |
- 3 |
- BXD45 |
- 58 |
- F |
-
-
- | 90 |
- R6610S |
- 3 |
- BXD45 |
- 55 |
- M |
-
-
- | 91 |
- R5922S |
- 2 |
- BXD48 |
- 64 |
- F |
-
-
- | 92 |
- R5925S |
- 2 |
- BXD48 |
- 60 |
- M |
-
-
- | 93 |
- R6719S1 |
- 4 |
- BXD49 |
- 58 |
- F |
-
-
- | 94 |
- R6485S |
- 3 |
- BXD49 |
- 79 |
- M |
-
-
- | 95 |
- R5781S |
- 1 |
- BXD50 |
- 61 |
- F |
-
-
- | 96 |
- R6464S |
- 3 |
- BXD51 |
- 65 |
- F |
-
-
- | 97 |
- R6585S |
- 3 |
- BXD51 |
- 63 |
- M |
-
-
- | 98 |
- R6500S |
- 3 |
- BXD55 |
- 58 |
- F |
-
-
- | 99 |
- R5938S |
- 2 |
- BXD55 |
- 93 |
- M |
-
-
- | 100 |
- R6504S |
- 3 |
- BXD56 |
- 58 |
- F |
-
-
- | 101 |
- R6503S |
- 3 |
- BXD56 |
- 58 |
- M |
-
-
- | 102 |
- R5783S |
- 1 |
- BXD60 |
- 111 |
- F |
-
-
- | 103 |
- R5784S |
- 1 |
- BXD60 |
- 85 |
- M |
-
-
- | 104 |
- R5786S |
- 1 |
- BXD61 |
- 86 |
- F |
-
-
- | 105 |
- R6449S |
- 3 |
- BXD61 |
- 65 |
- M |
-
-
- | 106 |
- R6716S1 |
- 4 |
- BXD62 |
- 54 |
- F |
-
-
- | 107 |
- R5790S |
- 1 |
- BXD62 |
- 115 |
- M |
-
-
- | 108 |
- R6519S |
- 3 |
- BXD63 |
- 54 |
- F |
-
-
- | 109 |
- R6717S1 |
- 4 |
- BXD63 |
- 70 |
- M |
-
-
- | 110 |
- R5792S |
- 1 |
- BXD64 |
- 167 |
- F |
-
-
- | 111 |
- R6641S4 |
- 4 |
- BXD64 |
- 68 |
- M |
-
-
- | 112 |
- R6630S |
- 3 |
- BXD64 |
- 68 |
- M |
-
-
- | 113 |
- R6477S |
- 3 |
- BXD65 |
- 58 |
- F |
-
-
- | 114 |
- R6628S |
- 3 |
- BXD65 |
- 70 |
- M |
-
-
- | 115 |
- R6511S |
- 3 |
- BXD66 |
- 70 |
- F |
-
-
- | 116 |
- R6448S |
- 3 |
- BXD66 |
- 61 |
- M |
-
-
- | 117 |
- R5794S |
- 1 |
- BXD66 |
- 144 |
- M |
-
-
- | 118 |
- R6502S |
- 3 |
- BXD67 |
- 66 |
- F |
-
-
- | 119 |
- R6545S |
- 3 |
- BXD67 |
- 61 |
- M |
-
-
- | 120 |
- R6337S |
- 3 |
- BXD68 |
- 56 |
- F |
-
-
- | 121 |
- R6594S |
- 3 |
- BXD68 |
- 64 |
- M |
-
-
- | 122 |
- R5796S |
- 1 |
- BXD69 |
- 85 |
- F |
-
-
- | 123 |
- R5798S |
- 1 |
- BXD69 |
- 98 |
- M |
-
-
- | 124 |
- R6402S |
- 3 |
- BXD70 |
- 93 |
- F |
-
-
- | 125 |
- R5841S |
- 1 |
- BXD70 |
- 121 |
- F |
-
-
- | 126 |
- R6592S |
- 3 |
- BXD70 |
- 59 |
- M |
-
-
- | 127 |
- R6328S |
- 3 |
- BXD71 |
- 87 |
- F |
-
-
- | 128 |
- R5967S |
- 2 |
- BXD71 |
- 64 |
- M |
-
-
- | 129 |
- R5969S |
- 2 |
- BXD73 |
- 64 |
- F |
-
-
- | 130 |
- R5800S |
- 1 |
- BXD73 |
- 120 |
- M |
-
-
- | 131 |
- R6646S |
- 3 |
- BXD74 |
- 40 |
- F |
-
-
- | 132 |
- R6524S |
- 3 |
- BXD74 |
- 72 |
- M |
-
-
- | 133 |
- R6445S |
- 3 |
- BXD75 |
- 85 |
- F |
-
-
- | 134 |
- R5843S |
- 1 |
- BXD75 |
- 103 |
- F |
-
-
- | 135 |
- R5845S |
- 1 |
- BXD75 |
- 103 |
- M |
-
-
- | 136 |
- R6604S |
- 3 |
- BXD77 |
- 64 |
- F |
-
-
- | 137 |
- R6513S |
- 3 |
- BXD77 |
- 72 |
- M |
-
-
- | 138 |
- R6582S |
- 3 |
- BXD78 |
- 144 |
- F |
-
-
- | 139 |
- R6563S |
- 3 |
- BXD78 |
- 95 |
- M |
-
-
- | 140 |
- R6645S4 |
- 4 |
- BXD79 |
- 66 |
- F |
-
-
- | 141 |
- R5806S |
- 1 |
- BXD79 |
- 78 |
- M |
-
-
- | 142 |
- R5847S |
- 1 |
- BXD80 |
- 89 |
- F |
-
-
- | 143 |
- R5852S |
- 1 |
- BXD80 |
- 79 |
- M |
-
-
- | 144 |
- R6562S |
- 3 |
- BXD81 |
- 99 |
- F |
-
-
- | 145 |
- R6468S |
- 3 |
- BXD81 |
- 65 |
- M |
-
-
- | 146 |
- R6560S |
- 3 |
- BXD82 |
- 85 |
- F |
-
-
- | 147 |
- R6512S |
- 3 |
- BXD83 |
- 68 |
- F |
-
-
- | 148 |
- R5810S |
- 1 |
- BXD83 |
- 139 |
- M |
-
-
- | 149 |
- R6510S |
- 3 |
- BXD84 |
- 87 |
- F |
-
-
- | 150 |
- R5970S |
- 2 |
- BXD84 |
- 107 |
- F |
-
-
- | 151 |
- R6603S |
- 3 |
- BXD84 |
- 99 |
- M |
-
-
- | 152 |
- R6517S |
- 3 |
- BXD85 |
- 58 |
- F |
-
-
- | 153 |
- R6718S1 |
- 4 |
- BXD85 |
- 86 |
- M |
-
-
- | 154 |
- R5812S |
- 1 |
- BXD86 |
- 61 |
- F |
-
-
- | 155 |
- R5814S |
- 1 |
- BXD86 |
- 59 |
- M |
-
-
- | 156 |
- R5816S |
- 1 |
- BXD87 |
- 112 |
- F |
-
-
- | 157 |
- R6488S |
- 3 |
- BXD87 |
- 137 |
- M |
-
-
- | 158 |
- R6580S |
- 3 |
- BXD88 |
- 125 |
- F |
-
-
- | 159 |
- R5977S |
- 2 |
- BXD89 |
- 68 |
- F |
-
-
- | 160 |
- R5979S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 161 |
- R5978S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 162 |
- R5818S |
- 1 |
- BXD90 |
- 106 |
- F |
-
-
- | 163 |
- R5820S |
- 1 |
- BXD90 |
- 131 |
- M |
-
-
- | 164 |
- R6343S |
- 3 |
- BXD92 |
- 62 |
- F |
-
-
- | 165 |
- R5984S |
- 2 |
- BXD92 |
- 55 |
- M |
-
-
- | 166 |
- R6581S |
- 3 |
- BXD93 |
- 173 |
- M |
-
-
- | 167 |
- R6557S |
- 3 |
- BXD93 |
- 126 |
- M |
-
-
- | 168 |
- R6509S |
- 3 |
- BXD95 |
- 59 |
- F |
-
-
- | 169 |
- R5822S |
- 1 |
- BXD95 |
- 89 |
- M |
-
-
- | 170 |
- R6640S4 |
- 4 |
- BXD96 |
- 70 |
- F |
-
-
- | 171 |
- R6514S |
- 3 |
- BXD96 |
- 64 |
- M |
-
-
- | 172 |
- R6506S |
- 3 |
- BXD97 |
- 78 |
- F |
-
-
- | 173 |
- R5849S |
- 1 |
- BXD97 |
- 130 |
- F |
-
-
- | 174 |
- R6591S |
- 3 |
- BXD97 |
- 122 |
- M |
-
-
- | 175 |
- R5990S |
- 2 |
- BXD98 |
- 65 |
- F |
-
-
- | 176 |
- R6596S |
- 3 |
- BXD98 |
- 67 |
- M |
-
-
- | 177 |
- R5993S |
- 2 |
- BXD99 |
- 74 |
- F |
-
-
- | 178 |
- R5995S |
- 2 |
- BXD99 |
- 50 |
- M |
-
-
- | 179 |
- R6607S |
- 3 |
- BXD100 |
- 75 |
- F |
-
-
- | 180 |
- R6411S |
- 3 |
- BXD100 |
- 104 |
- M |
-
-
- | 181 |
- R6508S |
- 3 |
- BXD101 |
- 59 |
- F |
-
-
- | 182 |
- R5593S |
- 1 |
- BXD101 |
- 59 |
- M |
-
-
- | 183 |
- R6523S |
- 3 |
- BXD102 |
- 60 |
- F |
-
-
- | 184 |
- R6466S |
- 3 |
- BXD102 |
- 50 |
- M |
-
-
- | 185 |
- R6404S |
- 3 |
- BXD103 |
- 72 |
- F |
-
-
- | 186 |
- R6609S |
- 3 |
- BXD103 |
- 57 |
- M |
-
-
- | 187 |
- R6555S |
- 3 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 188 |
- R5596S |
- 1 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 189 |
- R5597S |
- 1 |
- C57BL/6ByJ |
- 51 |
- F |
-
-
- | 190 |
- R5598S |
- 1 |
- C57BL/6ByJ |
- 69 |
- M |
-
-
- | 191 |
- R5600S |
- 1 |
- C57BL/6J |
- 79 |
- F |
-
-
- | 192 |
- R5599S |
- 1 |
- C57BL/6J |
- 60 |
- F |
-
-
- | 193 |
- R6451S |
- 3 |
- C57BL/6J |
- 77 |
- M |
-
-
- | 194 |
- R6410S |
- 3 |
- C57BL/6J |
- 85 |
- M |
-
-
- | 195 |
- R5603S |
- 1 |
- C57BLKS/J |
- 66 |
- F |
-
-
- | 196 |
- R5604S |
- 1 |
- C57BLKS/J |
- 66 |
- M |
-
-
- | 197 |
- R5996S |
- 2 |
- CBA/CaJ |
- 66 |
- F |
-
-
- | 198 |
- R6349S |
- 3 |
- CBA/CaJ |
- 66 |
- M |
-
-
- | 199 |
- R6458S |
- 3 |
- D2B6F1 |
- 64 |
- F |
-
-
- | 200 |
- R6353S |
- 3 |
- D2B6F1 |
- 60 |
- M |
-
-
- | 201 |
- R5605S |
- 1 |
- DBA/2J |
- 79 |
- F |
-
-
- | 202 |
- R6446S |
- 3 |
- DBA/2J |
- 83 |
- M |
-
-
- | 203 |
- R6597S |
- 3 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 204 |
- R5643S |
- 1 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 205 |
- R6598S |
- 3 |
- FVB/NJ |
- 60 |
- M |
-
-
- | 206 |
- R5606S |
- 1 |
- ILS |
- 74 |
- F |
-
-
- | 207 |
- R5607S |
- 1 |
- ILS |
- 74 |
- M |
-
-
- | 208 |
- R5610S |
- 1 |
- ISS |
- 97 |
- M |
-
-
- | 209 |
- R6627S |
- 3 |
- KK/HlJ |
- 64 |
- F |
-
-
- | 210 |
- R6444S |
- 3 |
- KK/HlJ |
- 65 |
- M |
-
-
- | 211 |
- R5702S |
- 1 |
- KK/HlJ |
- 61 |
- M |
-
-
- | 212 |
- R5613S |
- 1 |
- LG/J |
- 63 |
- F |
-
-
- | 213 |
- R5704S |
- 1 |
- LG/J |
- 65 |
- M |
-
-
- | 214 |
- R5614S |
- 1 |
- LP/J |
- 65 |
- F |
-
-
- | 215 |
- R5615S |
- 1 |
- LP/J |
- 65 |
- M |
-
-
- | 216 |
- R6599S |
- 3 |
- MOLF/EiJ |
- 60 |
- F |
-
-
- | 217 |
- R6606S |
- 3 |
- MOLF/EiJ |
- 60 |
- M |
-
-
- | 218 |
- R6544S |
- 3 |
- NOD/LtJ |
- 77 |
- F |
-
-
- | 219 |
- R5709S |
- 1 |
- NOD/LtJ |
- 58 |
- M |
-
-
- | 220 |
- R6601S |
- 3 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 221 |
- R5711S |
- 1 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 222 |
- R6427S |
- 3 |
- NZB/BlNJ |
- 58 |
- M |
-
-
- | 223 |
- R6150S |
- 2 |
- NZO/HlLtJ |
- 71 |
- F |
-
-
- | 224 |
- R6155S |
- 2 |
- NZW/LacJ |
- 65 |
- F |
-
-
- | 225 |
- R5654S |
- 1 |
- NZW/LacJ |
- 60 |
- M |
-
-
- | 226 |
- R5721S |
- 1 |
- PL/J |
- 59 |
- M |
-
-
- | 227 |
- R5616S |
- 1 |
- PWD/PhJ |
- 60 |
- M |
-
-
- | 228 |
- R5725S |
- 1 |
- PWK/PhJ |
- 121 |
- M |
-
-
- | 229 |
- R6174S |
- 2 |
- SJL/J |
- 63 |
- F |
-
-
- | 230 |
- R6350S |
- 3 |
- SJL/J |
- 65 |
- M |
-
-
- | 231 |
- R6419S |
- 3 |
- WSB/EiJ |
- 60 |
- F |
-
-
- | 232 |
- R5620S |
- 1 |
- WSB/EiJ |
- 60 |
- M |
-
-
-
-
- |
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/UTHSC_SPL_RMA_1010/summary.rtf b/general/datasets/UTHSC_SPL_RMA_1010/summary.rtf
deleted file mode 100644
index d9478f8..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1010/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This is a near final release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. The initial data enterted in 2010 had many errors described below. The data set is much improved and has no known errors of strain assignment.
-
-Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/UTHSC_SPL_RMA_1210/cases.rtf b/general/datasets/UTHSC_SPL_RMA_1210/cases.rtf
deleted file mode 100644
index 7fa108f..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 111 strains, including 81 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1), and 26 other common inbred strains were quantified. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by Lu Lu and colleagues. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. XX strains have matched male and female samples. XX strains have male only samples (BXDX, XX, XX, XXX and XXX). XX strains have only female samples (BXDXX, XX, and XX.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210/experiment-design.rtf b/general/datasets/UTHSC_SPL_RMA_1210/experiment-design.rtf
deleted file mode 100644
index a0aeba6..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-RNA Processing. Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-Array Processing: All arrays were processed by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. The spleen was dissected by both Dr. Lu Lu and colleagues and Dr. Abdeltawab and colleagues. All arrays were run together (interleaved) as a single large batch.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210/notes.rtf b/general/datasets/UTHSC_SPL_RMA_1210/notes.rtf
deleted file mode 100644
index c7bb873..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210/notes.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-Data Status and Use. This is a provisional release that will soon be replaced by a final corrected data set. In the interim this data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210/processing.rtf b/general/datasets/UTHSC_SPL_RMA_1210/processing.rtf
deleted file mode 100644
index deaf264..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210/processing.rtf
+++ /dev/null
@@ -1,1932 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required some correction for batch effects and the data in this initial release incorporate any additional corrections. There are several additional confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest probe sets in this spleen data set accounts of XX% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the spleen data set can be mapped as a trait.
-
-
-Data Release. This data set was first uploaded into GeneNetwork by Arthur Centeno, October 11, 2010 and made accessible without a password to all users on November 1, 2010. The initial data release had numerous strain identification errors that have now largely been fixed. Based on an analysis of the top 20 Mendelian loci, the following 21 strains were likely to have been incorrectly identified or assigned in the current release:
-
-
- - BXD8, e.g., Probe set 10450161, 1036098. 10338684
- - BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
- - BXD21 (may be ok, only one probe set 10338684 is problematic)
- - BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
- - BXD36 (may be ok, only one probe set 10421128 is problematic)
- - BXD40, e.g., Probe set 10341070
- - BXD43, e.g., Probe set 10450161, 1036098, 10338684
- - BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
- - BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
- - BXD68 (may be ok, only one probe set 10338684 is problematic)
- - BXD69, e.g., Probe set 10450161
- - BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
- - BXD74, e.g., Probe set 10402390
- - BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
- - BXD83, e.g., Probe set 10450161, 10338684
- - BXD87 (may be ok, only one probe set 10421128 is problematic)
- - BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
- - BXD93, e.g., Probe set 10402390, 10357381
- - BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
- - LP/J, e.g., Probe set 10592493
- - DBA/2J, e.g., Probe set 10592493
-
-
-Data Evaluation Summary
-
-
- - Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
- - After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
- - Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 237.9
- - After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 278.1
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
Table 1 (please confirm that these assignments are after correction)
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Phase |
- Strain |
- Age |
- Sex |
-
-
- | 1 |
- R5583S |
- 1 |
- 129P3/J |
- 65 |
- F |
-
-
- | 2 |
- R5584S |
- 1 |
- 129P3/J |
- 66 |
- M |
-
-
- | 3 |
- R5585S |
- 1 |
- 129S1/SvImJ |
- 66 |
- F |
-
-
- | 4 |
- R5586S |
- 1 |
- 129S1/SvImJ |
- 66 |
- M |
-
-
- | 5 |
- R5587S |
- 1 |
- 129X1/SvJ |
- 65 |
- F |
-
-
- | 6 |
- R5588S |
- 1 |
- 129X1/SvJ |
- 66 |
- M |
-
-
- | 7 |
- R6348S |
- 3 |
- B6D2F1 |
- 67 |
- F |
-
-
- | 8 |
- R6347S |
- 3 |
- B6D2F1 |
- 62 |
- F |
-
-
- | 9 |
- R5590S |
- 1 |
- B6D2F1 |
- 79 |
- M |
-
-
- | 10 |
- R5662S |
- 1 |
- BALB/cByJ |
- 59 |
- F |
-
-
- | 11 |
- R5664S |
- 1 |
- BALB/cByJ |
- 59 |
- M |
-
-
- | 12 |
- R5591S |
- 1 |
- BALB/cJ |
- 51 |
- F |
-
-
- | 13 |
- R5592S |
- 1 |
- BALB/cJ |
- 51 |
- M |
-
-
- | 14 |
- R6154S |
- 2 |
- BTBR T+ tf/J |
- 60 |
- F |
-
-
- | 15 |
- R6516S |
- 3 |
- BXD1 |
- 82 |
- F |
-
-
- | 16 |
- R6584S |
- 3 |
- BXD1 |
- 95 |
- M |
-
-
- | 17 |
- R5759S |
- 1 |
- BXD2 |
- N/A |
- F |
-
-
- | 18 |
- R5837S |
- 1 |
- BXD2 |
- 106 |
- M |
-
-
- | 19 |
- R5874S |
- 2 |
- BXD5 |
- 86 |
- F |
-
-
- | 20 |
- R6554S |
- 3 |
- BXD5 |
- 60 |
- M |
-
-
- | 21 |
- R6359S |
- 3 |
- BXD6 |
- 72 |
- F |
-
-
- | 22 |
- R5777S |
- 1 |
- BXD6 |
- 149 |
- M |
-
-
- | 23 |
- R6364S |
- 3 |
- BXD8 |
- 76 |
- F |
-
-
- | 24 |
- R5637S |
- 1 |
- BXD8 |
- 71 |
- F |
-
-
- | 25 |
- R6365S |
- 3 |
- BXD8 |
- 76 |
- M |
-
-
- | 26 |
- R5746S |
- 1 |
- BXD9 |
- 70 |
- F |
-
-
- | 27 |
- R5981S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 28 |
- R5980S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 29 |
- R6182S |
- 2 |
- BXD11 |
- 84 |
- F |
-
-
- | 30 |
- R6486S |
- 3 |
- BXD11 |
- 58 |
- M |
-
-
- | 31 |
- R6711S2 |
- 4 |
- BXD12 |
- 71 |
- F |
-
-
- | 32 |
- R6608S |
- 3 |
- BXD12 |
- 48 |
- F |
-
-
- | 33 |
- R5885S |
- 2 |
- BXD12 |
- 44 |
- M |
-
-
- | 34 |
- R5755S |
- 1 |
- BXD13 |
- 160 |
- F |
-
-
- | 35 |
- R5887S |
- 2 |
- BXD13 |
- 53 |
- M |
-
-
- | 36 |
- R6180S |
- 2 |
- BXD14 |
- 70 |
- F |
-
-
- | 37 |
- R5669S |
- 1 |
- BXD14 |
- 91 |
- M |
-
-
- | 38 |
- R6456S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 39 |
- R6622S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 40 |
- R6626S |
- 3 |
- BXD15 |
- 60 |
- M |
-
-
- | 41 |
- R6181S |
- 2 |
- BXD16 |
- 74 |
- F |
-
-
- | 42 |
- R6515S |
- 3 |
- BXD16 |
- 64 |
- M |
-
-
- | 43 |
- R5673S |
- 1 |
- BXD18 |
- 80 |
- F |
-
-
- | 44 |
- R5674S |
- 1 |
- BXD18 |
- 65 |
- M |
-
-
- | 45 |
- R6553S |
- 3 |
- BXD19 |
- 158 |
- F |
-
-
- | 46 |
- R6551S |
- 3 |
- BXD19 |
- 60 |
- M |
-
-
- | 47 |
- R6643S4 |
- 4 |
- BXD20 |
- 59 |
- F |
-
-
- | 48 |
- R6595S |
- 3 |
- BXD20 |
- 60 |
- M |
-
-
- | 49 |
- R5735S |
- 1 |
- BXD21 |
- 64 |
- F |
-
-
- | 50 |
- R5892S |
- 2 |
- BXD21 |
- 99 |
- M |
-
-
- | 51 |
- R5896S |
- 2 |
- BXD22 |
- 60 |
- F |
-
-
- | 52 |
- R6414S |
- 3 |
- BXD22 |
- 73 |
- M |
-
-
- | 53 |
- R6550S |
- 3 |
- BXD23 |
- 74 |
- F |
-
-
- | 54 |
- R6586S |
- 3 |
- BXD23 |
- 102 |
- F |
-
-
- | 55 |
- R5630S |
- 1 |
- BXD24 |
- 71 |
- F |
-
-
- | 56 |
- R6356S |
- 3 |
- BXD24 |
- 57 |
- M |
-
-
- | 57 |
- R6162S |
- 2 |
- BXD25 |
- 67 |
- F |
-
-
- | 58 |
- R6625S |
- 3 |
- BXD25 |
- 67 |
- F |
-
-
- | 59 |
- R6642S4 |
- 4 |
- BXD25 |
- 58 |
- M |
-
-
- | 60 |
- R5761S |
- 1 |
- BXD27 |
- N/A |
- F |
-
-
- | 61 |
- R5763S |
- 1 |
- BXD27 |
- 90 |
- M |
-
-
- | 62 |
- R6621S |
- 3 |
- BXD28 |
- 113 |
- F |
-
-
- | 63 |
- R6548S |
- 3 |
- BXD28 |
- 60 |
- M |
-
-
- | 64 |
- R6547S |
- 3 |
- BXD29 |
- 60 |
- F |
-
-
- | 65 |
- R6453S |
- 3 |
- BXD31 |
- 48 |
- F |
-
-
- | 66 |
- R6452S |
- 3 |
- BXD31 |
- 48 |
- M |
-
-
- | 67 |
- R6583S |
- 3 |
- BXD32 |
- 60 |
- F |
-
-
- | 68 |
- R5765S |
- 1 |
- BXD32 |
- 71 |
- M |
-
-
- | 69 |
- R5689S |
- 1 |
- BXD33 |
- 65 |
- F |
-
-
- | 70 |
- R6450S |
- 3 |
- BXD33 |
- 55 |
- M |
-
-
- | 71 |
- R5767S |
- 1 |
- BXD34 |
- 72 |
- F |
-
-
- | 72 |
- R5900S |
- 2 |
- BXD34 |
- 70 |
- M |
-
-
- | 73 |
- R6588S |
- 3 |
- BXD36 |
- 61 |
- F |
-
-
- | 74 |
- R6490S |
- 3 |
- BXD36 |
- 63 |
- M |
-
-
- | 75 |
- R6417S |
- 3 |
