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| author | acenteno | 2021-06-15 13:32:05 -0500 |
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| committer | acenteno | 2021-06-15 13:32:05 -0500 |
| commit | ed4f7f871fd2b615ba1416455065eb08da302b2b (patch) | |
| tree | e36aa5c807a3de8c484e8cae95f6052ff5191fb1 | |
| parent | 64a7d385cfdb5429682e51e62555466619854b97 (diff) | |
| download | gn-docs-ed4f7f871fd2b615ba1416455065eb08da302b2b.tar.gz | |
Update news.md
| -rw-r--r-- | general/news/news.md | 2044 |
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diff --git a/general/news/news.md b/general/news/news.md index f36c9b4..7b71df4 100644 --- a/general/news/news.md +++ b/general/news/news.md @@ -1,1029 +1,1029 @@ ### GeneNetwork News -> **2019-Sep-24: BXD Genotypes file: Sequence-based improvements coming -> soon** -> -> The BXD sequencing consortium has generated full genome sequence for -> 152 extant BXD strains. Dr. David Ashbrook has extracted the most -> informative 40,000 SNPs from sequence data, and compared -> sequence-based genotypes with those based on array platforms (see -> entries below). In general there is excellent concordance for all but -> a handful of the BXD strains that are in widespread use (BXD1 to -> BXD102). However, there are some problems and mixups that we list -> below. We are currently working on harmonizing data when possible, and -> understanding and fixing errors, when not. -> -> This evaluation of genotypes is based on data extracted from whole-genome sequencing of BXD male spleen samples obtained in January 2017 from the Jackson Laboratory whenever possible, and from the UTHSC colony in all other cases. All animals were born between January and December 2016. -> -> #### 1. BXD65b (sourced from JAX). The sequence-based genotypes correlate better to array-based 2017 genotypes of BXD65 and BXD65a than with the BXD65b array-based genotypes. It is possible that there are two somewhat distinct sub-strains now called BXD65b—one at JAX and one at UTHSC. **Recommended Action:**Sourcing BXD65b animals from JAX. {style="margin-left:40px"}** -> -> #### 2. BXD53 array-based genotypes do not correlate well with sequence-based genotypes for BXD53/2. BXD53 was rederived a second time by JAX and is now referred to formally at BXD53/2RwwJ (Stock 017749). The likely reason for the discrepancy is that we sequenced BXD53/2RwwJ (Stock 017749) rather than the older BXD53 (sourced from UTHSC) for array-based genotyping. BXD53 sequence-based genotypes correlate well with eQTL data for BXD53. **Recommended Action:**If using BXD53/2RwwJ, please obtain current sequence-based genotypes from David Ashbrook. {style="margin-left:40px"}** -> -> #### 3. BXD68 animals at UTHSC used from about 2012 to 2017 were BXD34 animals. Genotypes in the 2017 array-based file HAVE or HAVE NOT been corrected. We have corrected this error in some phenotype data sets. BXD68 from The Jackson Laboratory are genuine BXD68. We sequenced BXD68 DNA from JAX. **Recommended Action: **None unless you have used BXD68 animals obtained from UTHSC between 2012 and 2017. If so, these animals should be relabeled BXD34. {style="margin-left:40px"}** -> -> #### 4. BXD81 sequence-based genotypes correlate well with the new array-based genotypes (r = 0.81) but less well with old array-based genotypes (r = 0.66). This is presumably due to more complete inbreeding. The new sequence-based genotypes are for BXD81 sources from JAX. **Recommended Action: **None {style="margin-left:40px"}** -> -> #### 5. BXD88 sequence-based genotypes do not correlate well with either of the two array-based genotype files (r = 0.50 and 0.54). Like BXD53, BXD88 was rederived a second time by JAX and is now referred to formally at BXD88/2RwwJ (Stock 007110). BXD88 was admixed at some point in the last decade that has since been rederived. BXD88/2RwwJ is only available at JAX. **Recommended Action:**Sourcing BXD88/2RwwJ from JAX; do not treat as equivalent to old BXD88. {style="margin-left:40px"}** -> -> #### 6. BXD100 (JAX stock 007143) sequence-based genotypes correlates well with the older array-based genotypes (r = 0.96) but not so well with newer 2017 array data (r = 0.55). This suggests some admixture in the last decade at UTHSC that has since been fixed. **Recommended Action:**If you used BXD100s between 2006 and 2014, we recommend using genotypes from the older array-based file for this strain. If you are using new BXD100 animals sourced from JAX, then use the newer 2017 array-based genotypes or the sequence-based genotypes. {style="margin-left:40px"}** -> -> #### 7. BXD151 (UTHSC stock) sequence-based genotypes do not correlate with the array-based genotypes at all (r = -0.79 and -0.06). BXD151 sequence-based genotypes correlate very well with older array-based sequence for the now (formally) extinct BXD128a (r = 0.97 and 0.99 with the two array-based files). We need to check sequence of BXD151/RwwJ (JAX 029868). **Recommended Action:**None. It appears likely that BXD151 may be equivalent to what we used to call BXD128a. BXD128a is no longer officially available and we will retain the name BXD151. {style="margin-left:40px"}** -> -> #### 8. BXD155 (UTHSC