- BXD38 |
- 64 |
- F |
-
-
- | 76 |
- R6439S |
- 3 |
- BXD38 |
- 72 |
- M |
-
-
- | 77 |
- R5769S |
- 1 |
- BXD39 |
- N/A |
- F |
-
-
- | 78 |
- R5771S |
- 1 |
- BXD39 |
- 74 |
- M |
-
-
- | 79 |
- R5773S |
- 1 |
- BXD40 |
- N/A |
- F |
-
-
- | 80 |
- R5775S |
- 1 |
- BXD40 |
- N/A |
- M |
-
-
- | 81 |
- R6494S |
- 3 |
- BXD41 |
- 72 |
- F |
-
-
- | 82 |
- R5910S |
- 2 |
- BXD42 |
- 79 |
- F |
-
-
- | 83 |
- R6493S |
- 3 |
- BXD42 |
- 69 |
- M |
-
-
- | 84 |
- R6341S |
- 3 |
- BXD43 |
- 59 |
- F |
-
-
- | 85 |
- R6401S |
- 3 |
- BXD43 |
- 99 |
- M |
-
-
- | 86 |
- R5916S |
- 2 |
- BXD43 |
- 79 |
- M |
-
-
- | 87 |
- R5839S |
- 1 |
- BXD44 |
- 141 |
- F |
-
-
- | 88 |
- R5779S |
- 1 |
- BXD44 |
- 124 |
- M |
-
-
- | 89 |
- R6405S |
- 3 |
- BXD45 |
- 58 |
- F |
-
-
- | 90 |
- R6610S |
- 3 |
- BXD45 |
- 55 |
- M |
-
-
- | 91 |
- R5922S |
- 2 |
- BXD48 |
- 64 |
- F |
-
-
- | 92 |
- R5925S |
- 2 |
- BXD48 |
- 60 |
- M |
-
-
- | 93 |
- R6719S1 |
- 4 |
- BXD49 |
- 58 |
- F |
-
-
- | 94 |
- R6485S |
- 3 |
- BXD49 |
- 79 |
- M |
-
-
- | 95 |
- R5781S |
- 1 |
- BXD50 |
- 61 |
- F |
-
-
- | 96 |
- R6464S |
- 3 |
- BXD51 |
- 65 |
- F |
-
-
- | 97 |
- R6585S |
- 3 |
- BXD51 |
- 63 |
- M |
-
-
- | 98 |
- R6500S |
- 3 |
- BXD55 |
- 58 |
- F |
-
-
- | 99 |
- R5938S |
- 2 |
- BXD55 |
- 93 |
- M |
-
-
- | 100 |
- R6504S |
- 3 |
- BXD56 |
- 58 |
- F |
-
-
- | 101 |
- R6503S |
- 3 |
- BXD56 |
- 58 |
- M |
-
-
- | 102 |
- R5783S |
- 1 |
- BXD60 |
- 111 |
- F |
-
-
- | 103 |
- R5784S |
- 1 |
- BXD60 |
- 85 |
- M |
-
-
- | 104 |
- R5786S |
- 1 |
- BXD61 |
- 86 |
- F |
-
-
- | 105 |
- R6449S |
- 3 |
- BXD61 |
- 65 |
- M |
-
-
- | 106 |
- R6716S1 |
- 4 |
- BXD62 |
- 54 |
- F |
-
-
- | 107 |
- R5790S |
- 1 |
- BXD62 |
- 115 |
- M |
-
-
- | 108 |
- R6519S |
- 3 |
- BXD63 |
- 54 |
- F |
-
-
- | 109 |
- R6717S1 |
- 4 |
- BXD63 |
- 70 |
- M |
-
-
- | 110 |
- R5792S |
- 1 |
- BXD64 |
- 167 |
- F |
-
-
- | 111 |
- R6641S4 |
- 4 |
- BXD64 |
- 68 |
- M |
-
-
- | 112 |
- R6630S |
- 3 |
- BXD64 |
- 68 |
- M |
-
-
- | 113 |
- R6477S |
- 3 |
- BXD65 |
- 58 |
- F |
-
-
- | 114 |
- R6628S |
- 3 |
- BXD65 |
- 70 |
- M |
-
-
- | 115 |
- R6511S |
- 3 |
- BXD66 |
- 70 |
- F |
-
-
- | 116 |
- R6448S |
- 3 |
- BXD66 |
- 61 |
- M |
-
-
- | 117 |
- R5794S |
- 1 |
- BXD66 |
- 144 |
- M |
-
-
- | 118 |
- R6502S |
- 3 |
- BXD67 |
- 66 |
- F |
-
-
- | 119 |
- R6545S |
- 3 |
- BXD67 |
- 61 |
- M |
-
-
- | 120 |
- R6337S |
- 3 |
- BXD68 |
- 56 |
- F |
-
-
- | 121 |
- R6594S |
- 3 |
- BXD68 |
- 64 |
- M |
-
-
- | 122 |
- R5796S |
- 1 |
- BXD69 |
- 85 |
- F |
-
-
- | 123 |
- R5798S |
- 1 |
- BXD69 |
- 98 |
- M |
-
-
- | 124 |
- R6402S |
- 3 |
- BXD70 |
- 93 |
- F |
-
-
- | 125 |
- R5841S |
- 1 |
- BXD70 |
- 121 |
- F |
-
-
- | 126 |
- R6592S |
- 3 |
- BXD70 |
- 59 |
- M |
-
-
- | 127 |
- R6328S |
- 3 |
- BXD71 |
- 87 |
- F |
-
-
- | 128 |
- R5967S |
- 2 |
- BXD71 |
- 64 |
- M |
-
-
- | 129 |
- R5969S |
- 2 |
- BXD73 |
- 64 |
- F |
-
-
- | 130 |
- R5800S |
- 1 |
- BXD73 |
- 120 |
- M |
-
-
- | 131 |
- R6646S |
- 3 |
- BXD74 |
- 40 |
- F |
-
-
- | 132 |
- R6524S |
- 3 |
- BXD74 |
- 72 |
- M |
-
-
- | 133 |
- R6445S |
- 3 |
- BXD75 |
- 85 |
- F |
-
-
- | 134 |
- R5843S |
- 1 |
- BXD75 |
- 103 |
- F |
-
-
- | 135 |
- R5845S |
- 1 |
- BXD75 |
- 103 |
- M |
-
-
- | 136 |
- R6604S |
- 3 |
- BXD77 |
- 64 |
- F |
-
-
- | 137 |
- R6513S |
- 3 |
- BXD77 |
- 72 |
- M |
-
-
- | 138 |
- R6582S |
- 3 |
- BXD78 |
- 144 |
- F |
-
-
- | 139 |
- R6563S |
- 3 |
- BXD78 |
- 95 |
- M |
-
-
- | 140 |
- R6645S4 |
- 4 |
- BXD79 |
- 66 |
- F |
-
-
- | 141 |
- R5806S |
- 1 |
- BXD79 |
- 78 |
- M |
-
-
- | 142 |
- R5847S |
- 1 |
- BXD80 |
- 89 |
- F |
-
-
- | 143 |
- R5852S |
- 1 |
- BXD80 |
- 79 |
- M |
-
-
- | 144 |
- R6562S |
- 3 |
- BXD81 |
- 99 |
- F |
-
-
- | 145 |
- R6468S |
- 3 |
- BXD81 |
- 65 |
- M |
-
-
- | 146 |
- R6560S |
- 3 |
- BXD82 |
- 85 |
- F |
-
-
- | 147 |
- R6512S |
- 3 |
- BXD83 |
- 68 |
- F |
-
-
- | 148 |
- R5810S |
- 1 |
- BXD83 |
- 139 |
- M |
-
-
- | 149 |
- R6510S |
- 3 |
- BXD84 |
- 87 |
- F |
-
-
- | 150 |
- R5970S |
- 2 |
- BXD84 |
- 107 |
- F |
-
-
- | 151 |
- R6603S |
- 3 |
- BXD84 |
- 99 |
- M |
-
-
- | 152 |
- R6517S |
- 3 |
- BXD85 |
- 58 |
- F |
-
-
- | 153 |
- R6718S1 |
- 4 |
- BXD85 |
- 86 |
- M |
-
-
- | 154 |
- R5812S |
- 1 |
- BXD86 |
- 61 |
- F |
-
-
- | 155 |
- R5814S |
- 1 |
- BXD86 |
- 59 |
- M |
-
-
- | 156 |
- R5816S |
- 1 |
- BXD87 |
- 112 |
- F |
-
-
- | 157 |
- R6488S |
- 3 |
- BXD87 |
- 137 |
- M |
-
-
- | 158 |
- R6580S |
- 3 |
- BXD88 |
- 125 |
- F |
-
-
- | 159 |
- R5977S |
- 2 |
- BXD89 |
- 68 |
- F |
-
-
- | 160 |
- R5979S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 161 |
- R5978S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 162 |
- R5818S |
- 1 |
- BXD90 |
- 106 |
- F |
-
-
- | 163 |
- R5820S |
- 1 |
- BXD90 |
- 131 |
- M |
-
-
- | 164 |
- R6343S |
- 3 |
- BXD92 |
- 62 |
- F |
-
-
- | 165 |
- R5984S |
- 2 |
- BXD92 |
- 55 |
- M |
-
-
- | 166 |
- R6581S |
- 3 |
- BXD93 |
- 173 |
- M |
-
-
- | 167 |
- R6557S |
- 3 |
- BXD93 |
- 126 |
- M |
-
-
- | 168 |
- R6509S |
- 3 |
- BXD95 |
- 59 |
- F |
-
-
- | 169 |
- R5822S |
- 1 |
- BXD95 |
- 89 |
- M |
-
-
- | 170 |
- R6640S4 |
- 4 |
- BXD96 |
- 70 |
- F |
-
-
- | 171 |
- R6514S |
- 3 |
- BXD96 |
- 64 |
- M |
-
-
- | 172 |
- R6506S |
- 3 |
- BXD97 |
- 78 |
- F |
-
-
- | 173 |
- R5849S |
- 1 |
- BXD97 |
- 130 |
- F |
-
-
- | 174 |
- R6591S |
- 3 |
- BXD97 |
- 122 |
- M |
-
-
- | 175 |
- R5990S |
- 2 |
- BXD98 |
- 65 |
- F |
-
-
- | 176 |
- R6596S |
- 3 |
- BXD98 |
- 67 |
- M |
-
-
- | 177 |
- R5993S |
- 2 |
- BXD99 |
- 74 |
- F |
-
-
- | 178 |
- R5995S |
- 2 |
- BXD99 |
- 50 |
- M |
-
-
- | 179 |
- R6607S |
- 3 |
- BXD100 |
- 75 |
- F |
-
-
- | 180 |
- R6411S |
- 3 |
- BXD100 |
- 104 |
- M |
-
-
- | 181 |
- R6508S |
- 3 |
- BXD101 |
- 59 |
- F |
-
-
- | 182 |
- R5593S |
- 1 |
- BXD101 |
- 59 |
- M |
-
-
- | 183 |
- R6523S |
- 3 |
- BXD102 |
- 60 |
- F |
-
-
- | 184 |
- R6466S |
- 3 |
- BXD102 |
- 50 |
- M |
-
-
- | 185 |
- R6404S |
- 3 |
- BXD103 |
- 72 |
- F |
-
-
- | 186 |
- R6609S |
- 3 |
- BXD103 |
- 57 |
- M |
-
-
- | 187 |
- R6555S |
- 3 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 188 |
- R5596S |
- 1 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 189 |
- R5597S |
- 1 |
- C57BL/6ByJ |
- 51 |
- F |
-
-
- | 190 |
- R5598S |
- 1 |
- C57BL/6ByJ |
- 69 |
- M |
-
-
- | 191 |
- R5600S |
- 1 |
- C57BL/6J |
- 79 |
- F |
-
-
- | 192 |
- R5599S |
- 1 |
- C57BL/6J |
- 60 |
- F |
-
-
- | 193 |
- R6451S |
- 3 |
- C57BL/6J |
- 77 |
- M |
-
-
- | 194 |
- R6410S |
- 3 |
- C57BL/6J |
- 85 |
- M |
-
-
- | 195 |
- R5603S |
- 1 |
- C57BLKS/J |
- 66 |
- F |
-
-
- | 196 |
- R5604S |
- 1 |
- C57BLKS/J |
- 66 |
- M |
-
-
- | 197 |
- R5996S |
- 2 |
- CBA/CaJ |
- 66 |
- F |
-
-
- | 198 |
- R6349S |
- 3 |
- CBA/CaJ |
- 66 |
- M |
-
-
- | 199 |
- R6458S |
- 3 |
- D2B6F1 |
- 64 |
- F |
-
-
- | 200 |
- R6353S |
- 3 |
- D2B6F1 |
- 60 |
- M |
-
-
- | 201 |
- R5605S |
- 1 |
- DBA/2J |
- 79 |
- F |
-
-
- | 202 |
- R6446S |
- 3 |
- DBA/2J |
- 83 |
- M |
-
-
- | 203 |
- R6597S |
- 3 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 204 |
- R5643S |
- 1 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 205 |
- R6598S |
- 3 |
- FVB/NJ |
- 60 |
- M |
-
-
- | 206 |
- R5606S |
- 1 |
- ILS |
- 74 |
- F |
-
-
- | 207 |
- R5607S |
- 1 |
- ILS |
- 74 |
- M |
-
-
- | 208 |
- R5610S |
- 1 |
- ISS |
- 97 |
- M |
-
-
- | 209 |
- R6627S |
- 3 |
- KK/HlJ |
- 64 |
- F |
-
-
- | 210 |
- R6444S |
- 3 |
- KK/HlJ |
- 65 |
- M |
-
-
- | 211 |
- R5702S |
- 1 |
- KK/HlJ |
- 61 |
- M |
-
-
- | 212 |
- R5613S |
- 1 |
- LG/J |
- 63 |
- F |
-
-
- | 213 |
- R5704S |
- 1 |
- LG/J |
- 65 |
- M |
-
-
- | 214 |
- R5614S |
- 1 |
- LP/J |
- 65 |
- F |
-
-
- | 215 |
- R5615S |
- 1 |
- LP/J |
- 65 |
- M |
-
-
- | 216 |
- R6599S |
- 3 |
- MOLF/EiJ |
- 60 |
- F |
-
-
- | 217 |
- R6606S |
- 3 |
- MOLF/EiJ |
- 60 |
- M |
-
-
- | 218 |
- R6544S |
- 3 |
- NOD/LtJ |
- 77 |
- F |
-
-
- | 219 |
- R5709S |
- 1 |
- NOD/LtJ |
- 58 |
- M |
-
-
- | 220 |
- R6601S |
- 3 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 221 |
- R5711S |
- 1 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 222 |
- R6427S |
- 3 |
- NZB/BlNJ |
- 58 |
- M |
-
-
- | 223 |
- R6150S |
- 2 |
- NZO/HlLtJ |
- 71 |
- F |
-
-
- | 224 |
- R6155S |
- 2 |
- NZW/LacJ |
- 65 |
- F |
-
-
- | 225 |
- R5654S |
- 1 |
- NZW/LacJ |
- 60 |
- M |
-
-
- | 226 |
- R5721S |
- 1 |
- PL/J |
- 59 |
- M |
-
-
- | 227 |
- R5616S |
- 1 |
- PWD/PhJ |
- 60 |
- M |
-
-
- | 228 |
- R5725S |
- 1 |
- PWK/PhJ |
- 121 |
- M |
-
-
- | 229 |
- R6174S |
- 2 |
- SJL/J |
- 63 |
- F |
-
-
- | 230 |
- R6350S |
- 3 |
- SJL/J |
- 65 |
- M |
-
-
- | 231 |
- R6419S |
- 3 |
- WSB/EiJ |
- 60 |
- F |
-
-
- | 232 |
- R5620S |
- 1 |
- WSB/EiJ |
- 60 |
- M |
-
-
-
-
- |
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/UTHSC_SPL_RMA_1210/summary.rtf b/general/datasets/UTHSC_SPL_RMA_1210/summary.rtf
deleted file mode 100644
index d9478f8..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This is a near final release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. The initial data enterted in 2010 had many errors described below. The data set is much improved and has no known errors of strain assignment.
-
-Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/UTHSC_SPL_RMA_1210F/cases.rtf b/general/datasets/UTHSC_SPL_RMA_1210F/cases.rtf
deleted file mode 100644
index 7fa108f..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210F/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 111 strains, including 81 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1), and 26 other common inbred strains were quantified. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by Lu Lu and colleagues. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. XX strains have matched male and female samples. XX strains have male only samples (BXDX, XX, XX, XXX and XXX). XX strains have only female samples (BXDXX, XX, and XX.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210F/experiment-design.rtf b/general/datasets/UTHSC_SPL_RMA_1210F/experiment-design.rtf
deleted file mode 100644
index a0aeba6..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210F/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-RNA Processing. Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-Array Processing: All arrays were processed by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. The spleen was dissected by both Dr. Lu Lu and colleagues and Dr. Abdeltawab and colleagues. All arrays were run together (interleaved) as a single large batch.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210F/notes.rtf b/general/datasets/UTHSC_SPL_RMA_1210F/notes.rtf
deleted file mode 100644
index c7bb873..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210F/notes.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-Data Status and Use. This is a provisional release that will soon be replaced by a final corrected data set. In the interim this data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210F/processing.rtf b/general/datasets/UTHSC_SPL_RMA_1210F/processing.rtf
deleted file mode 100644
index deaf264..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210F/processing.rtf
+++ /dev/null
@@ -1,1932 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required some correction for batch effects and the data in this initial release incorporate any additional corrections. There are several additional confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest probe sets in this spleen data set accounts of XX% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the spleen data set can be mapped as a trait.
-
-
-Data Release. This data set was first uploaded into GeneNetwork by Arthur Centeno, October 11, 2010 and made accessible without a password to all users on November 1, 2010. The initial data release had numerous strain identification errors that have now largely been fixed. Based on an analysis of the top 20 Mendelian loci, the following 21 strains were likely to have been incorrectly identified or assigned in the current release:
-
-
- - BXD8, e.g., Probe set 10450161, 1036098. 10338684
- - BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
- - BXD21 (may be ok, only one probe set 10338684 is problematic)
- - BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
- - BXD36 (may be ok, only one probe set 10421128 is problematic)
- - BXD40, e.g., Probe set 10341070
- - BXD43, e.g., Probe set 10450161, 1036098, 10338684
- - BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
- - BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
- - BXD68 (may be ok, only one probe set 10338684 is problematic)
- - BXD69, e.g., Probe set 10450161
- - BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
- - BXD74, e.g., Probe set 10402390
- - BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
- - BXD83, e.g., Probe set 10450161, 10338684
- - BXD87 (may be ok, only one probe set 10421128 is problematic)
- - BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
- - BXD93, e.g., Probe set 10402390, 10357381
- - BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
- - LP/J, e.g., Probe set 10592493
- - DBA/2J, e.g., Probe set 10592493
-
-
-Data Evaluation Summary
-
-
- - Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
- - After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
- - Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 237.9
- - After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 278.1
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
Table 1 (please confirm that these assignments are after correction)
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Phase |
- Strain |
- Age |
- Sex |
-
-
- | 1 |
- R5583S |
- 1 |
- 129P3/J |
- 65 |
- F |
-
-
- | 2 |
- R5584S |
- 1 |
- 129P3/J |
- 66 |
- M |
-
-
- | 3 |
- R5585S |
- 1 |
- 129S1/SvImJ |
- 66 |
- F |
-
-
- | 4 |
- R5586S |
- 1 |
- 129S1/SvImJ |
- 66 |
- M |
-
-
- | 5 |
- R5587S |
- 1 |
- 129X1/SvJ |
- 65 |
- F |
-
-
- | 6 |
- R5588S |
- 1 |
- 129X1/SvJ |
- 66 |
- M |
-
-
- | 7 |
- R6348S |
- 3 |
- B6D2F1 |
- 67 |
- F |
-
-
- | 8 |
- R6347S |
- 3 |
- B6D2F1 |
- 62 |
- F |
-
-
- | 9 |
- R5590S |
- 1 |
- B6D2F1 |
- 79 |
- M |
-
-
- | 10 |
- R5662S |
- 1 |
- BALB/cByJ |
- 59 |
- F |
-
-
- | 11 |
- R5664S |
- 1 |
- BALB/cByJ |
- 59 |
- M |
-
-
- | 12 |
- R5591S |
- 1 |
- BALB/cJ |
- 51 |
- F |
-
-
- | 13 |
- R5592S |
- 1 |
- BALB/cJ |
- 51 |
- M |
-
-
- | 14 |
- R6154S |
- 2 |
- BTBR T+ tf/J |
- 60 |
- F |
-
-
- | 15 |
- R6516S |
- 3 |
- BXD1 |
- 82 |
- F |
-
-
- | 16 |
- R6584S |
- 3 |
- BXD1 |
- 95 |
- M |
-
-
- | 17 |
- R5759S |
- 1 |
- BXD2 |
- N/A |
- F |
-
-
- | 18 |
- R5837S |
- 1 |
- BXD2 |
- 106 |
- M |
-
-
- | 19 |
- R5874S |
- 2 |
- BXD5 |
- 86 |
- F |
-
-
- | 20 |
- R6554S |
- 3 |
- BXD5 |
- 60 |
- M |
-
-
- | 21 |
- R6359S |
- 3 |
- BXD6 |
- 72 |
- F |
-
-
- | 22 |
- R5777S |
- 1 |
- BXD6 |
- 149 |
- M |
-
-
- | 23 |
- R6364S |
- 3 |
- BXD8 |
- 76 |
- F |
-
-
- | 24 |
- R5637S |
- 1 |
- BXD8 |
- 71 |
- F |
-
-
- | 25 |
- R6365S |
- 3 |
- BXD8 |
- 76 |
- M |
-
-
- | 26 |
- R5746S |
- 1 |
- BXD9 |
- 70 |
- F |
-
-
- | 27 |
- R5981S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 28 |
- R5980S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 29 |
- R6182S |
- 2 |
- BXD11 |
- 84 |
- F |
-
-
- | 30 |
- R6486S |
- 3 |
- BXD11 |
- 58 |
- M |
-
-
- | 31 |
- R6711S2 |
- 4 |
- BXD12 |
- 71 |
- F |
-
-
- | 32 |
- R6608S |
- 3 |
- BXD12 |
- 48 |
- F |
-
-
- | 33 |
- R5885S |
- 2 |
- BXD12 |
- 44 |
- M |
-
-
- | 34 |
- R5755S |
- 1 |
- BXD13 |
- 160 |
- F |
-
-
- | 35 |
- R5887S |
- 2 |
- BXD13 |
- 53 |
- M |
-
-
- | 36 |
- R6180S |
- 2 |
- BXD14 |
- 70 |
- F |
-
-
- | 37 |
- R5669S |
- 1 |
- BXD14 |
- 91 |
- M |
-
-
- | 38 |
- R6456S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 39 |
- R6622S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 40 |
- R6626S |
- 3 |
- BXD15 |
- 60 |
- M |
-
-
- | 41 |
- R6181S |
- 2 |
- BXD16 |
- 74 |
- F |
-
-
- | 42 |
- R6515S |
- 3 |
- BXD16 |
- 64 |
- M |
-
-
- | 43 |
- R5673S |
- 1 |
- BXD18 |
- 80 |
- F |
-
-
- | 44 |
- R5674S |
- 1 |
- BXD18 |
- 65 |
- M |
-
-
- | 45 |
- R6553S |
- 3 |
- BXD19 |
- 158 |
- F |
-
-
- | 46 |
- R6551S |
- 3 |
- BXD19 |
- 60 |
- M |
-
-
- | 47 |
- R6643S4 |
- 4 |
- BXD20 |
- 59 |
- F |
-
-
- | 48 |
- R6595S |
- 3 |
- BXD20 |
- 60 |
- M |
-
-
- | 49 |
- R5735S |
- 1 |
- BXD21 |
- 64 |
- F |
-
-
- | 50 |
- R5892S |
- 2 |
- BXD21 |
- 99 |
- M |
-
-
- | 51 |
- R5896S |
- 2 |
- BXD22 |
- 60 |
- F |
-
-
- | 52 |
- R6414S |
- 3 |
- BXD22 |
- 73 |
- M |
-
-
- | 53 |
- R6550S |
- 3 |
- BXD23 |
- 74 |
- F |
-
-
- | 54 |
- R6586S |
- 3 |
- BXD23 |
- 102 |
- F |
-
-
- | 55 |
- R5630S |
- 1 |
- BXD24 |
- 71 |
- F |
-
-
- | 56 |
- R6356S |
- 3 |
- BXD24 |
- 57 |
- M |
-
-
- | 57 |
- R6162S |
- 2 |
- BXD25 |
- 67 |
- F |
-
-
- | 58 |
- R6625S |
- 3 |
- BXD25 |
- 67 |
- F |
-
-
- | 59 |
- R6642S4 |
- 4 |
- BXD25 |
- 58 |
- M |
-
-
- | 60 |
- R5761S |
- 1 |
- BXD27 |
- N/A |
- F |
-
-
- | 61 |
- R5763S |
- 1 |
- BXD27 |
- 90 |
- M |
-
-
- | 62 |
- R6621S |
- 3 |
- BXD28 |
- 113 |
- F |
-
-
- | 63 |
- R6548S |
- 3 |
- BXD28 |
- 60 |
- M |
-
-
- | 64 |
- R6547S |
- 3 |
- BXD29 |
- 60 |
- F |
-
-
- | 65 |
- R6453S |
- 3 |
- BXD31 |
- 48 |
- F |
-
-
- | 66 |
- R6452S |
- 3 |
- BXD31 |
- 48 |
- M |
-
-
- | 67 |
- R6583S |
- 3 |
- BXD32 |
- 60 |
- F |
-
-
- | 68 |
- R5765S |
- 1 |
- BXD32 |
- 71 |
- M |
-
-
- | 69 |
- R5689S |
- 1 |
- BXD33 |
- 65 |
- F |
-
-
- | 70 |
- R6450S |
- 3 |
- BXD33 |
- 55 |
- M |
-
-
- | 71 |
- R5767S |
- 1 |
- BXD34 |
- 72 |
- F |
-
-
- | 72 |
- R5900S |
- 2 |
- BXD34 |
- 70 |
- M |
-
-
- | 73 |
- R6588S |
- 3 |
- BXD36 |
- 61 |
- F |
-
-
- | 74 |
- R6490S |
- 3 |
- BXD36 |
- 63 |
- M |
-
-
- | 75 |
- R6417S |
- 3 |
- BXD38 |
- 64 |
- F |
-
-
- | 76 |
- R6439S |
- 3 |
- BXD38 |
- 72 |
- M |
-
-
- | 77 |
- R5769S |
- 1 |
- BXD39 |
- N/A |
- F |
-
-
- | 78 |
- R5771S |
- 1 |
- BXD39 |
- 74 |
- M |
-
-
- | 79 |
- R5773S |
- 1 |
- BXD40 |
- N/A |
- F |
-
-
- | 80 |
- R5775S |
- 1 |
- BXD40 |
- N/A |
- M |
-
-
- | 81 |
- R6494S |
- 3 |
- BXD41 |
- 72 |
- F |
-
-
- | 82 |
- R5910S |
- 2 |
- BXD42 |
- 79 |
- F |
-
-
- | 83 |
- R6493S |
- 3 |
- BXD42 |
- 69 |
- M |
-
-
- | 84 |
- R6341S |
- 3 |
- BXD43 |
- 59 |
- F |
-
-
- | 85 |
- R6401S |
- 3 |
- BXD43 |
- 99 |
- M |
-
-
- | 86 |
- R5916S |
- 2 |
- BXD43 |
- 79 |
- M |
-
-
- | 87 |
- R5839S |
- 1 |
- BXD44 |
- 141 |
- F |
-
-
- | 88 |
- R5779S |
- 1 |
- BXD44 |
- 124 |
- M |
-
-
- | 89 |
- R6405S |
- 3 |
- BXD45 |
- 58 |
- F |
-
-
- | 90 |
- R6610S |
- 3 |
- BXD45 |
- 55 |
- M |
-
-
- | 91 |
- R5922S |
- 2 |
- BXD48 |
- 64 |
- F |
-
-
- | 92 |
- R5925S |
- 2 |
- BXD48 |
- 60 |
- M |
-
-
- | 93 |
- R6719S1 |
- 4 |
- BXD49 |
- 58 |
- F |
-
-
- | 94 |
- R6485S |
- 3 |
- BXD49 |
- 79 |
- M |
-
-
- | 95 |
- R5781S |
- 1 |
- BXD50 |
- 61 |
- F |
-
-
- | 96 |
- R6464S |
- 3 |
- BXD51 |
- 65 |
- F |
-
-
- | 97 |
- R6585S |
- 3 |
- BXD51 |
- 63 |
- M |
-
-
- | 98 |
- R6500S |
- 3 |
- BXD55 |
- 58 |
- F |
-
-
- | 99 |
- R5938S |
- 2 |
- BXD55 |
- 93 |
- M |
-
-
- | 100 |
- R6504S |
- 3 |
- BXD56 |
- 58 |
- F |
-
-
- | 101 |
- R6503S |
- 3 |
- BXD56 |
- 58 |
- M |
-
-
- | 102 |
- R5783S |
- 1 |
- BXD60 |
- 111 |
- F |
-
-
- | 103 |
- R5784S |
- 1 |
- BXD60 |
- 85 |
- M |
-
-
- | 104 |
- R5786S |
- 1 |
- BXD61 |
- 86 |
- F |
-
-
- | 105 |
- R6449S |
- 3 |
- BXD61 |
- 65 |
- M |
-
-
- | 106 |
- R6716S1 |
- 4 |
- BXD62 |
- 54 |
- F |
-
-
- | 107 |
- R5790S |
- 1 |
- BXD62 |
- 115 |
- M |
-
-
- | 108 |
- R6519S |
- 3 |
- BXD63 |
- 54 |
- F |
-
-
- | 109 |
- R6717S1 |
- 4 |
- BXD63 |
- 70 |
- M |
-
-
- | 110 |
- R5792S |
- 1 |
- BXD64 |
- 167 |
- F |
-
-
- | 111 |
- R6641S4 |
- 4 |
- BXD64 |
- 68 |
- M |
-
-
- | 112 |
- R6630S |
- 3 |
- BXD64 |
- 68 |
- M |
-
-
- | 113 |
- R6477S |
- 3 |
- BXD65 |
- 58 |
- F |
-
-
- | 114 |
- R6628S |
- 3 |
- BXD65 |
- 70 |
- M |
-
-
- | 115 |
- R6511S |
- 3 |
- BXD66 |
- 70 |
- F |
-
-
- | 116 |
- R6448S |
- 3 |
- BXD66 |
- 61 |
- M |
-
-
- | 117 |
- R5794S |
- 1 |
- BXD66 |
- 144 |
- M |
-
-
- | 118 |
- R6502S |
- 3 |
- BXD67 |
- 66 |
- F |
-
-
- | 119 |
- R6545S |
- 3 |
- BXD67 |
- 61 |
- M |
-
-
- | 120 |
- R6337S |
- 3 |
- BXD68 |
- 56 |
- F |
-
-
- | 121 |
- R6594S |
- 3 |
- BXD68 |
- 64 |
- M |
-
-
- | 122 |
- R5796S |
- 1 |
- BXD69 |
- 85 |
- F |
-
-
- | 123 |
- R5798S |
- 1 |
- BXD69 |
- 98 |
- M |
-
-
- | 124 |
- R6402S |
- 3 |
- BXD70 |
- 93 |
- F |
-
-
- | 125 |
- R5841S |
- 1 |
- BXD70 |
- 121 |
- F |
-
-
- | 126 |
- R6592S |
- 3 |
- BXD70 |
- 59 |
- M |
-
-
- | 127 |
- R6328S |
- 3 |
- BXD71 |
- 87 |
- F |
-
-
- | 128 |
- R5967S |
- 2 |
- BXD71 |
- 64 |
- M |
-
-
- | 129 |
- R5969S |
- 2 |
- BXD73 |
- 64 |
- F |
-
-
- | 130 |
- R5800S |
- 1 |
- BXD73 |
- 120 |
- M |
-
-
- | 131 |
- R6646S |
- 3 |
- BXD74 |
- 40 |
- F |
-
-
- | 132 |
- R6524S |
- 3 |
- BXD74 |
- 72 |
- M |
-
-
- | 133 |
- R6445S |
- 3 |
- BXD75 |
- 85 |
- F |
-
-
- | 134 |
- R5843S |
- 1 |
- BXD75 |
- 103 |
- F |
-
-
- | 135 |
- R5845S |
- 1 |
- BXD75 |
- 103 |
- M |
-
-
- | 136 |
- R6604S |
- 3 |
- BXD77 |
- 64 |
- F |
-
-
- | 137 |
- R6513S |
- 3 |
- BXD77 |
- 72 |
- M |
-
-
- | 138 |
- R6582S |
- 3 |
- BXD78 |
- 144 |
- F |
-
-
- | 139 |
- R6563S |
- 3 |
- BXD78 |
- 95 |
- M |
-
-
- | 140 |
- R6645S4 |
- 4 |
- BXD79 |
- 66 |
- F |
-
-
- | 141 |
- R5806S |
- 1 |
- BXD79 |
- 78 |
- M |
-
-
- | 142 |
- R5847S |
- 1 |
- BXD80 |
- 89 |
- F |
-
-
- | 143 |
- R5852S |
- 1 |
- BXD80 |
- 79 |
- M |
-
-
- | 144 |
- R6562S |
- 3 |
- BXD81 |
- 99 |
- F |
-
-
- | 145 |
- R6468S |
- 3 |
- BXD81 |
- 65 |
- M |
-
-
- | 146 |
- R6560S |
- 3 |
- BXD82 |
- 85 |
- F |
-
-
- | 147 |
- R6512S |
- 3 |
- BXD83 |
- 68 |
- F |
-
-
- | 148 |
- R5810S |
- 1 |
- BXD83 |
- 139 |
- M |
-
-
- | 149 |
- R6510S |
- 3 |
- BXD84 |
- 87 |
- F |
-
-
- | 150 |
- R5970S |
- 2 |
- BXD84 |
- 107 |
- F |
-
-
- | 151 |
- R6603S |
- 3 |
- BXD84 |
- 99 |
- M |
-
-
- | 152 |
- R6517S |
- 3 |
- BXD85 |
- 58 |
- F |
-
-
- | 153 |
- R6718S1 |
- 4 |
- BXD85 |
- 86 |
- M |
-
-
- | 154 |
- R5812S |
- 1 |
- BXD86 |
- 61 |
- F |
-
-
- | 155 |
- R5814S |
- 1 |
- BXD86 |
- 59 |
- M |
-
-
- | 156 |
- R5816S |
- 1 |
- BXD87 |
- 112 |
- F |
-
-
- | 157 |
- R6488S |
- 3 |
- BXD87 |
- 137 |
- M |
-
-
- | 158 |
- R6580S |
- 3 |
- BXD88 |
- 125 |
- F |
-
-
- | 159 |
- R5977S |
- 2 |
- BXD89 |
- 68 |
- F |
-
-
- | 160 |
- R5979S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 161 |
- R5978S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 162 |
- R5818S |
- 1 |
- BXD90 |
- 106 |
- F |
-
-
- | 163 |
- R5820S |
- 1 |
- BXD90 |
- 131 |
- M |
-
-
- | 164 |
- R6343S |
- 3 |
- BXD92 |
- 62 |
- F |
-
-
- | 165 |
- R5984S |
- 2 |
- BXD92 |
- 55 |
- M |
-
-
- | 166 |
- R6581S |
- 3 |
- BXD93 |
- 173 |
- M |
-
-
- | 167 |
- R6557S |
- 3 |
- BXD93 |
- 126 |
- M |
-
-
- | 168 |
- R6509S |
- 3 |
- BXD95 |
- 59 |
- F |
-
-
- | 169 |
- R5822S |
- 1 |
- BXD95 |
- 89 |
- M |
-
-
- | 170 |
- R6640S4 |
- 4 |
- BXD96 |
- 70 |
- F |
-
-
- | 171 |
- R6514S |
- 3 |
- BXD96 |
- 64 |
- M |
-
-
- | 172 |
- R6506S |
- 3 |
- BXD97 |
- 78 |
- F |
-
-
- | 173 |
- R5849S |
- 1 |
- BXD97 |
- 130 |
- F |
-
-
- | 174 |
- R6591S |
- 3 |
- BXD97 |
- 122 |
- M |
-
-
- | 175 |
- R5990S |
- 2 |
- BXD98 |
- 65 |
- F |
-
-
- | 176 |
- R6596S |
- 3 |
- BXD98 |
- 67 |
- M |
-
-
- | 177 |
- R5993S |
- 2 |
- BXD99 |
- 74 |
- F |
-
-
- | 178 |
- R5995S |
- 2 |
- BXD99 |
- 50 |
- M |
-
-
- | 179 |
- R6607S |
- 3 |
- BXD100 |
- 75 |
- F |
-
-
- | 180 |
- R6411S |
- 3 |
- BXD100 |
- 104 |
- M |
-
-
- | 181 |
- R6508S |
- 3 |
- BXD101 |
- 59 |
- F |
-
-
- | 182 |
- R5593S |
- 1 |
- BXD101 |
- 59 |
- M |
-
-
- | 183 |
- R6523S |
- 3 |
- BXD102 |
- 60 |
- F |
-
-
- | 184 |
- R6466S |
- 3 |
- BXD102 |
- 50 |
- M |
-
-
- | 185 |
- R6404S |
- 3 |
- BXD103 |
- 72 |
- F |
-
-
- | 186 |
- R6609S |
- 3 |
- BXD103 |
- 57 |
- M |
-
-
- | 187 |
- R6555S |
- 3 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 188 |
- R5596S |
- 1 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 189 |
- R5597S |
- 1 |
- C57BL/6ByJ |
- 51 |
- F |
-
-
- | 190 |
- R5598S |
- 1 |
- C57BL/6ByJ |
- 69 |
- M |
-
-
- | 191 |
- R5600S |
- 1 |
- C57BL/6J |
- 79 |
- F |
-
-
- | 192 |
- R5599S |
- 1 |
- C57BL/6J |
- 60 |
- F |
-
-
- | 193 |
- R6451S |
- 3 |
- C57BL/6J |
- 77 |
- M |
-
-
- | 194 |
- R6410S |
- 3 |
- C57BL/6J |
- 85 |
- M |
-
-
- | 195 |
- R5603S |
- 1 |
- C57BLKS/J |
- 66 |
- F |
-
-
- | 196 |
- R5604S |
- 1 |
- C57BLKS/J |
- 66 |
- M |
-
-
- | 197 |
- R5996S |
- 2 |
- CBA/CaJ |
- 66 |
- F |
-
-
- | 198 |
- R6349S |
- 3 |
- CBA/CaJ |
- 66 |
- M |
-
-
- | 199 |
- R6458S |
- 3 |
- D2B6F1 |
- 64 |
- F |
-
-
- | 200 |
- R6353S |
- 3 |
- D2B6F1 |
- 60 |
- M |
-
-
- | 201 |
- R5605S |
- 1 |
- DBA/2J |
- 79 |
- F |
-
-
- | 202 |
- R6446S |
- 3 |
- DBA/2J |
- 83 |
- M |
-
-
- | 203 |
- R6597S |
- 3 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 204 |
- R5643S |
- 1 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 205 |
- R6598S |
- 3 |
- FVB/NJ |
- 60 |
- M |
-
-
- | 206 |
- R5606S |
- 1 |
- ILS |
- 74 |
- F |
-
-
- | 207 |
- R5607S |
- 1 |
- ILS |
- 74 |
- M |
-
-
- | 208 |
- R5610S |
- 1 |
- ISS |
- 97 |
- M |
-
-
- | 209 |
- R6627S |
- 3 |
- KK/HlJ |
- 64 |
- F |
-
-
- | 210 |
- R6444S |
- 3 |
- KK/HlJ |
- 65 |
- M |
-
-
- | 211 |
- R5702S |
- 1 |
- KK/HlJ |
- 61 |
- M |
-
-
- | 212 |
- R5613S |
- 1 |
- LG/J |
- 63 |
- F |
-
-
- | 213 |
- R5704S |
- 1 |
- LG/J |
- 65 |
- M |
-
-
- | 214 |
- R5614S |
- 1 |
- LP/J |
- 65 |
- F |
-
-
- | 215 |
- R5615S |
- 1 |
- LP/J |
- 65 |
- M |
-
-
- | 216 |
- R6599S |
- 3 |
- MOLF/EiJ |
- 60 |
- F |
-
-
- | 217 |
- R6606S |
- 3 |
- MOLF/EiJ |
- 60 |
- M |
-
-
- | 218 |
- R6544S |
- 3 |
- NOD/LtJ |
- 77 |
- F |
-
-
- | 219 |
- R5709S |
- 1 |
- NOD/LtJ |
- 58 |
- M |
-
-
- | 220 |
- R6601S |
- 3 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 221 |
- R5711S |
- 1 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 222 |
- R6427S |
- 3 |
- NZB/BlNJ |
- 58 |
- M |
-
-
- | 223 |
- R6150S |
- 2 |
- NZO/HlLtJ |
- 71 |
- F |
-
-
- | 224 |
- R6155S |
- 2 |
- NZW/LacJ |
- 65 |
- F |
-
-
- | 225 |
- R5654S |
- 1 |
- NZW/LacJ |
- 60 |
- M |
-
-
- | 226 |
- R5721S |
- 1 |
- PL/J |
- 59 |
- M |
-
-
- | 227 |
- R5616S |
- 1 |
- PWD/PhJ |
- 60 |
- M |
-
-
- | 228 |
- R5725S |
- 1 |
- PWK/PhJ |
- 121 |
- M |
-
-
- | 229 |
- R6174S |
- 2 |
- SJL/J |
- 63 |
- F |
-
-
- | 230 |
- R6350S |
- 3 |
- SJL/J |
- 65 |
- M |
-
-
- | 231 |
- R6419S |
- 3 |
- WSB/EiJ |
- 60 |
- F |
-
-
- | 232 |
- R5620S |
- 1 |
- WSB/EiJ |
- 60 |
- M |
-
-
-
-
- |
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/UTHSC_SPL_RMA_1210F/summary.rtf b/general/datasets/UTHSC_SPL_RMA_1210F/summary.rtf
deleted file mode 100644
index d9478f8..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210F/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This is a near final release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. The initial data enterted in 2010 had many errors described below. The data set is much improved and has no known errors of strain assignment.
-
-Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/UTHSC_SPL_RMA_1210M/cases.rtf b/general/datasets/UTHSC_SPL_RMA_1210M/cases.rtf
deleted file mode 100644
index 7fa108f..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210M/cases.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Cases. A total of 111 strains, including 81 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1), and 26 other common inbred strains were quantified. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by Lu Lu and colleagues. Samples were pooled by sex and usually include at least two cases per sex and strain.
-
-Sex Balance. XX strains have matched male and female samples. XX strains have male only samples (BXDX, XX, XX, XXX and XXX). XX strains have only female samples (BXDXX, XX, and XX.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210M/experiment-design.rtf b/general/datasets/UTHSC_SPL_RMA_1210M/experiment-design.rtf
deleted file mode 100644
index a0aeba6..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210M/experiment-design.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-RNA Processing. Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).
-
-Array Processing: All arrays were processed by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. The spleen was dissected by both Dr. Lu Lu and colleagues and Dr. Abdeltawab and colleagues. All arrays were run together (interleaved) as a single large batch.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210M/notes.rtf b/general/datasets/UTHSC_SPL_RMA_1210M/notes.rtf
deleted file mode 100644
index c7bb873..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210M/notes.rtf
+++ /dev/null
@@ -1,4 +0,0 @@
-Data Status and Use. This is a provisional release that will soon be replaced by a final corrected data set. In the interim this data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
-This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.
-
-Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.
diff --git a/general/datasets/UTHSC_SPL_RMA_1210M/processing.rtf b/general/datasets/UTHSC_SPL_RMA_1210M/processing.rtf
deleted file mode 100644
index deaf264..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210M/processing.rtf
+++ /dev/null
@@ -1,1932 +0,0 @@
-Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.
-
-Batch Effects. This data set required some correction for batch effects and the data in this initial release incorporate any additional corrections. There are several additional confounder-like factors that should be considered:
-
-
- - Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
- - Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest probe sets in this spleen data set accounts of XX% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the spleen data set can be mapped as a trait.
-
-
-Data Release. This data set was first uploaded into GeneNetwork by Arthur Centeno, October 11, 2010 and made accessible without a password to all users on November 1, 2010. The initial data release had numerous strain identification errors that have now largely been fixed. Based on an analysis of the top 20 Mendelian loci, the following 21 strains were likely to have been incorrectly identified or assigned in the current release:
-
-
- - BXD8, e.g., Probe set 10450161, 1036098. 10338684
- - BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
- - BXD21 (may be ok, only one probe set 10338684 is problematic)
- - BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
- - BXD36 (may be ok, only one probe set 10421128 is problematic)
- - BXD40, e.g., Probe set 10341070
- - BXD43, e.g., Probe set 10450161, 1036098, 10338684
- - BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
- - BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
- - BXD68 (may be ok, only one probe set 10338684 is problematic)
- - BXD69, e.g., Probe set 10450161
- - BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
- - BXD74, e.g., Probe set 10402390
- - BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
- - BXD83, e.g., Probe set 10450161, 10338684
- - BXD87 (may be ok, only one probe set 10421128 is problematic)
- - BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
- - BXD93, e.g., Probe set 10402390, 10357381
- - BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
- - LP/J, e.g., Probe set 10592493
- - DBA/2J, e.g., Probe set 10592493
-
-
-Data Evaluation Summary
-
-
- - Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
- - After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
- - Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 237.9
- - After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 278.1
- - Lowest mean value: Trait ID 10344361, mean = 3.998
- - Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
- - Greatest sex difference: Trait ID: 10606178 (Xist)
- - Great variation within and among strains: Trait ID 10454192 (Ttr
-
Table 1 (please confirm that these assignments are after correction)
-
-
-
-
-
-
-
-
-
- | Index |
- Array ID |
- Phase |
- Strain |
- Age |
- Sex |
-
-
- | 1 |
- R5583S |
- 1 |
- 129P3/J |
- 65 |
- F |
-
-
- | 2 |
- R5584S |
- 1 |
- 129P3/J |
- 66 |
- M |
-
-
- | 3 |
- R5585S |
- 1 |
- 129S1/SvImJ |
- 66 |
- F |
-
-
- | 4 |
- R5586S |
- 1 |
- 129S1/SvImJ |
- 66 |
- M |
-
-
- | 5 |
- R5587S |
- 1 |
- 129X1/SvJ |
- 65 |
- F |
-
-
- | 6 |
- R5588S |
- 1 |
- 129X1/SvJ |
- 66 |
- M |
-
-
- | 7 |
- R6348S |
- 3 |
- B6D2F1 |
- 67 |
- F |
-
-
- | 8 |
- R6347S |
- 3 |
- B6D2F1 |
- 62 |
- F |
-
-
- | 9 |
- R5590S |
- 1 |
- B6D2F1 |
- 79 |
- M |
-
-
- | 10 |
- R5662S |
- 1 |
- BALB/cByJ |
- 59 |
- F |
-
-
- | 11 |
- R5664S |
- 1 |
- BALB/cByJ |
- 59 |
- M |
-
-
- | 12 |
- R5591S |
- 1 |
- BALB/cJ |
- 51 |
- F |
-
-
- | 13 |
- R5592S |
- 1 |
- BALB/cJ |
- 51 |
- M |
-
-
- | 14 |
- R6154S |
- 2 |
- BTBR T+ tf/J |
- 60 |
- F |
-
-
- | 15 |
- R6516S |
- 3 |
- BXD1 |
- 82 |
- F |
-
-
- | 16 |
- R6584S |
- 3 |
- BXD1 |
- 95 |
- M |
-
-
- | 17 |
- R5759S |
- 1 |
- BXD2 |
- N/A |
- F |
-
-
- | 18 |
- R5837S |
- 1 |
- BXD2 |
- 106 |
- M |
-
-
- | 19 |
- R5874S |
- 2 |
- BXD5 |
- 86 |
- F |
-
-
- | 20 |
- R6554S |
- 3 |
- BXD5 |
- 60 |
- M |
-
-
- | 21 |
- R6359S |
- 3 |
- BXD6 |
- 72 |
- F |
-
-
- | 22 |
- R5777S |
- 1 |
- BXD6 |
- 149 |
- M |
-
-
- | 23 |
- R6364S |
- 3 |
- BXD8 |
- 76 |
- F |
-
-
- | 24 |
- R5637S |
- 1 |
- BXD8 |
- 71 |
- F |
-
-
- | 25 |
- R6365S |
- 3 |
- BXD8 |
- 76 |
- M |
-
-
- | 26 |
- R5746S |
- 1 |
- BXD9 |
- 70 |
- F |
-
-
- | 27 |
- R5981S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 28 |
- R5980S |
- 2 |
- BXD9 |
- 67 |
- M |
-
-
- | 29 |
- R6182S |
- 2 |
- BXD11 |
- 84 |
- F |
-
-
- | 30 |
- R6486S |
- 3 |
- BXD11 |
- 58 |
- M |
-
-
- | 31 |
- R6711S2 |
- 4 |
- BXD12 |
- 71 |
- F |
-
-
- | 32 |
- R6608S |
- 3 |
- BXD12 |
- 48 |
- F |
-
-
- | 33 |
- R5885S |
- 2 |
- BXD12 |
- 44 |
- M |
-
-
- | 34 |
- R5755S |