stock) sequence-based genotypes do not correlate with arrays (r = 0.21 and 0.18). BXD155 has an excellent correlation with previous array-based genotypes for strain BXD152 (r = 0.95 and 0.95 with arrays, 0.99 with sequence). Likely reading error or strain swap at UTHSC. BXD152 (Stock 029869, non-agouti black coat color) can be obtained from JAX, but BXD155 (gray coat color) is not yet available from JAX. **Recommended Action:**Check with David Ashbrook or Rob Williams on whether this issue has been resolved. It seems likely that the BXD155 sample that we sequenced was actually at BXD152. {style="margin-left:40px"}** -> -> #### 9. BXD162 (UTHSC stock) sequence-based genotypes correlate poorly well with new array genotypes (r = 0.65 and 0.69). This strain also has a reasonable correlation with BXD170 in older array genotypes (r = 0.7). Possible admixture. BXD162 is not yet available from JAX. **Recommended Action:**Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. {style="margin-left:40px"}** -> -> #### 10. BXD194 (UTHSC stock) sequence-based genotypes correlated with BXD87 (JAX stock) sequence-based genotypes. Probably a sample error at UTHSC when preparing samples for sequencing. We need to check the JAX BXD194/RwwJ (Stock 030878). **Recommended Action:**Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. {style="margin-left:40px"}** - -> **2018-12-19: BXD Genotypes file status (December 2018)** -> -> In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, -> and Danny Arends released new genotype files for many of the original -> BXD strains (BXD1 through BXD102), and for all of the new strains -> (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs -> using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de -> Villena (University of North Carolina) and Gary Churchill (The Jackson -> Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with -> financial support from the University of Tennessee Center for -> Integrative and Translational Genomics. -> -> **Update**The new genotypes are now available in GeneNetwork as the -> [2019 Genotype -> file](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600). -> All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly -> and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 -> GigaMUGA and many other markers we have typed, only about 6800 are -> useful (informative) in defining recombination events in the current -> set of BXDs. These informative markers either define unique -> recombination patterns across the 198 BXD strains (including extinct -> strains) or they define the proximal and distal ends of regions that -> do not contain any known recombinations in the BXD family. -> -> This file provides consensus genotypes for 198 BXD strains and for the -> two progenitor strains and the reciprocal F1s. Of the 198 BXD strains, -> 191 are independent, whereas 7 are substrains (e.g., BXD48 and -> BXD48a). This file provides approximate locations of 10300 -> recombinations, an average of 52 per strain. Genotypes were generated -> using Affymetrix, MUGA, MegaMUGA, and GigaMUGA Illumina platforms. -> Microsatellites and eQTL genotypes were generated by the Williams/Lu -> laboratory. Unknown genotypes were imputed as B or D, or were called -> as H (heterozygous) if the genotype was uncertain. Genotypes were -> manually curated by RW Williams. Genotypes were smoothed to remove -> unlikely recombination events. Almost all recombinations are supported -> by multiple markers, although only one or two representative markers -> may be provided in this file. The original parent file -> (BXD\_El\_Grande\_Master\_Used\_to\_Proof\_Final\_Genotypes\_2016.xlxs) -> contains data for approximately 37000 markers. A subset of the most -> informative 7300 markers are included here. Genotypes for Chr Y and -> Chr M are provisional. -> -> The file does not include any markers for Chr Y or the mitochondrion. -> -> As of December 2018 GeneNetwork uses mm10 coordinates for mapping -> functions. -> -> (Updated Dec 19, 2018 by RW Williams) - -> **2018-09-12: GeneNetwork 1 will be supported in 2018 but GeneNetwork -> 2 will become the main production server** -> -> [GeneNetwork 2](http://gn2.genenetwork.org) is ready for testing and -> research projects. GeneNetwork 1 (GN1) and GeneNetwork 2 (GN2) share -> the a single database, but they use different code and algorithms for -> mapping and data analysis. There are some benefits of using GN2, -> including more powerful linear mixed model mapping methods that -> account for kinship structure. -> -> The interface of GN2 is still a work in progress. Please send any -> suggestion, requests, or bug reports to rwilliams@uthsc.edu. - -> **2018-09-12: Notes on new BXD names**. -> -> 1. [BXD73](http://jaxmice.jax.org/strain/007117), -> [BXD73a](http://jaxmice.jax.org/strain/007124) (original known as -> *BXD80*), and [BXD73b](http://jaxmice.jax.org/strain/007146) -> (originally known as *BXD103*) are genetically very similar. -> [BXD73](http://jaxmice.jax.org/strain/007117) and *BXD80* are -> genetically identical at 82264 of 100290 markers (82% identical by -> descent). [BXD73](http://jaxmice.jax.org/strain/007117) keeps its -> original name and JAX identifier