- 1 |
- BXD13 |
- 160 |
- F |
-
-
- | 35 |
- R5887S |
- 2 |
- BXD13 |
- 53 |
- M |
-
-
- | 36 |
- R6180S |
- 2 |
- BXD14 |
- 70 |
- F |
-
-
- | 37 |
- R5669S |
- 1 |
- BXD14 |
- 91 |
- M |
-
-
- | 38 |
- R6456S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 39 |
- R6622S |
- 3 |
- BXD15 |
- 60 |
- F |
-
-
- | 40 |
- R6626S |
- 3 |
- BXD15 |
- 60 |
- M |
-
-
- | 41 |
- R6181S |
- 2 |
- BXD16 |
- 74 |
- F |
-
-
- | 42 |
- R6515S |
- 3 |
- BXD16 |
- 64 |
- M |
-
-
- | 43 |
- R5673S |
- 1 |
- BXD18 |
- 80 |
- F |
-
-
- | 44 |
- R5674S |
- 1 |
- BXD18 |
- 65 |
- M |
-
-
- | 45 |
- R6553S |
- 3 |
- BXD19 |
- 158 |
- F |
-
-
- | 46 |
- R6551S |
- 3 |
- BXD19 |
- 60 |
- M |
-
-
- | 47 |
- R6643S4 |
- 4 |
- BXD20 |
- 59 |
- F |
-
-
- | 48 |
- R6595S |
- 3 |
- BXD20 |
- 60 |
- M |
-
-
- | 49 |
- R5735S |
- 1 |
- BXD21 |
- 64 |
- F |
-
-
- | 50 |
- R5892S |
- 2 |
- BXD21 |
- 99 |
- M |
-
-
- | 51 |
- R5896S |
- 2 |
- BXD22 |
- 60 |
- F |
-
-
- | 52 |
- R6414S |
- 3 |
- BXD22 |
- 73 |
- M |
-
-
- | 53 |
- R6550S |
- 3 |
- BXD23 |
- 74 |
- F |
-
-
- | 54 |
- R6586S |
- 3 |
- BXD23 |
- 102 |
- F |
-
-
- | 55 |
- R5630S |
- 1 |
- BXD24 |
- 71 |
- F |
-
-
- | 56 |
- R6356S |
- 3 |
- BXD24 |
- 57 |
- M |
-
-
- | 57 |
- R6162S |
- 2 |
- BXD25 |
- 67 |
- F |
-
-
- | 58 |
- R6625S |
- 3 |
- BXD25 |
- 67 |
- F |
-
-
- | 59 |
- R6642S4 |
- 4 |
- BXD25 |
- 58 |
- M |
-
-
- | 60 |
- R5761S |
- 1 |
- BXD27 |
- N/A |
- F |
-
-
- | 61 |
- R5763S |
- 1 |
- BXD27 |
- 90 |
- M |
-
-
- | 62 |
- R6621S |
- 3 |
- BXD28 |
- 113 |
- F |
-
-
- | 63 |
- R6548S |
- 3 |
- BXD28 |
- 60 |
- M |
-
-
- | 64 |
- R6547S |
- 3 |
- BXD29 |
- 60 |
- F |
-
-
- | 65 |
- R6453S |
- 3 |
- BXD31 |
- 48 |
- F |
-
-
- | 66 |
- R6452S |
- 3 |
- BXD31 |
- 48 |
- M |
-
-
- | 67 |
- R6583S |
- 3 |
- BXD32 |
- 60 |
- F |
-
-
- | 68 |
- R5765S |
- 1 |
- BXD32 |
- 71 |
- M |
-
-
- | 69 |
- R5689S |
- 1 |
- BXD33 |
- 65 |
- F |
-
-
- | 70 |
- R6450S |
- 3 |
- BXD33 |
- 55 |
- M |
-
-
- | 71 |
- R5767S |
- 1 |
- BXD34 |
- 72 |
- F |
-
-
- | 72 |
- R5900S |
- 2 |
- BXD34 |
- 70 |
- M |
-
-
- | 73 |
- R6588S |
- 3 |
- BXD36 |
- 61 |
- F |
-
-
- | 74 |
- R6490S |
- 3 |
- BXD36 |
- 63 |
- M |
-
-
- | 75 |
- R6417S |
- 3 |
- BXD38 |
- 64 |
- F |
-
-
- | 76 |
- R6439S |
- 3 |
- BXD38 |
- 72 |
- M |
-
-
- | 77 |
- R5769S |
- 1 |
- BXD39 |
- N/A |
- F |
-
-
- | 78 |
- R5771S |
- 1 |
- BXD39 |
- 74 |
- M |
-
-
- | 79 |
- R5773S |
- 1 |
- BXD40 |
- N/A |
- F |
-
-
- | 80 |
- R5775S |
- 1 |
- BXD40 |
- N/A |
- M |
-
-
- | 81 |
- R6494S |
- 3 |
- BXD41 |
- 72 |
- F |
-
-
- | 82 |
- R5910S |
- 2 |
- BXD42 |
- 79 |
- F |
-
-
- | 83 |
- R6493S |
- 3 |
- BXD42 |
- 69 |
- M |
-
-
- | 84 |
- R6341S |
- 3 |
- BXD43 |
- 59 |
- F |
-
-
- | 85 |
- R6401S |
- 3 |
- BXD43 |
- 99 |
- M |
-
-
- | 86 |
- R5916S |
- 2 |
- BXD43 |
- 79 |
- M |
-
-
- | 87 |
- R5839S |
- 1 |
- BXD44 |
- 141 |
- F |
-
-
- | 88 |
- R5779S |
- 1 |
- BXD44 |
- 124 |
- M |
-
-
- | 89 |
- R6405S |
- 3 |
- BXD45 |
- 58 |
- F |
-
-
- | 90 |
- R6610S |
- 3 |
- BXD45 |
- 55 |
- M |
-
-
- | 91 |
- R5922S |
- 2 |
- BXD48 |
- 64 |
- F |
-
-
- | 92 |
- R5925S |
- 2 |
- BXD48 |
- 60 |
- M |
-
-
- | 93 |
- R6719S1 |
- 4 |
- BXD49 |
- 58 |
- F |
-
-
- | 94 |
- R6485S |
- 3 |
- BXD49 |
- 79 |
- M |
-
-
- | 95 |
- R5781S |
- 1 |
- BXD50 |
- 61 |
- F |
-
-
- | 96 |
- R6464S |
- 3 |
- BXD51 |
- 65 |
- F |
-
-
- | 97 |
- R6585S |
- 3 |
- BXD51 |
- 63 |
- M |
-
-
- | 98 |
- R6500S |
- 3 |
- BXD55 |
- 58 |
- F |
-
-
- | 99 |
- R5938S |
- 2 |
- BXD55 |
- 93 |
- M |
-
-
- | 100 |
- R6504S |
- 3 |
- BXD56 |
- 58 |
- F |
-
-
- | 101 |
- R6503S |
- 3 |
- BXD56 |
- 58 |
- M |
-
-
- | 102 |
- R5783S |
- 1 |
- BXD60 |
- 111 |
- F |
-
-
- | 103 |
- R5784S |
- 1 |
- BXD60 |
- 85 |
- M |
-
-
- | 104 |
- R5786S |
- 1 |
- BXD61 |
- 86 |
- F |
-
-
- | 105 |
- R6449S |
- 3 |
- BXD61 |
- 65 |
- M |
-
-
- | 106 |
- R6716S1 |
- 4 |
- BXD62 |
- 54 |
- F |
-
-
- | 107 |
- R5790S |
- 1 |
- BXD62 |
- 115 |
- M |
-
-
- | 108 |
- R6519S |
- 3 |
- BXD63 |
- 54 |
- F |
-
-
- | 109 |
- R6717S1 |
- 4 |
- BXD63 |
- 70 |
- M |
-
-
- | 110 |
- R5792S |
- 1 |
- BXD64 |
- 167 |
- F |
-
-
- | 111 |
- R6641S4 |
- 4 |
- BXD64 |
- 68 |
- M |
-
-
- | 112 |
- R6630S |
- 3 |
- BXD64 |
- 68 |
- M |
-
-
- | 113 |
- R6477S |
- 3 |
- BXD65 |
- 58 |
- F |
-
-
- | 114 |
- R6628S |
- 3 |
- BXD65 |
- 70 |
- M |
-
-
- | 115 |
- R6511S |
- 3 |
- BXD66 |
- 70 |
- F |
-
-
- | 116 |
- R6448S |
- 3 |
- BXD66 |
- 61 |
- M |
-
-
- | 117 |
- R5794S |
- 1 |
- BXD66 |
- 144 |
- M |
-
-
- | 118 |
- R6502S |
- 3 |
- BXD67 |
- 66 |
- F |
-
-
- | 119 |
- R6545S |
- 3 |
- BXD67 |
- 61 |
- M |
-
-
- | 120 |
- R6337S |
- 3 |
- BXD68 |
- 56 |
- F |
-
-
- | 121 |
- R6594S |
- 3 |
- BXD68 |
- 64 |
- M |
-
-
- | 122 |
- R5796S |
- 1 |
- BXD69 |
- 85 |
- F |
-
-
- | 123 |
- R5798S |
- 1 |
- BXD69 |
- 98 |
- M |
-
-
- | 124 |
- R6402S |
- 3 |
- BXD70 |
- 93 |
- F |
-
-
- | 125 |
- R5841S |
- 1 |
- BXD70 |
- 121 |
- F |
-
-
- | 126 |
- R6592S |
- 3 |
- BXD70 |
- 59 |
- M |
-
-
- | 127 |
- R6328S |
- 3 |
- BXD71 |
- 87 |
- F |
-
-
- | 128 |
- R5967S |
- 2 |
- BXD71 |
- 64 |
- M |
-
-
- | 129 |
- R5969S |
- 2 |
- BXD73 |
- 64 |
- F |
-
-
- | 130 |
- R5800S |
- 1 |
- BXD73 |
- 120 |
- M |
-
-
- | 131 |
- R6646S |
- 3 |
- BXD74 |
- 40 |
- F |
-
-
- | 132 |
- R6524S |
- 3 |
- BXD74 |
- 72 |
- M |
-
-
- | 133 |
- R6445S |
- 3 |
- BXD75 |
- 85 |
- F |
-
-
- | 134 |
- R5843S |
- 1 |
- BXD75 |
- 103 |
- F |
-
-
- | 135 |
- R5845S |
- 1 |
- BXD75 |
- 103 |
- M |
-
-
- | 136 |
- R6604S |
- 3 |
- BXD77 |
- 64 |
- F |
-
-
- | 137 |
- R6513S |
- 3 |
- BXD77 |
- 72 |
- M |
-
-
- | 138 |
- R6582S |
- 3 |
- BXD78 |
- 144 |
- F |
-
-
- | 139 |
- R6563S |
- 3 |
- BXD78 |
- 95 |
- M |
-
-
- | 140 |
- R6645S4 |
- 4 |
- BXD79 |
- 66 |
- F |
-
-
- | 141 |
- R5806S |
- 1 |
- BXD79 |
- 78 |
- M |
-
-
- | 142 |
- R5847S |
- 1 |
- BXD80 |
- 89 |
- F |
-
-
- | 143 |
- R5852S |
- 1 |
- BXD80 |
- 79 |
- M |
-
-
- | 144 |
- R6562S |
- 3 |
- BXD81 |
- 99 |
- F |
-
-
- | 145 |
- R6468S |
- 3 |
- BXD81 |
- 65 |
- M |
-
-
- | 146 |
- R6560S |
- 3 |
- BXD82 |
- 85 |
- F |
-
-
- | 147 |
- R6512S |
- 3 |
- BXD83 |
- 68 |
- F |
-
-
- | 148 |
- R5810S |
- 1 |
- BXD83 |
- 139 |
- M |
-
-
- | 149 |
- R6510S |
- 3 |
- BXD84 |
- 87 |
- F |
-
-
- | 150 |
- R5970S |
- 2 |
- BXD84 |
- 107 |
- F |
-
-
- | 151 |
- R6603S |
- 3 |
- BXD84 |
- 99 |
- M |
-
-
- | 152 |
- R6517S |
- 3 |
- BXD85 |
- 58 |
- F |
-
-
- | 153 |
- R6718S1 |
- 4 |
- BXD85 |
- 86 |
- M |
-
-
- | 154 |
- R5812S |
- 1 |
- BXD86 |
- 61 |
- F |
-
-
- | 155 |
- R5814S |
- 1 |
- BXD86 |
- 59 |
- M |
-
-
- | 156 |
- R5816S |
- 1 |
- BXD87 |
- 112 |
- F |
-
-
- | 157 |
- R6488S |
- 3 |
- BXD87 |
- 137 |
- M |
-
-
- | 158 |
- R6580S |
- 3 |
- BXD88 |
- 125 |
- F |
-
-
- | 159 |
- R5977S |
- 2 |
- BXD89 |
- 68 |
- F |
-
-
- | 160 |
- R5979S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 161 |
- R5978S |
- 2 |
- BXD89 |
- 79 |
- M |
-
-
- | 162 |
- R5818S |
- 1 |
- BXD90 |
- 106 |
- F |
-
-
- | 163 |
- R5820S |
- 1 |
- BXD90 |
- 131 |
- M |
-
-
- | 164 |
- R6343S |
- 3 |
- BXD92 |
- 62 |
- F |
-
-
- | 165 |
- R5984S |
- 2 |
- BXD92 |
- 55 |
- M |
-
-
- | 166 |
- R6581S |
- 3 |
- BXD93 |
- 173 |
- M |
-
-
- | 167 |
- R6557S |
- 3 |
- BXD93 |
- 126 |
- M |
-
-
- | 168 |
- R6509S |
- 3 |
- BXD95 |
- 59 |
- F |
-
-
- | 169 |
- R5822S |
- 1 |
- BXD95 |
- 89 |
- M |
-
-
- | 170 |
- R6640S4 |
- 4 |
- BXD96 |
- 70 |
- F |
-
-
- | 171 |
- R6514S |
- 3 |
- BXD96 |
- 64 |
- M |
-
-
- | 172 |
- R6506S |
- 3 |
- BXD97 |
- 78 |
- F |
-
-
- | 173 |
- R5849S |
- 1 |
- BXD97 |
- 130 |
- F |
-
-
- | 174 |
- R6591S |
- 3 |
- BXD97 |
- 122 |
- M |
-
-
- | 175 |
- R5990S |
- 2 |
- BXD98 |
- 65 |
- F |
-
-
- | 176 |
- R6596S |
- 3 |
- BXD98 |
- 67 |
- M |
-
-
- | 177 |
- R5993S |
- 2 |
- BXD99 |
- 74 |
- F |
-
-
- | 178 |
- R5995S |
- 2 |
- BXD99 |
- 50 |
- M |
-
-
- | 179 |
- R6607S |
- 3 |
- BXD100 |
- 75 |
- F |
-
-
- | 180 |
- R6411S |
- 3 |
- BXD100 |
- 104 |
- M |
-
-
- | 181 |
- R6508S |
- 3 |
- BXD101 |
- 59 |
- F |
-
-
- | 182 |
- R5593S |
- 1 |
- BXD101 |
- 59 |
- M |
-
-
- | 183 |
- R6523S |
- 3 |
- BXD102 |
- 60 |
- F |
-
-
- | 184 |
- R6466S |
- 3 |
- BXD102 |
- 50 |
- M |
-
-
- | 185 |
- R6404S |
- 3 |
- BXD103 |
- 72 |
- F |
-
-
- | 186 |
- R6609S |
- 3 |
- BXD103 |
- 57 |
- M |
-
-
- | 187 |
- R6555S |
- 3 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 188 |
- R5596S |
- 1 |
- C57BL/10J |
- 73 |
- M |
-
-
- | 189 |
- R5597S |
- 1 |
- C57BL/6ByJ |
- 51 |
- F |
-
-
- | 190 |
- R5598S |
- 1 |
- C57BL/6ByJ |
- 69 |
- M |
-
-
- | 191 |
- R5600S |
- 1 |
- C57BL/6J |
- 79 |
- F |
-
-
- | 192 |
- R5599S |
- 1 |
- C57BL/6J |
- 60 |
- F |
-
-
- | 193 |
- R6451S |
- 3 |
- C57BL/6J |
- 77 |
- M |
-
-
- | 194 |
- R6410S |
- 3 |
- C57BL/6J |
- 85 |
- M |
-
-
- | 195 |
- R5603S |
- 1 |
- C57BLKS/J |
- 66 |
- F |
-
-
- | 196 |
- R5604S |
- 1 |
- C57BLKS/J |
- 66 |
- M |
-
-
- | 197 |
- R5996S |
- 2 |
- CBA/CaJ |
- 66 |
- F |
-
-
- | 198 |
- R6349S |
- 3 |
- CBA/CaJ |
- 66 |
- M |
-
-
- | 199 |
- R6458S |
- 3 |
- D2B6F1 |
- 64 |
- F |
-
-
- | 200 |
- R6353S |
- 3 |
- D2B6F1 |
- 60 |
- M |
-
-
- | 201 |
- R5605S |
- 1 |
- DBA/2J |
- 79 |
- F |
-
-
- | 202 |
- R6446S |
- 3 |
- DBA/2J |
- 83 |
- M |
-
-
- | 203 |
- R6597S |
- 3 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 204 |
- R5643S |
- 1 |
- FVB/NJ |
- 60 |
- F |
-
-
- | 205 |
- R6598S |
- 3 |
- FVB/NJ |
- 60 |
- M |
-
-
- | 206 |
- R5606S |
- 1 |
- ILS |
- 74 |
- F |
-
-
- | 207 |
- R5607S |
- 1 |
- ILS |
- 74 |
- M |
-
-
- | 208 |
- R5610S |
- 1 |
- ISS |
- 97 |
- M |
-
-
- | 209 |
- R6627S |
- 3 |
- KK/HlJ |
- 64 |
- F |
-
-
- | 210 |
- R6444S |
- 3 |
- KK/HlJ |
- 65 |
- M |
-
-
- | 211 |
- R5702S |
- 1 |
- KK/HlJ |
- 61 |
- M |
-
-
- | 212 |
- R5613S |
- 1 |
- LG/J |
- 63 |
- F |
-
-
- | 213 |
- R5704S |
- 1 |
- LG/J |
- 65 |
- M |
-
-
- | 214 |
- R5614S |
- 1 |
- LP/J |
- 65 |
- F |
-
-
- | 215 |
- R5615S |
- 1 |
- LP/J |
- 65 |
- M |
-
-
- | 216 |
- R6599S |
- 3 |
- MOLF/EiJ |
- 60 |
- F |
-
-
- | 217 |
- R6606S |
- 3 |
- MOLF/EiJ |
- 60 |
- M |
-
-
- | 218 |
- R6544S |
- 3 |
- NOD/LtJ |
- 77 |
- F |
-
-
- | 219 |
- R5709S |
- 1 |
- NOD/LtJ |
- 58 |
- M |
-
-
- | 220 |
- R6601S |
- 3 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 221 |
- R5711S |
- 1 |
- NZB/BlNJ |
- 61 |
- F |
-
-
- | 222 |
- R6427S |
- 3 |
- NZB/BlNJ |
- 58 |
- M |
-
-
- | 223 |
- R6150S |
- 2 |
- NZO/HlLtJ |
- 71 |
- F |
-
-
- | 224 |
- R6155S |
- 2 |
- NZW/LacJ |
- 65 |
- F |
-
-
- | 225 |
- R5654S |
- 1 |
- NZW/LacJ |
- 60 |
- M |
-
-
- | 226 |
- R5721S |
- 1 |
- PL/J |
- 59 |
- M |
-
-
- | 227 |
- R5616S |
- 1 |
- PWD/PhJ |
- 60 |
- M |
-
-
- | 228 |
- R5725S |
- 1 |
- PWK/PhJ |
- 121 |
- M |
-
-
- | 229 |
- R6174S |
- 2 |
- SJL/J |
- 63 |
- F |
-
-
- | 230 |
- R6350S |
- 3 |
- SJL/J |
- 65 |
- M |
-
-
- | 231 |
- R6419S |
- 3 |
- WSB/EiJ |
- 60 |
- F |
-
-
- | 232 |
- R5620S |
- 1 |
- WSB/EiJ |
- 60 |
- M |
-
-
-
-
- |
-
-
-
-
-
-
-
-
-
diff --git a/general/datasets/UTHSC_SPL_RMA_1210M/summary.rtf b/general/datasets/UTHSC_SPL_RMA_1210M/summary.rtf
deleted file mode 100644
index d9478f8..0000000
--- a/general/datasets/UTHSC_SPL_RMA_1210M/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This is a near final release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. The initial data enterted in 2010 had many errors described below. The data set is much improved and has no known errors of strain assignment.
-
-Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").
diff --git a/general/datasets/UTHSC_Str_RankInv_1210/summary.rtf b/general/datasets/UTHSC_Str_RankInv_1210/summary.rtf
deleted file mode 100644
index cc6ac0f..0000000
--- a/general/datasets/UTHSC_Str_RankInv_1210/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 42, Name: HQF BXD Striatum ILM6.1 (Dec10)
\ No newline at end of file
diff --git a/general/datasets/UTHSC_Striatum_RankInv_1210/summary.rtf b/general/datasets/UTHSC_Striatum_RankInv_1210/summary.rtf
deleted file mode 100644
index cc6ac0f..0000000
--- a/general/datasets/UTHSC_Striatum_RankInv_1210/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 42, Name: HQF BXD Striatum ILM6.1 (Dec10)
\ No newline at end of file
diff --git a/general/datasets/UTK_BXDSpl_VST_0110/experiment-design.rtf b/general/datasets/UTK_BXDSpl_VST_0110/experiment-design.rtf
deleted file mode 100644
index 3166cb9..0000000
--- a/general/datasets/UTK_BXDSpl_VST_0110/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Spleen gene expression was analyzed from 38 BXD strains. Adult mice (8-12 weeks) were euthanized by cervical dislocation and spleens were harvested and stabilized in RNAlater. Total RNA was extracted and gene expression profiling was performed on the Illumina Sentrix mouse-6 gene expression arrays v1.1. Each BXD sample profiled consisted of a pool of equal amounts of RNA from two individuals of the same sex and strain (approximately 15ug per strain). In addition, flow cytometry was used for the immunophenotyping of male and female mice (average of four mice/sex/strain) from 41 BXD strains (spleen expression profiling was performed on 34 of these strains) and the parental strains. Lymphoctes were identified as CD3+, CD79+, CD4+, or CD8+ to identify T cells, B cells, T helper cells, and cytotoxic T cells, respectively. These data are presented as percentage of lymphoctes with those cell surface markers (e.g. CD3%, CD79%, CD4%, CD8%). Lymphocyte subpopulations are also represented as natural log-transformed ratios (e.g. LN T:B, LN CD4:CD8). In addition, the median expression of MHCII on B cells is reported (LN MHC Med). The immunophenotype data is available in the supplementary file.
diff --git a/general/datasets/UTK_BXDSpl_VST_0110/summary.rtf b/general/datasets/UTK_BXDSpl_VST_0110/summary.rtf
deleted file mode 100644
index c456b82..0000000
--- a/general/datasets/UTK_BXDSpl_VST_0110/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The immune system plays a pivotal role in susceptibility to and progression of a variety of diseases. Due to its strong genetic basis, heritable differences in immune function may contribute to differential disease susceptibility between individuals. Genetic reference populations, such as the BXD (C57BL/6J X DBA/2J) panel of recombinant inbred (RI) mouse strains, provide a unique model through which to integrate baseline phenotypes in healthy individuals with heritable risk for disease because of the ability to combine data collected from these populations across multiple studies and time. We performed basic immunophenotyping (e.g. percentage of circulating B and T lymphocytes and CD4+ and CD8+ T cell subpopulations) in peripheral blood of healthy mice from 41 BXD RI strains to define the phenotypic variation in this model system and to characterize the genetic architecture that unlerlies these traits. Significant QTL models that explained the majority (50-77%) of phenotypic variance were derived for each trait and for the T:B cell and CD4+:CD8+ ratios. Combining QTL mapping with spleen gene expression data uncovered two quantitative trait transcripts (QTTs), Ptprk and Acp1, that which are candidates for heritable differences in the relative abundance of helper and cytotoxic T cells. These data will be valuable in extracting genetic correlates of the immune system in the BXD panel. In addition, they will be a useful resource in prospective, phenotype-driven model selection to test hypotheses about differential disease or environmental susceptibility between individuals with baseline differences in the composition of the immune system.
diff --git a/general/datasets/UT_CEPH_RankInv0909/acknowledgment.rtf b/general/datasets/UT_CEPH_RankInv0909/acknowledgment.rtf
deleted file mode 100644
index 7d66250..0000000
--- a/general/datasets/UT_CEPH_RankInv0909/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Financial support for this project was provided by Dr. Barrett Haik and the Hamilton Eye Institute, by NIH grant support to Malak Kotb, Robert W. Williams, Rita G. Kasal and colleagues, and by the UT Center for Integrative and Translational Genomics.
diff --git a/general/datasets/UT_CEPH_RankInv0909/cases.rtf b/general/datasets/UT_CEPH_RankInv0909/cases.rtf
deleted file mode 100644
index f4f6663..0000000
--- a/general/datasets/UT_CEPH_RankInv0909/cases.rtf
+++ /dev/null
@@ -1,2009 +0,0 @@
-About the CEPH/UTAH families used to generate this data set:
-
-The CEPH/UTAH families used in this data set are part of CEPH repository linkage families of National Institute of General Medical Sciences (NIGMS) human genetic cell repository. These are immortalized human B-lymphocytes (EBV-transformed) from Caucasian donors of UTAH/Mormon ethnicity. The CEPH/UTAH families contain 48 families; the present data set includes 14 of these families with available DNA/genotypes for each member of these pedigrees. There are five families common with the published Monks et al (2004), namely families: 1346, 1362, 1418, 1421, and 1424.
-
-
-
-
-
-
-
-
- | Index |
- Repository
- Number |
- Case ID |
- Gender |
- Family ID |
- Family Member ID |
- Sentrix ID |
- Sentrix
- Position |
- Batch ID |
-
-
- | 1 |
- GM07038 |
- 1333001 |
- Male |
- 1333 |
- 1 |
- 4256249060 |
- A |
- 5 |
-
-
- | 2 |
- GM06987 |
- 1333002 |
- Female |
- 1333 |
- 2 |
- 4158260019 |
- B |
- 4 |
-
-
- | 3 |
- GM07004 |
- 1333003 |
- Male |
- 1333 |
- 3 |
- 4256249103 |
- A |
- 7 |
-
-
- | 4 |
- GM07052 |
- 1333004 |
- Male |
- 1333 |
- 4 |
- 4256249051 |
- A |
- 6 |
-
-
- | 5 |
- GM06982 |
- 1333005 |
- Male |
- 1333 |
- 5 |
- 4158260009 |
- F |
- 3 |
-
-
- | 6 |
- GM07011 |
- 1333006 |
- Female |
- 1333 |
- 6 |
- 4158260012 |
- C |
- 3 |
-
-
- | 7 |
- GM07009 |
- 1333007 |
- Male |
- 1333 |
- 7 |
- 4256249101 |
- F |
- 6 |
-
-
- | 8 |
- GM07678 |
- 1333008 |
- Male |
- 1333 |
- 8 |
- 4158260005 |
- B |
- 4 |
-
-
- | 9 |
- GM07026 |
- 1333009 |
- Male |
- 1333 |
- 9 |
- 4158260026 |
- C |
- 3 |
-
-
- | 10 |
- GM07679 |
- 1333010 |
- Male |
- 1333 |
- 10 |
- 4158260030 |
- C |
- 3 |
-
-
- | 11 |
- GM07049 |
- 1333011 |
- Male |
- 1333 |
- 11 |
- 4256249059 |
- A |
- 5 |
-
-
- | 12 |
- GM07002 |
- 1333012 |
- Female |
- 1333 |
- 12 |
- 4158260001 |
- B |
- 4 |
-
-
- | 13 |
- GM07017 |
- 1333013 |
- Male |
- 1333 |
- 13 |
- 4158260027 |
- B |
- 5 |
-
-
- | 14 |
- GM07341 |
- 1333014 |
- Female |
- 1333 |
- 14 |
- 4256249042 |
- A |
- 6 |
-
-
- | 15 |
- GM11820 |
- 1333015 |
- Female |
- 1333 |
- 15 |
- 4256249104 |
- E |
- 7 |
-
-
- | 16 |
- GM07048 |
- 1341001 |
- Male |
- 1341 |
- 1 |
- 4256249103 |
- B |
- 7 |
-
-
- | 17 |
- GM06991 |
- 1341002 |
- Female |
- 1341 |
- 2 |
- 4158260027 |
- A |
- 5 |
-
-
- | 18 |
- GM07343 |
- 1341003 |
- Female |
- 1341 |
- 3 |
- 4256249095 |
- C |
- 7 |
-
-
- | 19 |
- GM07044 |
- 1341004 |
- Female |
- 1341 |
- 4 |
- 4158260002 |
- C |
- 4 |
-
-
- | 20 |
- GM07012 |
- 1341005 |
- Female |
- 1341 |
- 5 |
- 4158260026 |
- D |
- 3 |
-
-
- | 21 |
- GM07344 |
- 1341006 |
- Female |
- 1341 |
- 6 |
- 4158260030 |
- B |
- 3 |
-
-
- | 22 |
- GM07021 |
- 1341007 |
- Male |
- 1341 |
- 7 |
- 4256249097 |
- B |
- 7 |
-
-
- | 23 |
- GM07006 |
- 1341008 |
- Female |
- 1341 |
- 8 |
- 4158260001 |
- C |
- 4 |
-
-
- | 24 |
- GM07010 |
- 1341009 |
- Female |
- 1341 |
- 9 |
- 41582600011 |
- A |
- 2 |
-
-
- | 25 |
- GM07020 |
- 1341010 |
- Male |
- 1341 |
- 10 |
- 4158260007 |
- A |
- 1 |
-
-
- | 26 |
- GM07034 |
- 1341011 |
- Male |
- 1341 |
- 11 |
- 4158260007 |
- B |
- 1 |
-
-
- | 27 |
- GM07055 |
- 1341012 |
- Female |
- 1341 |
- 12 |
- 4158260012 |
- E |
- 3 |
-
-
- | 28 |
- GM06993 |
- 1341013 |
- Male |
- 1341 |
- 13 |
- 4256249059 |
- C |
- 5 |
-
-
- | 29 |
- GM06985 |
- 1341014 |
- Female |
- 1341 |
- 14 |
- 4158260007 |
- C |
- 1 |
-
-
- | 30 |
- GM10852 |
- 1346002 |
- Female |
- 1346 |
- 2 |
- 4256249098 |
- D |
- 7 |
-
-
- | 31 |
- GM12035 |
- 1346003 |
- Male |
- 1346 |
- 3 |
- 4158260007 |
- D |
- 1 |
-
-
- | 32 |
- GM12036 |
- 1346004 |
- Male |
- 1346 |
- 4 |
- 4256249047 |
- A |
- 6 |
-
-
- | 33 |
- GM12037 |
- 1346005 |
- Male |
- 1346 |
- 5 |
- 4158260027 |
- E |
- 5 |
-
-
- | 34 |
- GM12038 |
- 1346006 |
- Male |
- 1346 |
- 6 |
- 4158260001 |
- E |
- 4 |
-
-
- | 35 |
- GM12039 |
- 1346007 |
- Male |
- 1346 |
- 7 |
- 4256249097 |
- C |
- 7 |
-
-
- | 36 |
- GM12041 |
- 1346009 |
- Female |
- 1346 |
- 9 |
- 4256249099 |
- B |
- 7 |
-
-
- | 37 |
- GM12042 |
- 1346010 |
- Female |
- 1346 |
- 10 |
- 41582600011 |
- D |
- 2 |
-
-
- | 38 |
- GM12043 |
- 1346011 |
- Male |
- 1346 |
- 11 |
- 4158260007 |
- E |
- 1 |
-
-
- | 39 |
- GM12044 |
- 1346012 |
- Female |
- 1346 |
- 12 |
- 4256249096 |
- F |
- 7 |
-
-
- | 40 |
- GM12046 |
- 1346014 |
- Female |
- 1346 |
- 14 |
- 4158260007 |
- F |
- 1 |
-
-
- | 41 |
- GM10858 |
- 1347001 |
- Male |
- 1347 |
- 1 |
- 4158260030 |
- A |
- 3 |
-
-
- | 42 |
- GM10859 |
- 1347002 |
- Female |
- 1347 |
- 2 |
- 4158260027 |
- C |
- 5 |
-
-
- | 43 |
- GM11870 |
- 1347003 |
- Female |
- 1347 |
- 3 |
- 4158260018 |
- C |
- 2 |
-
-
- | 44 |
- GM11871 |
- 1347004 |
- Male |
- 1347 |
- 4 |
- 4256249060 |
- B |
- 5 |
-
-
- | 45 |
- GM11872 |
- 1347005 |
- Male |
- 1347 |
- 5 |
- 4256249097 |
- A |
- 7 |
-
-
- | 46 |
- GM11873 |
- 1347006 |
- Male |
- 1347 |
- 6 |
- 4158260001 |
- A |
- 4 |
-
-
- | 47 |
- GM11875 |
- 1347008 |
- Female |
- 1347 |
- 8 |
- 4256249095 |
- E |
- 7 |
-
-
- | 48 |
- GM11876 |
- 1347009 |
- Male |
- 1347 |
- 9 |
- 4256249059 |
- E |
- 5 |
-
-
- | 49 |
- GM11877 |
- 1347010 |
- Male |
- 1347 |
- 10 |
- 4158260021 |
- A |
- 2 |
-
-
- | 50 |
- GM11878 |
- 1347011 |
- Male |
- 1347 |
- 11 |
- 4158260008 |
- A |
- 1 |
-
-
- | 51 |
- GM11879 |
- 1347012 |
- Male |
- 1347 |
- 12 |
- 4158260019 |
- D |
- 4 |
-
-
- | 52 |
- GM11880 |
- 1347013 |
- Female |
- 1347 |
- 13 |
- 4158260008 |
- B |
- 1 |
-
-
- | 53 |
- GM11881 |
- 1347014 |
- Male |
- 1347 |
- 14 |
- 4256249101 |
- C |
- 6 |
-
-
- | 54 |
- GM11882 |
- 1347015 |
- Female |
- 1347 |
- 15 |
- 4158260008 |
- C |
- 1 |
-
-
- | 55 |
- GM11883 |
- 1347016 |
- Male |
- 1347 |
- 16 |
- 41582600011 |
- B |
- 2 |
-
-
- | 56 |
- GM10860 |
- 1362001 |
- Male |
- 1362 |
- 1 |
- 4256249097 |
- E |
- 7 |
-
-
- | 57 |
- GM10861 |
- 1362002 |
- Female |
- 1362 |
- 2 |
- 4158260027 |
- D |
- 5 |
-
-
- | 58 |
- GM11982 |
- 1362003 |
- Female |
- 1362 |
- 3 |
- 4158260019 |
- F |
- 4 |
-
-
- | 59 |
- GM11983 |
- 1362004 |
- Female |
- 1362 |
- 4 |
- 4158260030 |
- D |
- 3 |
-
-
- | 60 |
- GM11984 |
- 1362005 |
- Male |
- 1362 |
- 5 |
- 4158260008 |
- D |
- 1 |
-
-
- | 61 |
- GM11985 |
- 1362006 |
- Female |
- 1362 |
- 6 |
- 4158260002 |
- F |
- 4 |
-
-
- | 62 |
- GM11986 |
- 1362007 |
- Female |
- 1362 |
- 7 |
- 4256249060 |
- C |
- 5 |
-
-
- | 63 |
- GM11987 |
- 1362008 |
- Male |
- 1362 |
- 8 |
- 4158260005 |
- F |
- 4 |
-
-
- | 64 |
- GM11988 |
- 1362009 |
- Female |
- 1362 |
- 9 |
- 4256249042 |
- B |
- 6 |
-
-
- | 65 |
- GM11989 |
- 1362010 |
- Female |
- 1362 |
- 10 |
- 4158260001 |
- F |
- 4 |
-
-
- | 66 |
- GM11990 |
- 1362011 |
- Male |
- 1362 |
- 11 |
- 4256249094 |
- A |
- 6 |
-
-
- | 67 |
- GM11991 |
- 1362012 |
- Female |
- 1362 |
- 12 |
- 4158260018 |
- E |
- 2 |
-
-
- | 68 |
- GM11992 |
- 1362013 |
- Male |
- 1362 |
- 13 |
- 4256249059 |
- B |
- 5 |
-
-
- | 69 |
- GM11993 |
- 1362014 |
- Female |
- 1362 |
- 14 |
- 4256249059 |
- F |
- 5 |
-
-
- | 70 |
- GM11994 |
- 1362015 |
- Male |
- 1362 |
- 15 |
- 4158260008 |
- E |
- 1 |
-
-
- | 71 |
- GM11995 |
- 1362016 |
- Female |
- 1362 |
- 16 |
- 4158260008 |
- F |
- 1 |
-
-
- | 72 |
- GM11996 |
- 1362017 |
- Male |
- 1362 |
- 17 |
- 4158260021 |
- C |
- 2 |
-
-
- | 73 |
- GM10835 |
- 1416001 |
- Male |
- 1416 |
- 1 |
- 4256249060 |
- F |
- 5 |
-
-
- | 74 |
- GM10834 |
- 1416002 |
- Female |
- 1416 |
- 2 |
- 4158260018 |
- A |
- 2 |
-
-
- | 75 |
- GM12240 |
- 1416003 |
- Male |
- 1416 |
- 3 |
- 4158260019 |
- E |
- 4 |
-
-
- | 76 |
- GM12241 |
- 1416004 |
- Male |
- 1416 |
- 4 |
- 4256249059 |
- D |
- 5 |
-
-
- | 77 |
- GM12243 |
- 1416006 |
- Male |
- 1416 |
- 6 |
- 4256249096 |
- C |
- 7 |
-
-
- | 78 |
- GM12244 |
- 1416007 |
- Female |
- 1416 |
- 7 |
- 4256249047 |
- B |
- 6 |
-
-
- | 79 |
- GM12245 |
- 1416008 |
- Male |
- 1416 |
- 8 |
- 41582600011 |
- E |
- 2 |
-
-
- | 80 |
- GM12246 |
- 1416009 |
- Female |
- 1416 |
- 9 |
- 4158260026 |
- E |
- 3 |
-
-
- | 81 |
- GM12247 |
- 1416010 |
- Female |
- 1416 |
- 10 |
- 4158260021 |
- D |
- 2 |
-
-
- | 82 |
- GM12248 |
- 1416011 |
- Male |
- 1416 |
- 11 |
- 4256249094 |
- B |
- 6 |
-
-
- | 83 |
- GM12249 |
- 1416012 |
- Female |
- 1416 |
- 12 |
- 4256249041 |
- A |
- 6 |
-
-
- | 84 |
- GM12250 |
- 1416013 |
- Male |
- 1416 |
- 13 |
- 4256249044 |
- F |
- 7 |
-
-
- | 85 |
- GM12251 |
- 1416014 |
- Female |
- 1416 |
- 14 |
- 4158260005 |
- D |
- 4 |
-
-
- | 86 |
- GM12252 |
- 1416015 |
- Female |
- 1416 |
- 15 |
- 4158260009 |
- E |
- 3 |
-
-
- | 87 |
- GM12253 |
- 1416016 |
- Female |
- 1416 |
- 16 |
- 4158260027 |
- F |
- 5 |
-
-
- | 88 |
- GM10836 |
- 1418002 |
- Female |
- 1418 |
- 2 |
- 4158260018 |
- B |
- 2 |
-
-
- | 89 |
- GM12328 |
- 1418003 |
- Female |
- 1418 |
- 3 |
- 4256249047 |
- C |
- 6 |
-
-
- | 90 |
- GM12266 |
- 1418005 |
- Female |
- 1418 |
- 5 |
- 41582600011 |
- F |
- 2 |
-
-
- | 91 |
- GM12267 |
- 1418006 |
- Male |
- 1418 |
- 6 |
- 4158260009 |
- D |
- 3 |
-
-
- | 92 |
- GM12270 |
- 1418009 |
- Female |
- 1418 |
- 9 |
- 4158260001 |
- D |
- 4 |
-
-
- | 93 |
- GM12271 |
- 1418010 |
- Female |
- 1418 |
- 10 |
- 4158260012 |
- D |
- 3 |
-
-
- | 94 |
- GM12272 |
- 1418011 |
- Male |
- 1418 |
- 11 |
- 4256249060 |
- E |
- 5 |
-
-
- | 95 |
- GM12273 |
- 1418012 |
- Female |
- 1418 |
- 12 |
- 4158260002 |
- D |
- 4 |
-
-
- | 96 |
- GM12274 |
- 1418013 |
- Male |
- 1418 |
- 13 |
- 4256249101 |
- A |
- 6 |
-
-
- | 97 |
- GM12275 |
- 1418014 |
- Female |
- 1418 |
- 14 |
- 4158260005 |
- C |
- 4 |
-
-
- | 98 |
- GM10841 |
- 1421001 |
- Male |
- 1421 |
- 1 |
- 4158260030 |
- E |
- 3 |
-
-
- | 99 |
- GM10840 |
- 1421002 |
- Female |
- 1421 |
- 2 |
- 4256249098 |
- C |
- 7 |
-
-
- | 100 |
- GM12276 |
- 1421003 |
- Female |
- 1421 |
- 3 |
- 4158260012 |
- F |
- 3 |
-
-
- | 101 |
- GM12278 |
- 1421005 |
- Female |
- 1421 |
- 5 |
- 4256249042 |
- C |
- 6 |
-
-
- | 102 |
- GM12280 |
- 1421007 |
- Female |
- 1421 |
- 7 |
- 4256249041 |
- B |
- 6 |
-
-
- | 103 |
- GM12281 |
- 1421008 |
- Male |
- 1421 |
- 8 |
- 4256249047 |
- D |
- 6 |
-
-
- | 104 |
- GM12282 |
- 1421009 |
- Male |
- 1421 |
- 9 |
- 4158260026 |
- F |
- 3 |
-
-
- | 105 |
- GM12283 |
- 1421010 |
- Female |
- 1421 |
- 10 |
- 4256249101 |
- B |
- 6 |
-
-
- | 106 |
- GM12284 |
- 1421011 |
- Male |
- 1421 |
- 11 |
- 4256249094 |
- C |
- 6 |
-
-
- | 107 |
- GM12285 |
- 1421012 |
- Male |
- 1421 |
- 12 |
- 4256249104 |
- B |
- 7 |
-
-
- | 108 |
- GM12287 |
- 1421014 |
- Female |
- 1421 |
- 14 |
- 4256249051 |
- B |
- 6 |
-
-
- | 109 |
- GM11910 |
- 1423004 |
- Female |
- 1423 |
- 4 |
- 4256249103 |
- D |
- 7 |
-
-
- | 110 |
- GM11911 |
- 1423005 |
- Female |
- 1423 |
- 5 |
- 4256249096 |
- E |
- 7 |
-
-
- | 111 |
- GM11912 |
- 1423006 |
- Male |
- 1423 |
- 6 |
- 4158260009 |
- C |
- 3 |
-
-
- | 112 |
- GM11913 |
- 1423007 |
- Male |
- 1423 |
- 7 |
- 4256249044 |
- D |
- 7 |
-
-
- | 113 |
- GM11914 |
- 1423008 |
- Female |
- 1423 |
- 8 |
- 4256249098 |
- A |
- 7 |
-
-
- | 114 |
- GM11915 |
- 1423009 |
- Female |
- 1423 |
- 9 |
- 41582600011 |
- C |
- 2 |
-
-
- | 115 |
- GM11916 |
- 1423010 |
- Male |
- 1423 |
- 10 |
- 4158260018 |
- D |
- 2 |
-
-
- | 116 |
- GM11917 |
- 1423011 |
- Male |
- 1423 |
- 11 |
- 4256249097 |
- F |
- 7 |
-
-
- | 117 |
- GM11919 |
- 1423013 |
- Male |
- 1423 |
- 13 |
- 4256249104 |
- F |
- 7 |
-
-
- | 118 |
- GM11920 |
- 1423014 |
- Female |
- 1423 |
- 14 |
- 4256249095 |
- D |
- 7 |
-
-
- | 119 |
- GM11921 |
- 1423015 |
- Female |
- 1423 |
- 15 |
- 4256249099 |
- A |
- 7 |
-
-
- | 120 |
- GM10845 |
- 1424001 |
- Male |
- 1424 |
- 1 |
- 4256249104 |
- C |
- 7 |
-
-
- | 121 |
- GM10844 |
- 1424002 |
- Female |
- 1424 |
- 2 |
- 4256249103 |
- F |
- 7 |
-
-
- | 122 |
- GM11922 |
- 1424003 |
- Male |
- 1424 |
- 3 |
- 4256249044 |
- A |
- 7 |
-
-
- | 123 |
- GM11923 |
- 1424004 |
- Male |
- 1424 |
- 4 |
- 4256249097 |
- D |
- 7 |
-
-
- | 124 |
- GM11924 |
- 1424005 |
- Female |
- 1424 |
- 5 |
- 4256249096 |
- A |
- 7 |
-
-
- | 125 |
- GM11925 |
- 1424006 |
- Male |
- 1424 |
- 6 |
- 4158260021 |
- B |
- 2 |
-
-
- | 126 |
- GM11926 |
- 1424007 |
- Female |
- 1424 |
- 7 |
- 4256249051 |
- C |
- 6 |
-
-
- | 127 |
- GM11927 |
- 1424008 |
- Male |
- 1424 |
- 8 |
- 4256249042 |
- D |
- 6 |
-
-
- | 128 |
- GM11928 |
- 1424009 |
- Male |
- 1424 |
- 9 |
- 4256249098 |
- B |
- 7 |
-
-
- | 129 |
- GM11929 |
- 1424010 |
- Male |
- 1424 |
- 10 |
- 4256249094 |
- D |
- 6 |
-
-
- | 130 |
- GM11930 |
- 1424011 |
- Male |
- 1424 |
- 11 |
- 4256249041 |
- C |
- 6 |
-
-
- | 131 |
- GM11931 |
- 1424012 |
- Female |
- 1424 |
- 12 |
- 4158260002 |
- A |
- 4 |
-
-
- | 132 |
- GM11932 |
- 1424013 |
- Male |
- 1424 |
- 13 |
- 4256249095 |
- A |
- 7 |
-
-
- | 133 |
- GM11933 |
- 1424014 |
- Female |
- 1424 |
- 14 |
- 4158260005 |
- E |
- 4 |
-
-
- | 134 |
- GM12752 |
- 1447001 |
- Male |
- 1447 |
- 1 |
- 4158260021 |
- E |
- 2 |
-
-
- | 135 |
- GM12754 |
- 1447003 |
- Female |
- 1447 |
- 3 |
- 4256249044 |
- E |
- 7 |
-
-
- | 136 |
- GM12756 |
- 1447005 |
- Male |
- 1447 |
- 5 |
- 4256249098 |
- F |
- 7 |
-
-
- | 137 |
- GM12758 |
- 1447007 |
- Female |
- 1447 |
- 7 |
- 4256249099 |
- D |
- 7 |
-
-
- | 138 |
- GM12759 |
- 1447008 |
- Female |
- 1447 |
- 8 |
- 4158260002 |
- E |
- 4 |
-
-
- | 139 |
- GM12760 |
- 1447009 |
- Male |
- 1447 |
- 9 |
- 4256249103 |
- E |
- 7 |
-
-
- | 140 |
- GM12761 |
- 1447010 |
- Female |
- 1447 |
- 10 |
- 4158260009 |
- A |
- 3 |
-
-
- | 141 |
- GM12762 |
- 1447011 |
- Male |
- 1447 |
- 11 |
- 4158260018 |
- F |
- 2 |
-
-
- | 142 |
- GM12763 |
- 1447012 |
- Female |
- 1447 |
- 12 |
- 4158260012 |
- A |
- 3 |
-
-
- | 143 |
- GM12764 |
- 1447013 |
- Male |
- 1447 |
- 13 |
- 4256249042 |
- E |
- 6 |
-
-
- | 144 |
- GM12765 |
- 1447014 |
- Male |
- 1447 |
- 14 |
- 4158260026 |
- A |
- 3 |
-
-
- | 145 |
- GM12766 |
- 1451001 |
- Male |
- 1451 |
- 1 |
- 4158260009 |
- B |
- 3 |
-
-
- | 146 |
- GM12767 |
- 1451002 |
- Female |
- 1451 |
- 2 |
- 4158260012 |
- B |
- 3 |
-
-
- | 147 |
- GM12768 |
- 1451003 |
- Male |
- 1451 |
- 3 |
- 4256249041 |
- D |
- 6 |
-
-
- | 148 |
- GM12769 |
- 1451004 |
- Female |
- 1451 |
- 4 |
- 4158260021 |
- F |
- 2 |
-
-
- | 149 |
- GM12770 |
- 1451005 |
- Female |
- 1451 |
- 5 |
- 4158260005 |
- A |
- 4 |
-
-
- | 150 |
- GM12771 |
- 1451006 |
- Male |
- 1451 |
- 6 |
- 4256249047 |
- E |
- 6 |
-
-
- | 151 |
- GM12772 |
- 1451007 |
- Female |
- 1451 |
- 7 |
- 4158260019 |
- A |
- 4 |
-
-
- | 152 |
- GM12773 |
- 1451008 |
- Female |
- 1451 |
- 8 |
- 4158260002 |
- B |
- 4 |
-
-
- | 153 |
- GM12848 |
- 1451009 |
- Female |
- 1451 |
- 9 |
- 4256249051 |
- D |
- 6 |
-
-
- | 154 |
- GM12774 |
- 1451010 |
- Male |
- 1451 |
- 10 |
- 4158260030 |
- F |
- 3 |
-
-
- | 155 |
- GM12776 |
- 1451012 |
- Female |
- 1451 |
- 12 |
- 4256249099 |
- E |
- 7 |
-
-
- | 156 |
- GM12777 |
- 1451013 |
- Male |
- 1451 |
- 13 |
- 4256249060 |
- D |
- 5 |
-
-
- | 157 |
- GM12801 |
- 1454001 |
- Male |
- 1454 |
- 1 |
- 4256249103 |
- C |
- 7 |
-
-
- | 158 |
- GM12803 |
- 1454003 |
- Female |
- 1454 |
- 3 |
- 4158260019 |
- C |
- 4 |
-
-
- | 159 |
- GM12804 |
- 1454004 |
- Female |
- 1454 |
- 4 |
- 4256249101 |
- D |
- 6 |
-
-
- | 160 |
- GM12805 |
- 1454005 |
- Male |
- 1454 |
- 5 |
- 4256249095 |
- F |
- 7 |
-
-
- | 161 |
- GM12806 |
- 1454006 |
- Male |
- 1454 |
- 6 |
- 4256249098 |
- E |
- 7 |
-
-
- | 162 |
- GM12808 |
- 1454008 |
- Female |
- 1454 |
- 8 |
- 4256249099 |
- C |
- 7 |
-
-
- | 163 |
- GM12809 |
- 1454009 |
- Female |
- 1454 |
- 9 |
- 4256249051 |
- E |
- 6 |
-
-
- | 164 |
- GM12810 |
- 1454010 |
- Male |
- 1454 |
- 10 |
- 4256249104 |
- A |
- 7 |
-
-
- | 165 |
- GM12811 |
- 1454011 |
- Male |
- 1454 |
- 11 |
- 4256249044 |
- B |
- 7 |
-
-
- | 166 |
- GM12812 |
- 1454012 |
- Male |
- 1454 |
- 12 |
- 4256249042 |
- F |
- 6 |
-
-
- | 167 |
- GM12813 |
- 1454013 |
- Female |
- 1454 |
- 13 |
- 4256249094 |
- E |
- 6 |
-
-
- | 168 |
- GM12814 |
- 1454014 |
- Male |
- 1454 |
- 14 |
- 4256249096 |
- D |
- 7 |
-
-
- | 169 |
- GM12815 |
- 1454015 |
- Female |
- 1454 |
- 15 |
- 4256249041 |
- E |
- 6 |
-
-
- | 170 |
- GM12816 |
- 1454016 |
- Male |
- 1454 |
- 16 |
- 4256249047 |
- F |
- 6 |
-
-
- | 171 |
- GM12817 |
- 1456001 |
- Male |
- 1456 |
- 1 |
- 4256249051 |
- F |
- 6 |
-
-
- | 172 |
- GM12818 |
- 1456002 |
- Female |
- 1456 |
- 2 |
- 4256249101 |
- E |
- 6 |
-
-
- | 173 |
- GM12819 |
- 1456003 |
- Male |
- 1456 |
- 3 |
- 4256249095 |
- B |
- 7 |
-
-
- | 174 |
- GM12821 |
- 1456005 |
- Female |
- 1456 |
- 5 |
- 4256249044 |
- C |
- 7 |
-
-
- | 175 |
- GM12822 |
- 1456006 |
- Male |
- 1456 |
- 6 |
- 4256249094 |
- F |
- 6 |
-
-
- | 176 |
- GM12823 |
- 1456007 |
- Male |
- 1456 |
- 7 |
- 4256249096 |
- B |
- 7 |
-
-
- | 177 |
- GM12824 |
- 1456008 |
- Female |
- 1456 |
- 8 |
- 4256249104 |
- D |
- 7 |
-
-
- | 178 |
- GM12825 |
- 1456009 |
- Male |
- 1456 |
- 9 |
- 4158260026 |
- B |
- 3 |
-
-
- | 179 |
- GM12826 |
- 1456010 |
- Female |
- 1456 |
- 10 |
- 4256249041 |
- F |
- 6 |
-
-
- | 180 |
- GM12828 |
- 1456012 |
- Female |
- 1456 |
- 12 |
- 4256249099 |
- F |
- 7 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/UT_CEPH_RankInv0909/experiment-design.rtf b/general/datasets/UT_CEPH_RankInv0909/experiment-design.rtf
deleted file mode 100644
index d525b2e..0000000
--- a/general/datasets/UT_CEPH_RankInv0909/experiment-design.rtf
+++ /dev/null
@@ -1,13 +0,0 @@
-Experimental Design and Batch Structure:
-
-This data set consists of arrays processed in seven groups. Groups consisted of 2, 3, 4, 4, 3, 6, and then 8 beadchips at a time, batch IDs are indicated in table 1. Samples from same family were scattered among array groups, with samples from six different families were run on one chip. This was done to ensure balance and to minimize batch effects and group-by-family statistical confounds in normalization. This was done with the exception of the first two chips, which were run with 3 generations of the same family on one chip. A single operator, Yan Jiao, processed all arrays using illumina protocol for hybridization, washing and scanning. All samples in a group were labeled on one day, hybridization station accommodates up to 24 samples, or 4 beadchips. Chips were scanned using BeadArray Reader in sets of three.
-
-About the processing of cell lines:
-
-CEPH/UTAH families cell lines were purchased from Coriell repository of cell lines part of NIGMS. Upon arrival from the Coriell institute, we incubated the cell lines in 25ml flasks upright overnight at 37 ºC humidified incubator, with 5% carbon dioxide. We maintained the cells at a density of 5 X 105 cells/ml. The composition of the media used was RPMI-1640, 15% fetal bovine serum (FBS) and 2mM L-Glutamine; all FBS used was from the same lot. At 48 hours or when cell counts were ≥ 8 x 106 cells total, we harvested the cells and tested each cell line for mycoplasma contamination using e-Myco Mycoplasma PCR detection kit (iNtRON Biotechnology) according to manufacturer protocol. Cell lysates free of mycoplasma were used for RNA extraction as detailed below. We froze duplicates of each cell line at a concentration of ~2–6 x106 cells/ml according to standard procedures and stored in liquid nitrogen.
-
-About RNA processing:
-
-Two hundred and five cell lines were used for isolation of RNA. Ms. Sarah Rowe Hasty performed initial RNA isolation, purification and re-precipitation from 205 cell lines in Dr. Malak Kotb laboratory at VAMC. After initial RNA isolation, Ms. Nourtan Abdeltawab treated all samples for removal of contaminating DNA, along with further purification and re-precipitation of all samples. RNA samples that passed quality control were used to generate cRNA samples, those that didn't pass QC were re-extracted as we had duplicates of all cell lines lysates. RNA Extraction details: We used Qiagen RNeasy Mini purification of total RNA from tissues and cells spin protocol. RNA was isolated from 7.5 X 105 cells in duplicates. We froze cell lysates in RLT buffer and ß-mercaptoethanol at -80 ºC in 96 well plates until processed at a later time. We thawed samples, one 96 well plate at a time, and proceeded with RNA isolation steps and resuspended the pellets in RNase-free water. We then treated RNA to remove any DNA contamination using DNase digestion with RNase-free DNase kit (Qiagen) according to manufacturer protocol. RNA was finally purified by re-precipitation using ethanol precipitation using Purescript RNA purification kit (Gentra). Final purified RNA was resuspended in RNase-free water. RNA quality control: RNA samples were checked for RNA purity and integrity. RNA purity was evaluated using the 260/280 and 260/230 absorbance ratios. We used RNA samples with 260/280 ratio values ≥ 1.8 and 260/230 of ≥1.7. In cases were RNA samples did not meet these ratios, the RNA was purified by re-precipitation as above. RNA integrity was assessed using 1% RNA denaturing agrose gels. We required clear sharp bands of 18S and 28S rRNA for all samples compared to a control RNA sample to ensure intactness of rRNA.
-
-All RNA samples were processed by Yan Jiao at Dr. Weikuan Gu’s microarray core facility at VA medical center, Memphis, TN. We used only RNA samples that passed quality control as detailed above and of concentration ≥ 50ng/ul for cRNA synthesis using Illumina TotalPrep RNA amplification kit (Ambion) according to manufacturer protocol. The basic outline of the procedure involves reverse transcription of RNA to synthesize cDNA using oligo (dT) primer, followed by in vitro transcription of purified dsDNA to synthesize amplified biotinylated cRNA (aRNA). We evaluated purified labeled cRNA using same methods as mentioned above for RNA samples. cRNA samples of good quality (passing QC), were then used to hybridize to Illumina Human-6WG v2.0 according to Illumina standard protocols.
diff --git a/general/datasets/UT_CEPH_RankInv0909/platform.rtf b/general/datasets/UT_CEPH_RankInv0909/platform.rtf
deleted file mode 100644
index a7a8769..0000000
--- a/general/datasets/UT_CEPH_RankInv0909/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Illumina HumanGW-6 v2.0 BeadChip: The Human-6 v2 beadchip simultaneously assays six samples, therefore, known as ‘array of arrays’. Each chip has ~1.8 million beads, beads have several hundred thousands copies of optimized 50-mer gene-specific probes. These probes cover more than 48,000 transcripts per sample, targeting genes and known alternative splice variants from the RefSeq database release 17 and UniGene build 188.
diff --git a/general/datasets/UT_CEPH_RankInv0909/processing.rtf b/general/datasets/UT_CEPH_RankInv0909/processing.rtf
deleted file mode 100644
index d144cac..0000000
--- a/general/datasets/UT_CEPH_RankInv0909/processing.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-About array data processing and analysis:
-
-RNA samples (n = 180) were processed using a total of 30 Illumina HumanWG-6 BeadChips, each beadchip analyses six samples covering 48,000 transcripts per sample. All chips passed quality control and error checking. This data set was extracted and processed using the Bead Studio 3. We applied Rank-invariant normalization to all the samples and the resulting expression values along with gene ID were exported in GeneSpring format. Dr. Rita Kansal performed the normalization steps.
diff --git a/general/datasets/UT_CEPH_RankInv0909/summary.rtf b/general/datasets/UT_CEPH_RankInv0909/summary.rtf
deleted file mode 100644
index 4394cb5..0000000
--- a/general/datasets/UT_CEPH_RankInv0909/summary.rtf
+++ /dev/null
@@ -1,7 +0,0 @@
-The Illumina Human Whole Genome 6 v2.0 Rank Invariant data for CEPH lymphoblastoid cell lines obtained from the Coriell Institute for Medical Research. All cell lines were processed in Memphis in the UTHSC laboratory of Dr. Malak Kotb (2007-2009), by Dr. Rita G. Kasal, Nourtan Abdeltawab, and colleagues.
-
-Selection of CEPH families and members was done by Dr. Roel Ophoff (Utrecht and UCLA).
-
-Array data were generated at microarray core facility in laboratory of Dr. Weikuan Gu at VA medical center, Memphis, TN.
-
-Analysis by Mark Reimers, Stephanie Santorico, and Roel Ophoff
diff --git a/general/datasets/UT_HippRatEx_RMA_0709/acknowledgment.rtf b/general/datasets/UT_HippRatEx_RMA_0709/acknowledgment.rtf
deleted file mode 100644
index ded4315..0000000
--- a/general/datasets/UT_HippRatEx_RMA_0709/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with NIAAA grants U01AA13499 to Robert W. Williams and a grant to Gerd Kempermann, Genomics of Regeneration in the Central Nervous System, Center for Regenerative Therapies, Dresden.
diff --git a/general/datasets/UT_HippRatEx_RMA_0709/cases.rtf b/general/datasets/UT_HippRatEx_RMA_0709/cases.rtf
deleted file mode 100644
index 85b4b4b..0000000
--- a/general/datasets/UT_HippRatEx_RMA_0709/cases.rtf
+++ /dev/null
@@ -1,1392 +0,0 @@
-
-
-
-
-
-
-
- | Index |
- run order |
- case ID |
- strain |
- RNA ID |
- Tube ID |
- tissue |
- out ID |
- BORN |
- SEX |
- age |
- from |
- Extracted |
- RIN |
- 260:280 |
- 260:230 |
- ng/ul |
- 8ug |
-
-
- | 1 |
- 1 |
- 100908.03 |
- BN.Lx |
- R5448H |
- R5448H1 |
- hippo |
- BN.Lx |
- 12/25/10 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.03 |
- 2.2 |
- 1042.14 |
- 8 |
-
-
- | 2 |
- 16 |
- 100908.02 |
- BN.Lx |
- R5446H |
- R5446H1 |
- hippo |
- BN.Lx |
- 12/25/10 |
- male 2 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.02 |
- 2.24 |
- 392.64 |
- 20 |
-
-
- | 3 |
- 57 |
- 100908.04 |
- BN.Lx |
- R5450H |
- R5450H1 |
- hippo |
- BN.Lx |
- 12/25/10 |
- female 2 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.06 |
- 2.18 |
- 1233.45 |
- 6 |
-
-
- | 4 |
- 68 |
- 100908.01 |
- BN.Lx |
- R5444H |
- R5444H1 |
- hippo |
- BN.Lx |
- 12/25/10 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.05 |
- 2.05 |
- 640.56 |
- 12 |
-
-
- | 5 |
- 3 |
- 101308.03 |
- BXH10 |
- R5390H |
- R5390H1 |
- hippo |
- RI 10C |
- 6/8/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/4/13 |
- |
- 1.97 |
- 2.26 |
- 444.35 |
- 18 |
-
-
- | 6 |
- 66 |
- 101308.01 |
- BXH10 |
- R5386H |
- R5386H1 |
- hippo |
- RI 10C |
- 2/6/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/4/13 |
- |
- 2.04 |
- 2.25 |
- 746.6 |
- 11 |
-
-
- | 7 |
- 5 |
- 110608.19 |
- BXH11 |
- R5380H |
- R5380H1 |
- hippo |
- RI 11C |
- 5/25/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/4/13 |
- |
- 1.97 |
- 2.35 |
- 269.58 |
- 30 |
-
-
- | 8 |
- 64 |
- 110608.17 |
- BXH11 |
- R5378H |
- R5378H1 |
- hippo |
- RI 11C |
- 5/25/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/4/13 |
- |
- 2.04 |
- 2.28 |
- 811.02 |
- 10 |
-
-
- | 9 |
- 7 |
- 110608.23 |
- BXH12 |
- R5384H |
- R5384H1 |
- hippo |
- RI 12C |
- 3/26/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/4/13 |
- |
- 2.06 |
- 2.28 |
- 923.13 |
- 9 |
-
-
- | 10 |
- 62 |
- 110608.21 |
- BXH12 |
- R5382H |
- R5382H1 |
- hippo |
- RI 12C |
- 3/26/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/4/13 |
- |
- 1.96 |
- 2.33 |
- 260.39 |
- 31 |
-
-
- | 11 |
- 9 |
- 101508.19 |
- BXH13 |
- R5438H |
- R5438H1 |
- hippo |
- RI 13C |
- 4/20/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 1.98 |
- 2.33 |
- 274.04 |
- 29 |
-
-
- | 12 |
- 60 |
- 101508.17 |
- BXH13 |
- R5436H |
- R5436H1 |
- hippo |
- RI 13C |
- 4/20/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 1.98 |
- 2.26 |
- 334.92 |
- 24 |
-
-
- | 13 |
- 11 |
- 110608.27 |
- BXH2 |
- R5462H |
- R5462H1 |
- hippo |
- RI 2C |
- 4/1/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.06 |
- 2.3 |
- 1050.29 |
- 8 |
-
-
- | 14 |
- 58 |
- 110608.25 |
- BXH2 |
- R5464H |
- R5464H1 |
- hippo |
- RI 2C |
- 4/1/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.04 |
- 2.29 |
- 804.77 |
- 10 |
-
-
- | 15 |
- 56 |
- 100908.05 |
- BXH3 |
- R5452H |
- R5452H1 |
- hippo |
- RI 3C |
- 1/14/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/5/13 |
- |
- 1.97 |
- 2.36 |
- 306.01 |
- 26 |
-
-
- | 16 |
- 59 |
- 100908.08 |
- BXH3 |
- R5394H |
- R5394H1 |
- hippo |
- RI 3C |
- 1/14/11 |
- female 2 |
- 6 weeks |
- Pravence's lab |
- 3/5/13 |
- |
- 1.97 |
- 2.28 |
- 409.78 |
- 20 |
-
-
- | 17 |
- 13 |
- 110608.31 |
- BXH5 |
- R5368H |
- R5368H1 |
- hippo |
- RI 5C |
- 4/1/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- |
- 2.07 |
- 2.3 |
- 1235.02 |
- 6 |
-
-
- | 18 |
- 54 |
- 110608.29 |
- BXH5 |
- R5366H |
- R5366H1 |
- hippo |
- RI 5C |
- 4/1/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- |
- 2.04 |
- 2.28 |
- 905 |
- 9 |
-
-
- | 19 |
- 15 |
- 110608.11 |
- BXH6 |
- R5372H |
- R5372H1 |
- hippo |
- RI 6C |
- 6/4/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- |
- 2.05 |
- 1.95 |
- 692.63 |
- 12 |
-
-
- | 20 |
- 52 |
- 110608.09 |
- BXH6 |
- R5370H |
- R5370H1 |
- hippo |
- RI 6C |
- 6/4/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- 8.1 |
- 2.06 |
- 2.08 |
- 954.85 |
- 8 |
-
-
- | 21 |
- 17 |
- 112008.07 |
- BXH8 |
- R5360H |
- R5360H1 |
- hippo |
- RI 8C |
- 4/17/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- 9.1 |
- 2.07 |
- 2.27 |
- 1127.86 |
- 7 |
-
-
- | 22 |
- 50 |
- 112008.05 |
- BXH8 |
- R5358H |
- R5358H1 |
- hippo |
- RI 8C |
- 4/17/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- 9.1 |
- 2.08 |
- 2.2 |
- 682.5 |
- 12 |
-
-
- | 23 |
- 19 |
- 110608.15 |
- BXH9 |
- R5376H |
- R5376H1 |
- hippo |
- RI 9C |
- 6/16/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- 9.5 |
- 2.08 |
- 2.24 |
- 736.93 |
- 11 |
-
-
- | 24 |
- 48 |
- 110608.13 |
- BXH9 |
- R5374H |
- R5374H1 |
- hippo |
- RI 9C |
- 6/16/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- 8.9 |
- 1.98 |
- 2.25 |
- 434.51 |
- 18 |
-
-
- | 25 |
- 21 |
- 110608.03 |
- HXB1 |
- R5422H |
- R5422H1 |
- hippo |
- RI 1 |
- 3/13/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 1.99 |
- 2.22 |
- 401.83 |
- 20 |
-
-
- | 26 |
- 46 |
- 110608.01 |
- HXB1 |
- R5420H |
- R5420H1 |
- hippo |
- RI 1 |
- 3/13/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 1.97 |
- 2.29 |
- 351.01 |
- 23 |
-
-
- | 27 |
- 23 |
- 112008.51 |
- HXB10 |
- R5470H |
- R5470H1 |
- hippo |
- RI 10 |
- 3/30/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/17/13 |
- |
- 2.04 |
- 2.26 |
- 743.27 |
- 11 |
-
-
- | 28 |
- 44 |
- 112008.49 |
- HXB10 |
- R5472H |
- R5472H1 |
- hippo |
- RI 10 |
- 3/30/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/17/13 |
- |
- 2.05 |
- 2.21 |
- 958.07 |
- 8 |
-
-
- | 29 |
- 25 |
- 112008.55 |
- HXB13 |
- R5352H |
- R5352H1 |
- hippo |
- RI 13 |
- 3/3/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 2.06 |
- 2.13 |
- 306.01 |
- 26 |
-
-
- | 30 |
- 42 |
- 112008.53 |
- HXB13 |
- R5350H |
- R5350H1 |
- hippo |
- RI 13 |
- 3/3/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- 9.1 |
- 2.09 |
- 2.24 |
- 965.01 |
- 8 |
-
-
- | 31 |
- 27 |
- 112008.11 |
- HXB15 |
- R5414H |
- R5414H1 |
- hippo |
- RI 15 |
- 1/22/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- 8.7 |
- 2.03 |
- 2.31 |
- 788.08 |
- 10 |
-
-
- | 32 |
- 40 |
- 112008.09 |
- HXB15 |
- R5412H |
- R5412H1 |
- hippo |
- RI 15 |
- 1/22/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- |
- 2.05 |
- 2.3 |
- 1041.66 |
- 8 |
-
-
- | 33 |
- 29 |
- 112008.47 |
- HXB17 |
- R5474H |
- R5474H1 |
- hippo |
- RI 17 |
- 4/13/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/17/13 |
- |
- 2.03 |
- 2.28 |
- 758.42 |
- 11 |
-
-
- | 34 |
- 38 |
- 112008.45 |
- HXB17 |
- R5476H |
- R5476H1 |
- hippo |
- RI 17 |
- 4/13/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/17/13 |
- |
- 2.05 |
- 2.27 |
- 1112.55 |
- 7 |
-
-
- | 35 |
- 14 |
- 112008.22 |
- HXB18 |
- R5409H |
- R5409H1 |
- hippo |
- RI 18 |
- 2/2/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- |
- 2.06 |
- 2.27 |
- 1281.26 |
- 6 |
-
-
- | 36 |
- 31 |
- 112008.23 |
- HXB18 |
- R5410H |
- R5410H1 |
- hippo |
- RI 18 |
- 2/2/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- 8.9 |
- 1.98 |
- 2.29 |
- 356.56 |
- 22 |
-
-
- | 37 |
- 36 |
- 112008.13 |
- HXB2 |
- R5416H |
- R5416H1 |
- hippo |
- RI 2 |
- 1/10/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- 8.2 |
- 2.06 |
- 2.3 |
- 1471.72 |
- 5 |
-
-
- | 38 |
- 67 |
- 112008.15 |
- HXB2 |
- R5418H |
- R5418H1 |
- hippo |
- RI 2 |
- 1/10/11 |
- female1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- |
- 2.01 |
- 2.29 |
- 690.65 |
- 12 |
-
-
- | 39 |
- 33 |
- 112008.19 |
- HXB20 |
- R5406H |
- R5406H1 |
- hippo |
- RI 20 |
- 5/24/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- |
- 2.07 |
- 2.24 |
- 1386.52 |
- 6 |
-
-
- | 40 |
- 34 |
- 112008.17 |
- HXB20 |
- R5404H |
- R5404H1 |
- hippo |
- RI 20 |
- 2/16/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/6/13 |
- 8.6 |
- 2.05 |
- 2.26 |
- 1072.81 |
- 7 |
-
-
- | 41 |
- 12 |
- 101508.02 |
- HXB21 |
- R5458H |
- R5458H1 |
- hippo |
- RI 21 |
- 2/3/11 |
- male 2 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2 |
- 2.23 |
- 791.4 |
- 10 |
-
-
- | 42 |
- 35 |
- 101508.04 |
- HXB21 |
- R5460H |
- R5460H1 |
- hippo |
- RI 21 |
- 2/3/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 1.97 |
- 2.29 |
- 413.19 |
- 19 |
-
-
- | 43 |
- 32 |
- 112008.33 |
- HXB22 |
- R5484H |
- R5484H1 |
- hippo |
- RI 22 |
- 4/5/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/18/13 |
- |
- 2.08 |
- 2.16 |
- 755.61 |
- 11 |
-
-
- | 44 |
- 37 |
- 112008.35 |
- HXB22 |
- R5482H |
- R5482H1 |
- hippo |
- RI 22 |
- 4/5/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/18/13 |
- |
- 2.02 |
- 2.3 |
- 978.86 |
- 8 |
-
-
- | 45 |
- 10 |
- 101508.06 |
- HXB23 |
- R5454H |
- R5454H1 |
- hippo |
- RI 23 |
- 3/15/11 |
- male 2 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.05 |
- 2.3 |
- 1052.18 |
- 8 |
-
-
- | 46 |
- 61 |
- 101508.08 |
- HXB23 |
- R5456H |
- R5456H1 |
- hippo |
- RI 23 |
- 3/15/11 |
- female 2 |
- 6 weeks |
- Pravence's lab |
- 3/14/13 |
- |
- 2.06 |
- 2.27 |
- 1281.26 |
- 6 |
-
-
- | 47 |
- 30 |
- 100908.09 |
- HXB24 |
- R5396H |
- R5396H1 |
- hippo |
- RI 24 |
- 2/6/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/5/13 |
- 8.4 |
- 2.08 |
- 1.74 |
- 764.68 |
- 10 |
-
-
- | 48 |
- 39 |
- 100908.11 |
- HXB24 |
- R5400H |
- R5400H1 |
- hippo |
- RI 24 |
- 2/15/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/5/13 |
- 8.8 |
- 2.04 |
- 2.26 |
- 906.15 |
- 9 |
-
-
- | 49 |
- 28 |
- 101508.09 |
- HXB25 |
- R5428H |
- R5428H1 |
- hippo |
- RI 25 |
- 3/1/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- 8.5 |
- 2.05 |
- 2.3 |
- 966.92 |
- 8 |
-
-
- | 50 |
- 41 |
- 101508.11 |
- HXB25 |
- R5430H |
- R5430H1 |
- hippo |
- RI 25 |
- 3/1/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 2.03 |
- 2.3 |
- 811.64 |
- 10 |
-
-
- | 51 |
- 8 |
- 101508.22 |
- HXB27 |
- R5441H |
- R5441H1 |
- hippo |
- RI 27 |
- 4/19/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 2.02 |
- 2.24 |
- 428.61 |
- 19 |
-
-
- | 52 |
- 43 |
- 101508.23 |
- HXB27 |
- R5442H |
- R5442H1 |
- hippo |
- RI 27 |
- 4/19/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 2.02 |
- 2.27 |
- 767.32 |
- 10 |
-
-
- | 53 |
- 6 |
- 112008.26 |
- HXB29 |
- R5364H |
- R5364H1 |
- hippo |
- RI 29 |
- 2/13/11 |
- male 2 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- |
- 2.06 |
- 2.29 |
- 961 |
- 8 |
-
-
- | 54 |
- 63 |
- 112008.28 |
- HXB29 |
- R5362H |
- R5362H1 |
- hippo |
- RI 29 |
- 2/13/11 |
- female 2 |
- 6 weeks |
- Pravence's lab |
- 3/3/13 |
- 8.8 |
- 2.07 |
- 2.26 |
- 830.15 |
- 10 |
-
-
- | 55 |
- 26 |
- 112008.37 |
- HXB3 |
- R5480H |
- R5480H1 |
- hippo |
- RI 3 |
- 3/16/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/18/13 |
- 8.7 |
- 2.05 |
- 2.26 |
- 1169.97 |
- 7 |
-
-
- | 56 |
- 45 |
- 112008.39 |
- HXB3 |
- R5478H |
- R5478H1 |
- hippo |
- RI 3 |
- 3/16/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/18/13 |
- |
- 2.01 |
- 2.18 |
- 864.52 |
- 9 |
-
-
- | 57 |
- 4 |
- 112008.30 |
- HXB31 |
- R5347H |
- R5347H1 |
- hippo |
- RI 31 |
- 3/27/11 |
- male 2 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 2.1 |
- 2.29 |
- 881.39 |
- 9 |
-
-
- | 58 |
- 47 |
- 112008.31 |
- HXB31 |
- R5348H |
- R5348H1 |
- hippo |
- RI 31 |
- 3/27/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 1.96 |
- 2.37 |
- 194.23 |
- 41 |
-
-
- | 59 |
- 24 |
- 101508.13 |
- HXB4 |
- R5432H |
- R5432H1 |
- hippo |
- RI 4 |
- 2/25/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- 8.4 |
- 2.06 |
- 2.29 |
- 1345.87 |
- 6 |
-
-
- | 60 |
- 49 |
- 101508.15 |
- HXB4 |
- R5434H |
- R5434H1 |
- hippo |
- RI 4 |
- 2/25/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 2.05 |
- 2.21 |
- 663.4 |
- 12 |
-
-
- | 61 |
- 22 |
- 112008.41 |
- HXB5 |
- R5468H |
- R5468H1 |
- hippo |
- RI 5 |
- 4/20/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/17/13 |
- |
- 2.05 |
- 2.26 |
- 961.62 |
- 8 |
-
-
- | 62 |
- 51 |
- 112008.43 |
- HXB5 |
- R5466H |
- R5466H1 |
- hippo |
- RI 5 |
- 4/20/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/17/13 |
- |
- 1.99 |
- 2.32 |
- 349.47 |
- 23 |
-
-
- | 63 |
- 20 |
- 110608.05 |
- HXB7 |
- R5424H |
- R5424H1 |
- hippo |
- RI 7 |
- 1/19/11 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- 8.5 |
- 2.04 |
- 2.29 |
- 911.71 |
- 9 |
-
-
- | 64 |
- 53 |
- 110608.07 |
- HXB7 |
- R5426H |
- R5426H1 |
- hippo |
- RI 7 |
- 3/28/11 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 3/10/13 |
- |
- 1.97 |
- 2.28 |
- 423.45 |
- 19 |
-
-
- | 65 |
- 2 |
- 112008.02 |
- SHR |
- R5355H |
- R5355H1 |
- hippo |
- SHR |
- 12/25/10 |
- male 2 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 2.08 |
- 2.24 |
- 684.67 |
- 12 |
-
-
- | 66 |
- 18 |
- 112008.01 |
- SHR |
- R5354H |
- R5354H1 |
- hippo |
- SHR |
- 12/25/10 |
- male 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 2.07 |
- 2.29 |
- 728.58 |
- 11 |
-
-
- | 67 |
- 55 |
- 112008.03 |
- SHR |
- R5356H |
- R5356H1 |
- hippo |
- SHR |
- 12/25/10 |
- female 1 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 1.97 |
- 2.36 |
- 265.66 |
- 30 |
-
-
- | 68 |
- 65 |
- 112008.04 |
- SHR |
- R5357H |
- R5357H1 |
- hippo |
- SHR |
- 12/25/10 |
- female 2 |
- 6 weeks |
- Pravence's lab |
- 2/28/13 |
- |
- 2.05 |
- 2.29 |
- 967.24 |
- 8 |
-
-
-
- |
-
-
-
diff --git a/general/datasets/UT_HippRatEx_RMA_0709/summary.rtf b/general/datasets/UT_HippRatEx_RMA_0709/summary.rtf
deleted file mode 100644
index 8ea4a28..0000000
--- a/general/datasets/UT_HippRatEx_RMA_0709/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-The HXB/BXH data provides estimates of Hippocampus mRNA expression. Affymetrix Rat Exon 1.0ST microarrays were used for hybridization using standard procedures. Total of 68 samples come from 30 BXH/HXB strain (one male and one female) and 2 parental strains (two males and two females).
diff --git a/general/datasets/UT_ILM_BXD_hipp_5T_1112/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_5T_1112/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_5T_1112/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_5T_1112/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_5T_1112/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_5T_1112/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_NOE_0909/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_NOE_0909/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NOE_0909/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_NOE_0909/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_NOE_0909/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NOE_0909/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_NON_0909/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_NON_0909/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NON_0909/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_NON_0909/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_NON_0909/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NON_0909/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_NON_1112/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_NON_1112/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NON_1112/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_NON_1112/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_NON_1112/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NON_1112/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_NOS_0909/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_NOS_0909/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NOS_0909/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_NOS_0909/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_NOS_0909/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NOS_0909/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_NOS_1112/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_NOS_1112/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NOS_1112/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_NOS_1112/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_NOS_1112/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_NOS_1112/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_RSE_0909/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_RSE_0909/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_RSE_0909/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_RSE_0909/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_RSE_0909/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_RSE_0909/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_RSE_1112/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_RSE_1112/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_RSE_1112/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_RSE_1112/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_RSE_1112/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_RSE_1112/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/UT_ILM_BXD_hipp_RSS_0909/notes.rtf b/general/datasets/UT_ILM_BXD_hipp_RSS_0909/notes.rtf
deleted file mode 100644
index 35247b6..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_RSS_0909/notes.rtf
+++ /dev/null
@@ -1,23 +0,0 @@
-Hippocampus 5 Conditions
-Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
-Batch and Outlier Analysis on Partek Genomic Suite 6.6
-ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
-K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
-Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
-Number of samples = 284
-Number of probes = 46643
-
-
- - UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
- - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
- - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
- ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
- - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
- ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
- - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
- ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
- - UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
- ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1
-
diff --git a/general/datasets/UT_ILM_BXD_hipp_RSS_0909/summary.rtf b/general/datasets/UT_ILM_BXD_hipp_RSS_0909/summary.rtf
deleted file mode 100644
index 5aeb69c..0000000
--- a/general/datasets/UT_ILM_BXD_hipp_RSS_0909/summary.rtf
+++ /dev/null
@@ -1,39 +0,0 @@
-This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.
-
-For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.
-
-Restraint Stress Protocol
-
-
- - Weigh animals all animals to be tested and record body weight.
- - Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
- - Place animals in immobilization tubes for 15 minutes.
- - Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
- - Place each animal into zero-maze for 10 minutes.
- - Return animal to home cage.
- - Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.
-
-
-Ethanol and saline injections
-Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).
-
-"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."
-
-Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.
-
-Quality Control Data
-Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe
-
-
- - NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- - NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- - NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- - RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- - RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)
-
-
-Entered by Arthur Centeno, September 20, 2010.
-
-Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.
-
-Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.
diff --git a/general/datasets/Umutaffyexon_0209_rma/experiment-type.rtf b/general/datasets/Umutaffyexon_0209_rma/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Umutaffyexon_0209_rma/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Umutaffyexon_0209_rma_mdp/experiment-type.rtf b/general/datasets/Umutaffyexon_0209_rma_mdp/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Umutaffyexon_0209_rma_mdp/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Ut_ilm_bxd_hipp_non_0909/experiment-type.rtf b/general/datasets/Ut_ilm_bxd_hipp_non_0909/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Ut_ilm_bxd_hipp_non_0909/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Uthsc_spl_rma_1210f/experiment-type.rtf b/general/datasets/Uthsc_spl_rma_1210f/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Uthsc_spl_rma_1210f/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Uthsc_spl_rma_1210m/experiment-type.rtf b/general/datasets/Uthsc_spl_rma_1210m/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Uthsc_spl_rma_1210m/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/VCUEtOH_0609_R/notes.rtf b/general/datasets/VCUEtOH_0609_R/notes.rtf
deleted file mode 100644
index 3b773ce..0000000
--- a/general/datasets/VCUEtOH_0609_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All samples were processed by Nate Bruce at VCU between April and May 2009. The BioRad Experion RNA analyzer and used to assess total RNA integrity and verify equal molar ratios of 18S and 28S ribosomal RNA. All RNA Quality Index (RQI) calculations were > 8. Standard Affymetrix reagents and protocols were used for generation of cDNA and biotinylated cRNA from total RNA samples. Integrity of cRNA was checked by Experion analysis prior to microarray hybridizations. All probes exceeded a maximum size of 3000 nt for the upper border of the cRNA size distribution.
diff --git a/general/datasets/VCUEtOH_0609_R/platform.rtf b/general/datasets/VCUEtOH_0609_R/platform.rtf
deleted file mode 100644
index b7370c8..0000000
--- a/general/datasets/VCUEtOH_0609_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-GEO: GPL1261 Affymetrix GeneChip Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCUEtOH_0609_R/specifics.rtf b/general/datasets/VCUEtOH_0609_R/specifics.rtf
deleted file mode 100644
index bab9fcf..0000000
--- a/general/datasets/VCUEtOH_0609_R/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to ethanol.
\ No newline at end of file
diff --git a/general/datasets/VCUEtOH_0609_R/summary.rtf b/general/datasets/VCUEtOH_0609_R/summary.rtf
deleted file mode 100644
index ad6106d..0000000
--- a/general/datasets/VCUEtOH_0609_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This BXD data set provides estimates of ventral tegmental area (VTA) mRNA expression in response to ethanol (1.8 g/kg x 4 hours) across 35 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 596 adult male animals obtained from Jackson Laboratory (27 classical BXD strains) or Oak Ridge National Laboratory (extended BXD series) and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and ethanol (IP) treatment in the light-dark transition model of anxiety.
-
-All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to ethanol or saline and transforming these data using the S-score method to compare ethanol vs. saline expression from pairs of arrays for each strain (Kerns et al., Methods 31:274, 2003). The S-score is a method developed for Affymetrix oligonucleotide arrays that is particularly suited to comparing expression on 2 or a small number of chips. The S-score output for each probeset is not an indication of expression magnitude but rather, the change in expression between compared arrays. The S-score is essentially a z-score centered around zero with positive S-scores reflecting increased gene expression with ethanol and negative scores reflecting ethanol-induced decreases in expression. Larger magnitude S-scores show more significant changes in expression and are generally correlated with the fold-change.
diff --git a/general/datasets/VCUEtOH_0806_R/summary.rtf b/general/datasets/VCUEtOH_0806_R/summary.rtf
deleted file mode 100644
index 36e8ee4..0000000
--- a/general/datasets/VCUEtOH_0806_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 33, Name: VCU LXS PFC Et vs Sal M430A 2.0 (Aug06)
\ No newline at end of file
diff --git a/general/datasets/VCUEtOH_1007_R/experiment-design.rtf b/general/datasets/VCUEtOH_1007_R/experiment-design.rtf
deleted file mode 100644
index 9826853..0000000
--- a/general/datasets/VCUEtOH_1007_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Acute ethanol injection. Please ad dose, route, age, timing, etc.
diff --git a/general/datasets/VCUEtOH_1007_R/processing.rtf b/general/datasets/VCUEtOH_1007_R/processing.rtf
deleted file mode 100644
index 692987b..0000000
--- a/general/datasets/VCUEtOH_1007_R/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-These data use the S-score algorithm of Miles and colleagues (PMIDs: 16574698, 16545131, 14597311, 11902839) to evaluate the magnitude of change between the control condition and the ethanol-treated animals. Positive S-score values reflect increased expression with ethanol, negative S-scores reflect decreased expression after ethanol treatment.
diff --git a/general/datasets/VCUEtOH_1007_R/summary.rtf b/general/datasets/VCUEtOH_1007_R/summary.rtf
deleted file mode 100644
index 479039b..0000000
--- a/general/datasets/VCUEtOH_1007_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Summary of DatasetId 44, Name: VCU BXD NA Et vs Sal M430 2.0 (Oct07).
-
-Data set generated by Dr. Michael Miles at Virginia Commonwealth University <mfmiles@vcu.edu>.
diff --git a/general/datasets/VCUEtOH_1206_R/acknowledgment.rtf b/general/datasets/VCUEtOH_1206_R/acknowledgment.rtf
deleted file mode 100644
index 4463223..0000000
--- a/general/datasets/VCUEtOH_1206_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Michael F Miles from the NIAAA.
diff --git a/general/datasets/VCUEtOH_1206_R/cases.rtf b/general/datasets/VCUEtOH_1206_R/cases.rtf
deleted file mode 100644
index a9b6489..0000000
--- a/general/datasets/VCUEtOH_1206_R/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This BXD data set provides estimates of mRNA expression in the prefrontal cortex following ethanol treatment across 27 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 468 adult male animals obtained from Jackson Laboratory and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and treatment with 1.8g/kg ethanol in the light-dark transition model of anxiety. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected as previously described (Kerns et al., J. Neurosci. 25:2255, 2005). All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the prefrontal cortex following ethanol treatment using the Robust Multichip Average (RMA) method.
diff --git a/general/datasets/VCUEtOH_1206_R/experiment-design.rtf b/general/datasets/VCUEtOH_1206_R/experiment-design.rtf
deleted file mode 100644
index 05c600b..0000000
--- a/general/datasets/VCUEtOH_1206_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-This data set was generated concurrently with the VCU saline prefrontal cortex BXD RMA data and therefore consisted of 64 microarrays processed in 5 groups of 8 to 16 microarrays during the month of September 2006. All RNA extractions, cRNA synthesis, and hybridizations were randomized across strain and treatment groups to minimize batch effects.
-
-Many of the techniques used to generate this data set are described in a recent publication in the Journal of Neuroscience.
-
-Animals were injected intraperitoneally (IP) with saline or 1.8 g/kg of ethanol. As part of a parallel study of ethanol induced anxiolysis, all mice underwent behavioral testing that included 15 minutes of restraint in a 50 mL conical tube followed by 10 minutes in a light-dark chamber. Mice were killed by cervical dislocation four hours following IP injection. Immediately thereafter, brains were extracted and chilled for 1 minute in iced phosphate buffer before being microdissected into 8 constituent regions, including the medial prefrontal cortex. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represent a pooling of 4-5 animals.
diff --git a/general/datasets/VCUEtOH_1206_R/platform.rtf b/general/datasets/VCUEtOH_1206_R/platform.rtf
deleted file mode 100644
index ec67993..0000000
--- a/general/datasets/VCUEtOH_1206_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCUEtOH_1206_R/summary.rtf b/general/datasets/VCUEtOH_1206_R/summary.rtf
deleted file mode 100644
index ff7c56f..0000000
--- a/general/datasets/VCUEtOH_1206_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.
diff --git a/general/datasets/VCUEtOH_1206_R/tissue.rtf b/general/datasets/VCUEtOH_1206_R/tissue.rtf
deleted file mode 100644
index 6473075..0000000
--- a/general/datasets/VCUEtOH_1206_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-All animals were obtained at 8-9 weeks of age from the Jackson Laboratory (Bar Harbor, ME) and were treated, behaviorally tested and brains dissected by Alex Putman and colleagues at VCU. Following an hour acclimation period to the behavioral room, animals were restrained for 15 minutes, immediately injected (I.P.) with either saline (0.9%) or 1.8g/kg ethanol, and 5 minutes later placed in the light-dark box for a 10-minute test session. All behavioral testing occurred between 10 AM and 1 PM during the light phase over a 12 month period beginning August 2005. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected. Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediately frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation. A pool of dissected tissue from 3 mice of the same strain was used to generate RNA samples. All RNA samples were extracted at VCU by Alex Putman during October 2006 and the order of RNA isolation was randomized across all strains and treatment groups (since saline treated animals were processed concurrently).
-
-GEO Accession: GSE28515
diff --git a/general/datasets/VCUEt_vs_Sal_0806_R/summary.rtf b/general/datasets/VCUEt_vs_Sal_0806_R/summary.rtf
deleted file mode 100644
index 36e8ee4..0000000
--- a/general/datasets/VCUEt_vs_Sal_0806_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 33, Name: VCU LXS PFC Et vs Sal M430A 2.0 (Aug06)
\ No newline at end of file
diff --git a/general/datasets/VCUEtvsSal_0609_R/notes.rtf b/general/datasets/VCUEtvsSal_0609_R/notes.rtf
deleted file mode 100644
index 3b773ce..0000000
--- a/general/datasets/VCUEtvsSal_0609_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All samples were processed by Nate Bruce at VCU between April and May 2009. The BioRad Experion RNA analyzer and used to assess total RNA integrity and verify equal molar ratios of 18S and 28S ribosomal RNA. All RNA Quality Index (RQI) calculations were > 8. Standard Affymetrix reagents and protocols were used for generation of cDNA and biotinylated cRNA from total RNA samples. Integrity of cRNA was checked by Experion analysis prior to microarray hybridizations. All probes exceeded a maximum size of 3000 nt for the upper border of the cRNA size distribution.
diff --git a/general/datasets/VCUEtvsSal_0609_R/platform.rtf b/general/datasets/VCUEtvsSal_0609_R/platform.rtf
deleted file mode 100644
index b7370c8..0000000
--- a/general/datasets/VCUEtvsSal_0609_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-GEO: GPL1261 Affymetrix GeneChip Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCUEtvsSal_0609_R/specifics.rtf b/general/datasets/VCUEtvsSal_0609_R/specifics.rtf
deleted file mode 100644
index 5222820..0000000
--- a/general/datasets/VCUEtvsSal_0609_R/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to ethanol or saline and transforming these data using the S-score method to compare ethanol vs. saline expression from pairs of arrays for each strain (Kerns et al., Methods 31:274, 2003).
\ No newline at end of file
diff --git a/general/datasets/VCUEtvsSal_0609_R/summary.rtf b/general/datasets/VCUEtvsSal_0609_R/summary.rtf
deleted file mode 100644
index ad6106d..0000000
--- a/general/datasets/VCUEtvsSal_0609_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This BXD data set provides estimates of ventral tegmental area (VTA) mRNA expression in response to ethanol (1.8 g/kg x 4 hours) across 35 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 596 adult male animals obtained from Jackson Laboratory (27 classical BXD strains) or Oak Ridge National Laboratory (extended BXD series) and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and ethanol (IP) treatment in the light-dark transition model of anxiety.
-
-All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to ethanol or saline and transforming these data using the S-score method to compare ethanol vs. saline expression from pairs of arrays for each strain (Kerns et al., Methods 31:274, 2003). The S-score is a method developed for Affymetrix oligonucleotide arrays that is particularly suited to comparing expression on 2 or a small number of chips. The S-score output for each probeset is not an indication of expression magnitude but rather, the change in expression between compared arrays. The S-score is essentially a z-score centered around zero with positive S-scores reflecting increased gene expression with ethanol and negative scores reflecting ethanol-induced decreases in expression. Larger magnitude S-scores show more significant changes in expression and are generally correlated with the fold-change.
diff --git a/general/datasets/VCUSal_0609_R/notes.rtf b/general/datasets/VCUSal_0609_R/notes.rtf
deleted file mode 100644
index 3b773ce..0000000
--- a/general/datasets/VCUSal_0609_R/notes.rtf
+++ /dev/null
@@ -1 +0,0 @@
-All samples were processed by Nate Bruce at VCU between April and May 2009. The BioRad Experion RNA analyzer and used to assess total RNA integrity and verify equal molar ratios of 18S and 28S ribosomal RNA. All RNA Quality Index (RQI) calculations were > 8. Standard Affymetrix reagents and protocols were used for generation of cDNA and biotinylated cRNA from total RNA samples. Integrity of cRNA was checked by Experion analysis prior to microarray hybridizations. All probes exceeded a maximum size of 3000 nt for the upper border of the cRNA size distribution.
diff --git a/general/datasets/VCUSal_0609_R/platform.rtf b/general/datasets/VCUSal_0609_R/platform.rtf
deleted file mode 100644
index b7370c8..0000000
--- a/general/datasets/VCUSal_0609_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-GEO: GPL1261 Affymetrix GeneChip Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCUSal_0609_R/specifics.rtf b/general/datasets/VCUSal_0609_R/specifics.rtf
deleted file mode 100644
index cb1ae5d..0000000
--- a/general/datasets/VCUSal_0609_R/specifics.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to saline.
diff --git a/general/datasets/VCUSal_0609_R/summary.rtf b/general/datasets/VCUSal_0609_R/summary.rtf
deleted file mode 100644
index ad6106d..0000000
--- a/general/datasets/VCUSal_0609_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-This BXD data set provides estimates of ventral tegmental area (VTA) mRNA expression in response to ethanol (1.8 g/kg x 4 hours) across 35 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 596 adult male animals obtained from Jackson Laboratory (27 classical BXD strains) or Oak Ridge National Laboratory (extended BXD series) and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and ethanol (IP) treatment in the light-dark transition model of anxiety.
-
-All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to ethanol or saline and transforming these data using the S-score method to compare ethanol vs. saline expression from pairs of arrays for each strain (Kerns et al., Methods 31:274, 2003). The S-score is a method developed for Affymetrix oligonucleotide arrays that is particularly suited to comparing expression on 2 or a small number of chips. The S-score output for each probeset is not an indication of expression magnitude but rather, the change in expression between compared arrays. The S-score is essentially a z-score centered around zero with positive S-scores reflecting increased gene expression with ethanol and negative scores reflecting ethanol-induced decreases in expression. Larger magnitude S-scores show more significant changes in expression and are generally correlated with the fold-change.
diff --git a/general/datasets/VCUSal_0806_R/summary.rtf b/general/datasets/VCUSal_0806_R/summary.rtf
deleted file mode 100644
index 36e8ee4..0000000
--- a/general/datasets/VCUSal_0806_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 33, Name: VCU LXS PFC Et vs Sal M430A 2.0 (Aug06)
\ No newline at end of file
diff --git a/general/datasets/VCUSal_1006_R/acknowledgment.rtf b/general/datasets/VCUSal_1006_R/acknowledgment.rtf
deleted file mode 100644
index 4463223..0000000
--- a/general/datasets/VCUSal_1006_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Michael F Miles from the NIAAA.
diff --git a/general/datasets/VCUSal_1006_R/cases.rtf b/general/datasets/VCUSal_1006_R/cases.rtf
deleted file mode 100644
index a9b6489..0000000
--- a/general/datasets/VCUSal_1006_R/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This BXD data set provides estimates of mRNA expression in the prefrontal cortex following ethanol treatment across 27 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 468 adult male animals obtained from Jackson Laboratory and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and treatment with 1.8g/kg ethanol in the light-dark transition model of anxiety. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected as previously described (Kerns et al., J. Neurosci. 25:2255, 2005). All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the prefrontal cortex following ethanol treatment using the Robust Multichip Average (RMA) method.
diff --git a/general/datasets/VCUSal_1006_R/experiment-design.rtf b/general/datasets/VCUSal_1006_R/experiment-design.rtf
deleted file mode 100644
index 05c600b..0000000
--- a/general/datasets/VCUSal_1006_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-This data set was generated concurrently with the VCU saline prefrontal cortex BXD RMA data and therefore consisted of 64 microarrays processed in 5 groups of 8 to 16 microarrays during the month of September 2006. All RNA extractions, cRNA synthesis, and hybridizations were randomized across strain and treatment groups to minimize batch effects.
-
-Many of the techniques used to generate this data set are described in a recent publication in the Journal of Neuroscience.
-
-Animals were injected intraperitoneally (IP) with saline or 1.8 g/kg of ethanol. As part of a parallel study of ethanol induced anxiolysis, all mice underwent behavioral testing that included 15 minutes of restraint in a 50 mL conical tube followed by 10 minutes in a light-dark chamber. Mice were killed by cervical dislocation four hours following IP injection. Immediately thereafter, brains were extracted and chilled for 1 minute in iced phosphate buffer before being microdissected into 8 constituent regions, including the medial prefrontal cortex. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represent a pooling of 4-5 animals.
diff --git a/general/datasets/VCUSal_1006_R/platform.rtf b/general/datasets/VCUSal_1006_R/platform.rtf
deleted file mode 100644
index ec67993..0000000
--- a/general/datasets/VCUSal_1006_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCUSal_1006_R/summary.rtf b/general/datasets/VCUSal_1006_R/summary.rtf
deleted file mode 100644
index ff7c56f..0000000
--- a/general/datasets/VCUSal_1006_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.
diff --git a/general/datasets/VCUSal_1006_R/tissue.rtf b/general/datasets/VCUSal_1006_R/tissue.rtf
deleted file mode 100644
index 6473075..0000000
--- a/general/datasets/VCUSal_1006_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-All animals were obtained at 8-9 weeks of age from the Jackson Laboratory (Bar Harbor, ME) and were treated, behaviorally tested and brains dissected by Alex Putman and colleagues at VCU. Following an hour acclimation period to the behavioral room, animals were restrained for 15 minutes, immediately injected (I.P.) with either saline (0.9%) or 1.8g/kg ethanol, and 5 minutes later placed in the light-dark box for a 10-minute test session. All behavioral testing occurred between 10 AM and 1 PM during the light phase over a 12 month period beginning August 2005. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected. Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediately frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation. A pool of dissected tissue from 3 mice of the same strain was used to generate RNA samples. All RNA samples were extracted at VCU by Alex Putman during October 2006 and the order of RNA isolation was randomized across all strains and treatment groups (since saline treated animals were processed concurrently).
-
-GEO Accession: GSE28515
diff --git a/general/datasets/VCUSal_1007_R/experiment-design.rtf b/general/datasets/VCUSal_1007_R/experiment-design.rtf
deleted file mode 100644
index 9826853..0000000
--- a/general/datasets/VCUSal_1007_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Acute ethanol injection. Please ad dose, route, age, timing, etc.
diff --git a/general/datasets/VCUSal_1007_R/processing.rtf b/general/datasets/VCUSal_1007_R/processing.rtf
deleted file mode 100644
index 692987b..0000000
--- a/general/datasets/VCUSal_1007_R/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-These data use the S-score algorithm of Miles and colleagues (PMIDs: 16574698, 16545131, 14597311, 11902839) to evaluate the magnitude of change between the control condition and the ethanol-treated animals. Positive S-score values reflect increased expression with ethanol, negative S-scores reflect decreased expression after ethanol treatment.
diff --git a/general/datasets/VCUSal_1007_R/summary.rtf b/general/datasets/VCUSal_1007_R/summary.rtf
deleted file mode 100644
index 479039b..0000000
--- a/general/datasets/VCUSal_1007_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Summary of DatasetId 44, Name: VCU BXD NA Et vs Sal M430 2.0 (Oct07).
-
-Data set generated by Dr. Michael Miles at Virginia Commonwealth University <mfmiles@vcu.edu>.
diff --git a/general/datasets/VCUSal_1206_R/acknowledgment.rtf b/general/datasets/VCUSal_1206_R/acknowledgment.rtf
deleted file mode 100644
index 4463223..0000000
--- a/general/datasets/VCUSal_1206_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Michael F Miles from the NIAAA.
diff --git a/general/datasets/VCUSal_1206_R/cases.rtf b/general/datasets/VCUSal_1206_R/cases.rtf
deleted file mode 100644
index a9b6489..0000000
--- a/general/datasets/VCUSal_1206_R/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This BXD data set provides estimates of mRNA expression in the prefrontal cortex following ethanol treatment across 27 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 468 adult male animals obtained from Jackson Laboratory and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and treatment with 1.8g/kg ethanol in the light-dark transition model of anxiety. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected as previously described (Kerns et al., J. Neurosci. 25:2255, 2005). All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the prefrontal cortex following ethanol treatment using the Robust Multichip Average (RMA) method.
diff --git a/general/datasets/VCUSal_1206_R/experiment-design.rtf b/general/datasets/VCUSal_1206_R/experiment-design.rtf
deleted file mode 100644
index 05c600b..0000000
--- a/general/datasets/VCUSal_1206_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-This data set was generated concurrently with the VCU saline prefrontal cortex BXD RMA data and therefore consisted of 64 microarrays processed in 5 groups of 8 to 16 microarrays during the month of September 2006. All RNA extractions, cRNA synthesis, and hybridizations were randomized across strain and treatment groups to minimize batch effects.
-
-Many of the techniques used to generate this data set are described in a recent publication in the Journal of Neuroscience.
-
-Animals were injected intraperitoneally (IP) with saline or 1.8 g/kg of ethanol. As part of a parallel study of ethanol induced anxiolysis, all mice underwent behavioral testing that included 15 minutes of restraint in a 50 mL conical tube followed by 10 minutes in a light-dark chamber. Mice were killed by cervical dislocation four hours following IP injection. Immediately thereafter, brains were extracted and chilled for 1 minute in iced phosphate buffer before being microdissected into 8 constituent regions, including the medial prefrontal cortex. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represent a pooling of 4-5 animals.
diff --git a/general/datasets/VCUSal_1206_R/platform.rtf b/general/datasets/VCUSal_1206_R/platform.rtf
deleted file mode 100644
index ec67993..0000000
--- a/general/datasets/VCUSal_1206_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCUSal_1206_R/summary.rtf b/general/datasets/VCUSal_1206_R/summary.rtf
deleted file mode 100644
index ff7c56f..0000000
--- a/general/datasets/VCUSal_1206_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.
diff --git a/general/datasets/VCUSal_1206_R/tissue.rtf b/general/datasets/VCUSal_1206_R/tissue.rtf
deleted file mode 100644
index 6473075..0000000
--- a/general/datasets/VCUSal_1206_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-All animals were obtained at 8-9 weeks of age from the Jackson Laboratory (Bar Harbor, ME) and were treated, behaviorally tested and brains dissected by Alex Putman and colleagues at VCU. Following an hour acclimation period to the behavioral room, animals were restrained for 15 minutes, immediately injected (I.P.) with either saline (0.9%) or 1.8g/kg ethanol, and 5 minutes later placed in the light-dark box for a 10-minute test session. All behavioral testing occurred between 10 AM and 1 PM during the light phase over a 12 month period beginning August 2005. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected. Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediately frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation. A pool of dissected tissue from 3 mice of the same strain was used to generate RNA samples. All RNA samples were extracted at VCU by Alex Putman during October 2006 and the order of RNA isolation was randomized across all strains and treatment groups (since saline treated animals were processed concurrently).
-
-GEO Accession: GSE28515
diff --git a/general/datasets/VCUSalo_1007_R/experiment-design.rtf b/general/datasets/VCUSalo_1007_R/experiment-design.rtf
deleted file mode 100644
index 9826853..0000000
--- a/general/datasets/VCUSalo_1007_R/experiment-design.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Acute ethanol injection. Please ad dose, route, age, timing, etc.
diff --git a/general/datasets/VCUSalo_1007_R/processing.rtf b/general/datasets/VCUSalo_1007_R/processing.rtf
deleted file mode 100644
index 692987b..0000000
--- a/general/datasets/VCUSalo_1007_R/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-These data use the S-score algorithm of Miles and colleagues (PMIDs: 16574698, 16545131, 14597311, 11902839) to evaluate the magnitude of change between the control condition and the ethanol-treated animals. Positive S-score values reflect increased expression with ethanol, negative S-scores reflect decreased expression after ethanol treatment.
diff --git a/general/datasets/VCUSalo_1007_R/summary.rtf b/general/datasets/VCUSalo_1007_R/summary.rtf
deleted file mode 100644
index 479039b..0000000
--- a/general/datasets/VCUSalo_1007_R/summary.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-Summary of DatasetId 44, Name: VCU BXD NA Et vs Sal M430 2.0 (Oct07).
-
-Data set generated by Dr. Michael Miles at Virginia Commonwealth University <mfmiles@vcu.edu>.
diff --git a/general/datasets/VCU_NAc_AvE_0113_Ss/summary.rtf b/general/datasets/VCU_NAc_AvE_0113_Ss/summary.rtf
deleted file mode 100644
index c82b72c..0000000
--- a/general/datasets/VCU_NAc_AvE_0113_Ss/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 161, Name: VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13)
diff --git a/general/datasets/VCU_PF_Air_0111_R/acknowledgment.rtf b/general/datasets/VCU_PF_Air_0111_R/acknowledgment.rtf
deleted file mode 100644
index 4463223..0000000
--- a/general/datasets/VCU_PF_Air_0111_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Michael F Miles from the NIAAA.
diff --git a/general/datasets/VCU_PF_Air_0111_R/cases.rtf b/general/datasets/VCU_PF_Air_0111_R/cases.rtf
deleted file mode 100644
index a9b6489..0000000
--- a/general/datasets/VCU_PF_Air_0111_R/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This BXD data set provides estimates of mRNA expression in the prefrontal cortex following ethanol treatment across 27 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 468 adult male animals obtained from Jackson Laboratory and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and treatment with 1.8g/kg ethanol in the light-dark transition model of anxiety. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected as previously described (Kerns et al., J. Neurosci. 25:2255, 2005). All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the prefrontal cortex following ethanol treatment using the Robust Multichip Average (RMA) method.
diff --git a/general/datasets/VCU_PF_Air_0111_R/experiment-design.rtf b/general/datasets/VCU_PF_Air_0111_R/experiment-design.rtf
deleted file mode 100644
index 05c600b..0000000
--- a/general/datasets/VCU_PF_Air_0111_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-This data set was generated concurrently with the VCU saline prefrontal cortex BXD RMA data and therefore consisted of 64 microarrays processed in 5 groups of 8 to 16 microarrays during the month of September 2006. All RNA extractions, cRNA synthesis, and hybridizations were randomized across strain and treatment groups to minimize batch effects.
-
-Many of the techniques used to generate this data set are described in a recent publication in the Journal of Neuroscience.
-
-Animals were injected intraperitoneally (IP) with saline or 1.8 g/kg of ethanol. As part of a parallel study of ethanol induced anxiolysis, all mice underwent behavioral testing that included 15 minutes of restraint in a 50 mL conical tube followed by 10 minutes in a light-dark chamber. Mice were killed by cervical dislocation four hours following IP injection. Immediately thereafter, brains were extracted and chilled for 1 minute in iced phosphate buffer before being microdissected into 8 constituent regions, including the medial prefrontal cortex. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represent a pooling of 4-5 animals.
diff --git a/general/datasets/VCU_PF_Air_0111_R/platform.rtf b/general/datasets/VCU_PF_Air_0111_R/platform.rtf
deleted file mode 100644
index ec67993..0000000
--- a/general/datasets/VCU_PF_Air_0111_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCU_PF_Air_0111_R/summary.rtf b/general/datasets/VCU_PF_Air_0111_R/summary.rtf
deleted file mode 100644
index ff7c56f..0000000
--- a/general/datasets/VCU_PF_Air_0111_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.
diff --git a/general/datasets/VCU_PF_Air_0111_R/tissue.rtf b/general/datasets/VCU_PF_Air_0111_R/tissue.rtf
deleted file mode 100644
index 6473075..0000000
--- a/general/datasets/VCU_PF_Air_0111_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-All animals were obtained at 8-9 weeks of age from the Jackson Laboratory (Bar Harbor, ME) and were treated, behaviorally tested and brains dissected by Alex Putman and colleagues at VCU. Following an hour acclimation period to the behavioral room, animals were restrained for 15 minutes, immediately injected (I.P.) with either saline (0.9%) or 1.8g/kg ethanol, and 5 minutes later placed in the light-dark box for a 10-minute test session. All behavioral testing occurred between 10 AM and 1 PM during the light phase over a 12 month period beginning August 2005. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected. Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediately frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation. A pool of dissected tissue from 3 mice of the same strain was used to generate RNA samples. All RNA samples were extracted at VCU by Alex Putman during October 2006 and the order of RNA isolation was randomized across all strains and treatment groups (since saline treated animals were processed concurrently).
-
-GEO Accession: GSE28515
diff --git a/general/datasets/VCU_PF_AvE_0111_Ss/acknowledgment.rtf b/general/datasets/VCU_PF_AvE_0111_Ss/acknowledgment.rtf
deleted file mode 100644
index 4463223..0000000
--- a/general/datasets/VCU_PF_AvE_0111_Ss/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Michael F Miles from the NIAAA.
diff --git a/general/datasets/VCU_PF_AvE_0111_Ss/cases.rtf b/general/datasets/VCU_PF_AvE_0111_Ss/cases.rtf
deleted file mode 100644
index a9b6489..0000000
--- a/general/datasets/VCU_PF_AvE_0111_Ss/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This BXD data set provides estimates of mRNA expression in the prefrontal cortex following ethanol treatment across 27 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 468 adult male animals obtained from Jackson Laboratory and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and treatment with 1.8g/kg ethanol in the light-dark transition model of anxiety. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected as previously described (Kerns et al., J. Neurosci. 25:2255, 2005). All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the prefrontal cortex following ethanol treatment using the Robust Multichip Average (RMA) method.
diff --git a/general/datasets/VCU_PF_AvE_0111_Ss/experiment-design.rtf b/general/datasets/VCU_PF_AvE_0111_Ss/experiment-design.rtf
deleted file mode 100644
index 05c600b..0000000
--- a/general/datasets/VCU_PF_AvE_0111_Ss/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-This data set was generated concurrently with the VCU saline prefrontal cortex BXD RMA data and therefore consisted of 64 microarrays processed in 5 groups of 8 to 16 microarrays during the month of September 2006. All RNA extractions, cRNA synthesis, and hybridizations were randomized across strain and treatment groups to minimize batch effects.
-
-Many of the techniques used to generate this data set are described in a recent publication in the Journal of Neuroscience.
-
-Animals were injected intraperitoneally (IP) with saline or 1.8 g/kg of ethanol. As part of a parallel study of ethanol induced anxiolysis, all mice underwent behavioral testing that included 15 minutes of restraint in a 50 mL conical tube followed by 10 minutes in a light-dark chamber. Mice were killed by cervical dislocation four hours following IP injection. Immediately thereafter, brains were extracted and chilled for 1 minute in iced phosphate buffer before being microdissected into 8 constituent regions, including the medial prefrontal cortex. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represent a pooling of 4-5 animals.
diff --git a/general/datasets/VCU_PF_AvE_0111_Ss/platform.rtf b/general/datasets/VCU_PF_AvE_0111_Ss/platform.rtf
deleted file mode 100644
index ec67993..0000000
--- a/general/datasets/VCU_PF_AvE_0111_Ss/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCU_PF_AvE_0111_Ss/summary.rtf b/general/datasets/VCU_PF_AvE_0111_Ss/summary.rtf
deleted file mode 100644
index ff7c56f..0000000
--- a/general/datasets/VCU_PF_AvE_0111_Ss/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.
diff --git a/general/datasets/VCU_PF_AvE_0111_Ss/tissue.rtf b/general/datasets/VCU_PF_AvE_0111_Ss/tissue.rtf
deleted file mode 100644
index 6473075..0000000
--- a/general/datasets/VCU_PF_AvE_0111_Ss/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-All animals were obtained at 8-9 weeks of age from the Jackson Laboratory (Bar Harbor, ME) and were treated, behaviorally tested and brains dissected by Alex Putman and colleagues at VCU. Following an hour acclimation period to the behavioral room, animals were restrained for 15 minutes, immediately injected (I.P.) with either saline (0.9%) or 1.8g/kg ethanol, and 5 minutes later placed in the light-dark box for a 10-minute test session. All behavioral testing occurred between 10 AM and 1 PM during the light phase over a 12 month period beginning August 2005. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected. Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediately frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation. A pool of dissected tissue from 3 mice of the same strain was used to generate RNA samples. All RNA samples were extracted at VCU by Alex Putman during October 2006 and the order of RNA isolation was randomized across all strains and treatment groups (since saline treated animals were processed concurrently).
-
-GEO Accession: GSE28515
diff --git a/general/datasets/VCU_PF_Et_0111_R/acknowledgment.rtf b/general/datasets/VCU_PF_Et_0111_R/acknowledgment.rtf
deleted file mode 100644
index 4463223..0000000
--- a/general/datasets/VCU_PF_Et_0111_R/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Data were generated with funds to Michael F Miles from the NIAAA.
diff --git a/general/datasets/VCU_PF_Et_0111_R/cases.rtf b/general/datasets/VCU_PF_Et_0111_R/cases.rtf
deleted file mode 100644
index a9b6489..0000000
--- a/general/datasets/VCU_PF_Et_0111_R/cases.rtf
+++ /dev/null
@@ -1 +0,0 @@
-This BXD data set provides estimates of mRNA expression in the prefrontal cortex following ethanol treatment across 27 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 468 adult male animals obtained from Jackson Laboratory and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and treatment with 1.8g/kg ethanol in the light-dark transition model of anxiety. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected as previously described (Kerns et al., J. Neurosci. 25:2255, 2005). All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the prefrontal cortex following ethanol treatment using the Robust Multichip Average (RMA) method.
diff --git a/general/datasets/VCU_PF_Et_0111_R/experiment-design.rtf b/general/datasets/VCU_PF_Et_0111_R/experiment-design.rtf
deleted file mode 100644
index 05c600b..0000000
--- a/general/datasets/VCU_PF_Et_0111_R/experiment-design.rtf
+++ /dev/null
@@ -1,5 +0,0 @@
-This data set was generated concurrently with the VCU saline prefrontal cortex BXD RMA data and therefore consisted of 64 microarrays processed in 5 groups of 8 to 16 microarrays during the month of September 2006. All RNA extractions, cRNA synthesis, and hybridizations were randomized across strain and treatment groups to minimize batch effects.
-
-Many of the techniques used to generate this data set are described in a recent publication in the Journal of Neuroscience.
-
-Animals were injected intraperitoneally (IP) with saline or 1.8 g/kg of ethanol. As part of a parallel study of ethanol induced anxiolysis, all mice underwent behavioral testing that included 15 minutes of restraint in a 50 mL conical tube followed by 10 minutes in a light-dark chamber. Mice were killed by cervical dislocation four hours following IP injection. Immediately thereafter, brains were extracted and chilled for 1 minute in iced phosphate buffer before being microdissected into 8 constituent regions, including the medial prefrontal cortex. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represent a pooling of 4-5 animals.
diff --git a/general/datasets/VCU_PF_Et_0111_R/platform.rtf b/general/datasets/VCU_PF_Et_0111_R/platform.rtf
deleted file mode 100644
index ec67993..0000000
--- a/general/datasets/VCU_PF_Et_0111_R/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
diff --git a/general/datasets/VCU_PF_Et_0111_R/summary.rtf b/general/datasets/VCU_PF_Et_0111_R/summary.rtf
deleted file mode 100644
index ff7c56f..0000000
--- a/general/datasets/VCU_PF_Et_0111_R/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.
diff --git a/general/datasets/VCU_PF_Et_0111_R/tissue.rtf b/general/datasets/VCU_PF_Et_0111_R/tissue.rtf
deleted file mode 100644
index 6473075..0000000
--- a/general/datasets/VCU_PF_Et_0111_R/tissue.rtf
+++ /dev/null
@@ -1,3 +0,0 @@
-All animals were obtained at 8-9 weeks of age from the Jackson Laboratory (Bar Harbor, ME) and were treated, behaviorally tested and brains dissected by Alex Putman and colleagues at VCU. Following an hour acclimation period to the behavioral room, animals were restrained for 15 minutes, immediately injected (I.P.) with either saline (0.9%) or 1.8g/kg ethanol, and 5 minutes later placed in the light-dark box for a 10-minute test session. All behavioral testing occurred between 10 AM and 1 PM during the light phase over a 12 month period beginning August 2005. Four hours after treatment, animals were rapidly sacrificed by cervical dislocation, brains were removed, cooled and microdissected. Prefrontal cortex tissue was isolated by microdissection using a wedge-shaped slice taken from a 4 mm thick brain slice extending rostrally from the optic chiasm. The wedge was centered on the inter-hemispheric fissure and extending 2 mm laterally on each side and ventrally to just above the corpus callosum. This tissue and all other brain regions were dissected in less than 5 minutes per mouse and were immediately frozen in liquid nitrogen followed by storage at -80 oC prior to RNA isolation. A pool of dissected tissue from 3 mice of the same strain was used to generate RNA samples. All RNA samples were extracted at VCU by Alex Putman during October 2006 and the order of RNA isolation was randomized across all strains and treatment groups (since saline treated animals were processed concurrently).
-
-GEO Accession: GSE28515
diff --git a/general/datasets/VUBXDMouseMidBrainQ0512/cases.rtf b/general/datasets/VUBXDMouseMidBrainQ0512/cases.rtf
deleted file mode 100644
index 4a8704a..0000000
--- a/general/datasets/VUBXDMouseMidBrainQ0512/cases.rtf
+++ /dev/null
@@ -1,795 +0,0 @@
-
-
-
-
-
-
-
-
-
- | Index |
- Sample ID |
- Sex |
- Strain Assignment L14 |
-
-
- | 1 |
- 916-DCA-68 |
- M |
- BXD1 |
-
-
- | 2 |
- 916-DCA-165 |
- M |
- BXD1 |
-
-
- | 3 |
- 916-DCA-147 |
- M |
- BXD1 |
-
-
- | 4 |
- 916-DCA-114 |
- M |
- BXD1 |
-
-
- | 5 |
- 916-DCA-107 |
- M |
- BXD11 |
-
-
- | 6 |
- 916-DCA-187 |
- M |
- BXD11 |
-
-
- | 7 |
- 916-DCA-67 |
- M |
- BXD11 |
-
-
- | 8 |
- 916-DCA-158 |
- M |
- BXD12 |
-
-
- | 9 |
- 916-DCA-35 |
- M |
- BXD12 |
-
-
- | 10 |
- 916-DCA-36 |
- M |
- BXD12 |
-
-
- | 11 |
- 916-DCA-140 |
- M |
- BXD14 |
-
-
- | 12 |
- 916-DCA-45 |
- M |
- BXD14 |
-
-
- | 13 |
- 916-DCA-99 |
- M |
- BXD14 |
-
-
- | 14 |
- 916-DCA-191 |
- M |
- BXD14 |
-
-
- | 15 |
- 916-DCA-79 |
- M |
- BXD15 |
-
-
- | 16 |
- 916-DCA-38 |
- M |
- BXD15 |
-
-
- | 17 |
- 916-DCA-41 |
- M |
- BXD15 |
-
-
- | 18 |
- 916-DCA-88 |
- M |
- BXD15 |
-
-
- | 19 |
- 916-DCA-141 |
- M |
- BXD16 |
-
-
- | 20 |
- 916-DCA-97 |
- M |
- BXD16 |
-
-
- | 21 |
- 916-DCA-18 |
- M |
- BXD16 |
-
-
- | 22 |
- 916-DCA-179 |
- M |
- BXD16 |
-
-
- | 23 |
- 916-DCA-16 |
- M |
- BXD18 |
-
-
- | 24 |
- 916-DCA-23 |
- M |
- BXD18 |
-
-
- | 25 |
- 916-DCA-12 |
- M |
- BXD18 |
-
-
- | 26 |
- 916-DCA-175 |
- M |
- BXD18 |
-
-
- | 27 |
- 916-DCA-8 |
- M |
- BXD19 |
-
-
- | 28 |
- 916-DCA-174 |
- M |
- BXD19 |
-
-
- | 29 |
- 916-DCA-78 |
- M |
- BXD19 |
-
-
- | 30 |
- 916-DCA-24 |
- M |
- BXD19 |
-
-
- | 31 |
- 916-DCA-105 |
- M |
- BXD2 |
-
-
- | 32 |
- 916-DCA-57 |
- M |
- BXD2 |
-
-
- | 33 |
- 916-DCA-166 |
- M |
- BXD2 |
-
-
- | 34 |
- 916-DCA-181 |
- M |
- BXD2 |
-
-
- | 35 |
- 916-DCA-100 |
- M |
- BXD20 |
-
-
- | 36 |
- 916-DCA-82 |
- M |
- BXD20 |
-
-
- | 37 |
- 916-DCA-72 |
- M |
- BXD20 |
-
-
- | 38 |
- 916-DCA-131 |
- M |
- BXD20 |
-
-
- | 39 |
- 916-DCA-63 |
- M |
- BXD21 |
-
-
- | 40 |
- 916-DCA-13 |
- M |
- BXD21 |
-
-
- | 41 |
- 916-DCA-15 |
- M |
- BXD21 |
-
-
- | 42 |
- 916-DCA-109 |
- M |
- BXD22 |
-
-
- | 43 |
- 916-DCA-101 |
- M |
- BXD22 |
-
-
- | 44 |
- 916-DCA-69 |
- M |
- BXD22 |
-
-
- | 45 |
- 916-DCA-104 |
- M |
- BXD22 |
-
-
- | 46 |
- 916-DCA-125 |
- M |
- BXD24 |
-
-
- | 47 |
- 916-DCA-33 |
- M |
- BXD24 |
-
-
- | 48 |
- 916-DCA-108 |
- M |
- BXD24 |
-
-
- | 49 |
- 916-DCA-44 |
- M |
- BXD24 |
-
-
- | 50 |
- 916-DCA-80 |
- M |
- BXD27 |
-
-
- | 51 |
- 916-DCA-151 |
- M |
- BXD28 |
-
-
- | 52 |
- 916-DCA-47 |
- M |
- BXD28 |
-
-
- | 53 |
- 916-DCA-27 |
- M |
- BXD28 |
-
-
- | 54 |
- 916-DCA-154 |
- M |
- BXD28 |
-
-
- | 55 |
- 916-DCA-71 |
- M |
- BXD29 |
-
-
- | 56 |
- 916-DCA-54 |
- M |
- BXD29 |
-
-
- | 57 |
- 916-DCA-122 |
- M |
- BXD29 |
-
-
- | 58 |
- 916-DCA-51.1 |
- M |
- BXD29 |
-
-
- | 59 |
- 916-DCA-144 |
- M |
- BXD31 |
-
-
- | 60 |
- 916-DCA-76 |
- M |
- BXD31 |
-
-
- | 61 |
- 916-DCA-164 |
- M |
- BXD31 |
-
-
- | 62 |
- 916-DCA-37 |
- M |
- BXD32 |
-
-
- | 63 |
- 916-DCA-89 |
- M |
- BXD32 |
-
-
- | 64 |
- 916-DCA-25 |
- M |
- BXD32 |
-
-
- | 65 |
- 916-DCA-160 |
- M |
- BXD33 |
-
-
- | 66 |
- 916-DCA-65 |
- M |
- BXD33 |
-
-
- | 67 |
- 916-DCA-128 |
- M |
- BXD33 |
-
-
- | 68 |
- 916-DCA-73 |
- M |
- BXD34 |
-
-
- | 69 |
- 916-DCA-103 |
- M |
- BXD34 |
-
-
- | 70 |
- 916-DCA-137 |
- M |
- BXD34 |
-
-
- | 71 |
- 916-DCA-29 |
- M |
- BXD38 |
-
-
- | 72 |
- 916-DCA-112 |
- M |
- BXD38 |
-
-
- | 73 |
- 916-DCA-84 |
- M |
- BXD38 |
-
-
- | 74 |
- 916-DCA-132 |
- M |
- BXD38 |
-
-
- | 75 |
- 916-DCA-156 |
- M |
- BXD38 |
-
-
- | 76 |
- 916-DCA-130 |
- M |
- BXD39 |
-
-
- | 77 |
- 916-DCA-117 |
- M |
- BXD39 |
-
-
- | 78 |
- 916-DCA-111 |
- M |
- BXD39 |
-
-
- | 79 |
- 916-DCA-14 |
- M |
- BXD40 |
-
-
- | 80 |
- 916-DCA-188 |
- M |
- BXD40 |
-
-
- | 81 |
- 916-DCA-192 |
- M |
- BXD40 |
-
-
- | 82 |
- 916-DCA-90 |
- M |
- BXD40 |
-
-
- | 83 |
- 916-DCA-52 |
- M |
- BXD42 |
-
-
- | 84 |
- 916-DCA-2 |
- M |
- BXD42 |
-
-
- | 85 |
- 916-DCA-126 |
- M |
- BXD42 |
-
-
- | 86 |
- 916-DCA-81 |
- M |
- BXD42 |
-
-
- | 87 |
- 916-DCA-118 |
- M |
- BXD44 |
-
-
- | 88 |
- 916-DCA-42 |
- M |
- BXD44 |
-
-
- | 89 |
- 916-DCA-92 |
- M |
- BXD44 |
-
-
- | 90 |
- 916-DCA-39 |
- M |
- BXD49 |
-
-
- | 91 |
- 916-DCA-98 |
- M |
- BXD49 |
-
-
- | 92 |
- 916-DCA-83 |
- M |
- BXD49 |
-
-
- | 93 |
- 916-DCA-85 |
- M |
- BXD5 |
-
-
- | 94 |
- 916-DCA-6 |
- M |
- BXD5 |
-
-
- | 95 |
- 916-DCA-142 |
- M |
- BXD5 |
-
-
- | 96 |
- 916-DCA-11 |
- M |
- BXD55 |
-
-
- | 97 |
- 916-DCA-121 |
- M |
- BXD55 |
-
-
- | 98 |
- 916-DCA-77 |
- M |
- BXD55 |
-
-
- | 99 |
- 916-DCA-123 |
- M |
- BXD6 |
-
-
- | 100 |
- 916-DCA-28 |
- M |
- BXD6 |
-
-
- | 101 |
- 916-DCA-161 |
- M |
- BXD6 |
-
-
- | 102 |
- 916-DCA-124 |
- M |
- BXD6 |
-
-
- | 103 |
- 916-DCA-189 |
- M |
- BXD62 |
-
-
- | 104 |
- 916-DCA-143 |
- M |
- BXD62 |
-
-
- | 105 |
- 916-DCA-116 |
- M |
- BXD62 |
-
-
- | 106 |
- 916-DCA-159 |
- M |
- BXD73 |
-
-
- | 107 |
- 916-DCA-40 |
- M |
- BXD73 |
-
-
- | 108 |
- 916-DCA-169 |
- M |
- BXD73 |
-
-
- | 109 |
- 916-DCA-120 |
- M |
- BXD8 |
-
-
- | 110 |
- 916-DCA-64 |
- M |
- BXD8 |
-
-
- | 111 |
- 916-DCA-93 |
- M |
- BXD8 |
-
-
- | 112 |
- 916-DCA-148 |
- M |
- BXD86 |
-
-
- | 113 |
- 916-DCA-55 |
- M |
- BXD86 |
-
-
- | 114 |
- 916-DCA-170 |
- M |
- BXD86 |
-
-
- | 115 |
- 916-DCA-50 |
- M |
- BXD89 |
-
-
- | 116 |
- 916-DCA-127 |
- M |
- BXD89 |
-
-
- | 117 |
- 916-DCA-32 |
- M |
- BXD89 |
-
-
- | 118 |
- 916-DCA-62 |
- M |
- BXD89 |
-
-
- | 119 |
- 916-DCA-53 |
- M |
- BXD9 |
-
-
- | 120 |
- 916-DCA-138 |
- M |
- BXD9 |
-
-
- | 121 |
- 916-DCA-180 |
- M |
- BXD9 |
-
-
- | 122 |
- 916-DCA-46 |
- M |
- BXD9 |
-
-
- | 123 |
- 916-DCA-74 |
- M |
- BXD96 |
-
-
- | 124 |
- 916-DCA-110 |
- M |
- BXD96 |
-
-
- | 125 |
- 916-DCA-94 |
- M |
- BXD96 |
-
-
- | 126 |
- 916-DCA-49 |
- M |
- BXD96 |
-
-
- | 127 |
- 916-DCA-119 |
- M |
- BXD98 |
-
-
- | 128 |
- 916-DCA-135 |
- M |
- BXD98 |
-
-
- | 129 |
- 916-DCA-58 |
- M |
- BXD98 |
-
-
-
- |
-
-
-
-
diff --git a/general/datasets/VUBXDMouseMidBrainQ0512/summary.rtf b/general/datasets/VUBXDMouseMidBrainQ0512/summary.rtf
deleted file mode 100644
index 7ed558d..0000000
--- a/general/datasets/VUBXDMouseMidBrainQ0512/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-Summary of DatasetId 141, Name: VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12)
diff --git a/general/datasets/Vcu_pf_air_0111_r/experiment-type.rtf b/general/datasets/Vcu_pf_air_0111_r/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcu_pf_air_0111_r/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Vcu_pf_ave_0111_ss/experiment-type.rtf b/general/datasets/Vcu_pf_ave_0111_ss/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcu_pf_ave_0111_ss/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Vcu_pf_et_0111_r/experiment-type.rtf b/general/datasets/Vcu_pf_et_0111_r/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcu_pf_et_0111_r/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Vcuetoh_0609_r/experiment-type.rtf b/general/datasets/Vcuetoh_0609_r/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcuetoh_0609_r/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Vcuetvssal_0609_r/experiment-type.rtf b/general/datasets/Vcuetvssal_0609_r/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcuetvssal_0609_r/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Vcusal_0609_r/experiment-type.rtf b/general/datasets/Vcusal_0609_r/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcusal_0609_r/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
diff --git a/general/datasets/Vcusal_1206_r/experiment-type.rtf b/general/datasets/Vcusal_1206_r/experiment-type.rtf
deleted file mode 100644
index 4af1832..0000000
--- a/general/datasets/Vcusal_1206_r/experiment-type.rtf
+++ /dev/null
@@ -1 +0,0 @@
-None
\ No newline at end of file
--
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