number (JR\#7117), whereas -> *BXD80* is now referred to as -> [BXD73a](http://jaxmice.jax.org/strain/007124) (JR\#7124). -> [BXD73](http://jaxmice.jax.org/strain/007117) and BXD103 are -> genetically identical at 90917 of 100290 markers (90.6% identical -> by descent). *BXD103* is now referred to as -> [BXD73b](http://jaxmice.jax.org/strain/007146) (JR\#7146). -> 2. [BXD48](http://jaxmice.jax.org/strain/007097) and -> [BXD48a](http://jaxmice.jax.org/strain/007139) (originally known -> as *BXD96*) are sister substrains, and are genetically identical -> at 93485 of 100290 markers (93.2% identical by descent). -> [BXD48](http://jaxmice.jax.org/strain/007097) retains its original -> name and JAX identifier number (JAX JR\#7097) whereas BXD96 is now -> referred to as [BXD48a](http://jaxmice.jax.org/strain/007139) -> (JR\#7139). -> 3. [BXD65](http://jaxmice.jax.org/strain/007110), -> [BXD65a](http://jaxmice.jax.org/strain/007140) (originally known -> as *BXD97*), and [BXD65b](http://jaxmice.jax.org/strain/009677) -> (originally known as *BXD92*) are sister substrains. -> [BXD65](http://jaxmice.jax.org/strain/007110) and *BXD97* are -> genetically identical at 92225 of 100290 markers (92% identical by -> descent). *BXD97* is now referred to as -> [BXD65a](http://jaxmice.jax.org/strain/007140) (JR\#7140). -> [BXD65](http://jaxmice.jax.org/strain/007110) and *BXD92* are -> genetically identical at 6155 of 6459 markers (95.3% identical by -> descent). [BXD65](http://jaxmice.jax.org/strain/007110) retains -> its original name and JAX identifier (JR\#7110) whereas *BXD92* is -> now referred to as [BXD65b](http://jaxmice.jax.org/strain/009677) -> (JR\#9677). - -> **2018-09-08: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2 and raw -> data.** profiling by array entered into GeneNetwork. -> -> - [UConn-Rheaume Retina RGC (Sep18) scRNA-Seq -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=866) -> - [UConn-Rheaume Retina RGC (Sep18) scRNA-Seq -> Raw](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=865) -> - [UConn-Rheaume Retina RGC (Sep18) scRNA-Seq -> Siamak](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=867) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-08-23: HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog** -> profiling by array entered into GeneNetwork. -> -> - [HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) -> rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=864) -> - [HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) -> rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=863) -> - [HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) -> rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=862) -> - [HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) -> rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=861) -> - [HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) -> rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=860) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-08-14: EPFL/LISP BXD HFD+CD Liver Affy Mouse Gene 1.0 ST -> (Aug18) RMA** profiling by array entered into GeneNetwork. -> -> - [EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=859) -> - [EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=858) -> - [EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=857) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-08-10: NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2** profiling -> by array entered into GeneNetwork. -> -> - [NIA Aging BXD CD Liver RNA-Seq (Aug18) -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=856) -> - [NIA Aging BXD HFD Liver RNA-Seq (Aug18) -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=855) -> - [NIA Aging BXD CD+HFD Liver RNA-Seq (Aug18) -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=854) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-08-07: NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=853) -> - [NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=852) -> - [NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=851) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-08-06: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=850) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-04-27: JAX Retina (Apr18) RNA-Seq log2-Z** profiling by array -> entered into GeneNetwork. -> -> - [JAX Retina (Apr18) RNA-Seq -> log2-Z](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=847) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-04-11: UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq** profiling -> by array entered into GeneNetwork. -> -> - [UCSD AIL Prefrontal Cortex (Apr18) -> RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=846) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-04-11: UCSD AIL Striatum (Apr18) RNA-Seq** profiling by array -> entered into GeneNetwork. -> -> - [UCSD AIL Striatum (Apr18) -> RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=845) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-04-11: UCSD AIL Hippocampus (Apr18) RNA-Seq** profiling by -> array entered into GeneNetwork. -> -> - [UCSD AIL Hippocampus (Apr18) -> RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=844) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2018-01-04: UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 \*\*** -> profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=843) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-09-29: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=842) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-09-12: EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S -> GeneLevel Main (Sep17) RMA \*\*** profiling by array entered into -> GeneNetwork. -> -> - [EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main -> (Sep17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=841) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-09-12: EPFL/LISP BXD CD Gastrointestinal Affy Clariom S -> GeneLevel Main (Sep17) RMA \*\*** profiling by array entered into -> GeneNetwork. -> -> - [EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main -> (Sep17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=840) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-09-12: EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S -> GeneLevel Main (Sep17) RMA \*\*** profiling by array entered into -> GeneNetwork. -> -> - [EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel -> Main (Sep17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=839) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction -> B, HFD Cohorts (Mar 2017) log2** profiling by array entered into -> GeneNetwork. -> -> - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD -> Cohorts (Mar 2017) -> log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=838) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction -> B, Chow Diet Cohorts (Mar 2017) log2** profiling by array entered into -> GeneNetwork. -> -> - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow -> Diet Cohorts (Mar 2017) -> log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=837) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction -> A, HFD Cohorts (Mar 2017) log2** profiling by array entered into -> GeneNetwork. -> -> - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD -> Cohorts (Mar 2017) -> log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=836) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction -> A, Chow Diet Cohorts (Mar 2017) log2** profiling by array entered into -> GeneNetwork. -> -> - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, Chow -> Diet Cohorts (Mar 2017) -> log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=835) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-04-27: INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) -> RMA** profiling by array entered into GeneNetwork. -> -> - [INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=834) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-05-05: INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=833) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-05-05: INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel -> (Apr17) RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) -> RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=832) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-05-05: INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel -> (Mar18) RMA** profiling by array entered into GeneNetwork. -> -> - [INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel (Mar18) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=831) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-04-28: INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) -> RMA** profiling by array entered into GeneNetwork. -> -> - [INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=830) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-25: UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level -> (Mar17) RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) -> RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=829) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-26: UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=828) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-27: UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level -> (Mar17) RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=827) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-28: UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=826) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-29: UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level -> (Mar17) RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) -> RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=825) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-24: UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA -> \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=824) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-02: UCLA CXB Liver Affy M430 2.0 (Jan16) RMA** profiling by -> array entered into GeneNetwork. -> -> - [UCLA CXB Liver Affy M430 2.0 (Jan16) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=823) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-02: UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA** profiling -> by array entered into GeneNetwork. -> -> - [UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=822) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-02: UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA** profiling by -> array entered into GeneNetwork. -> -> - [UCLA CXB Aorta Affy M430 2.0 (Jan16) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=821) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-02: UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA** profiling -> by array entered into GeneNetwork. -> -> - [UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=820) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-02: UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA** profiling by -> array entered into GeneNetwork. -> -> - [UCLA BXD Aorta Affy M430 2.0 (Jan16) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=819) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-03-02: UCLA BXD Liver Affy M430 2.0 (Jan16) RMA** profiling by -> array entered into GeneNetwork. -> -> - [UCLA BXD Liver Affy M430 2.0 (Jan16) -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=818) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-02-04: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 -> Z-score** profiling by array entered into GeneNetwork. -> -> - [UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 -> Z-score](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=813) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-02-04: UCSD CFW Striatum (Jan17) RNA-Seq Log2 Z-score** -> profiling by array entered into GeneNetwork. -> -> - [UCSD CFW Striatum (Jan17) RNA-Seq Log2 -> Z-score](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=812) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-02-04: UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 Z-score** -> profiling by array entered into GeneNetwork. -> -> - [UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 -> Z-score](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=811) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-01-17: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq** profiling -> by array entered into GeneNetwork. -> -> - [UCSD CFW Prefrontal Cortex (Jan17) -> RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=810) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-01-17: UCSD CFW Striatum (Jan17) RNA-Seq** profiling by array -> entered into GeneNetwork. -> -> - [UCSD CFW Striatum (Jan17) -> RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=809) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2017-01-17: UCSD CFW Hippocampus (Jan17) RNA-Seq** profiling by -> array entered into GeneNetwork. -> -> - [UCSD CFW Hippocampus (Jan17) -> RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=808) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2016-11-28: EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) -> RMA Exon Level** profiling by array entered into GeneNetwork. -> -> - [EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon -> Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=849) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2016-11-28: EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) -> RMA Exon Level** profiling by array entered into GeneNetwork. -> -> - [EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon -> Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=848) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2016-11-04: UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA \*\*** -> profiling by array entered into GeneNetwork. -> -> - [UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=806) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2016-10-02: BXD Genotypes file status (October 2016)** -> -> In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, -> and Danny Arends released new genotype files for many of the original -> BXD strains (BXD1 through BXD102), and for all of the new strains -> (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs -> using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de -> Villena (University of North Carolina) and Gary Churchill (The Jackson -> Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with -> financial support from the University of Tennessee Center for -> Integrative and Translational Genomics. -> -> The new genotypes are now available in GeneNetwork as the [2017 -> Genotype -> file](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600). -> All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly -> and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 -> GigaMUGA and many other markers we have typed, only about 6800 are -> useful (informative) in defining recombination events in the current -> set of BXDs. These informative markers either define unique -> recombination patterns across the 198 BXD strains (including extinct -> strains) or they define the proximal and distal ends of regions that -> do not contain any known recombinations in the BXD family. -> -> The file does not include any markers for Chr Y or the mitochondrion. -> -> As of October 2016 GeneNetwork still uses mm9 coordinates for mapping -> functions. -> -> (Updated Oct 2, 2016 by RW Williams) - -> **2016-09-29: TIGEM Human Retina RNA-Seq (Sep16) RPKM log2** profiling -> by array entered into GeneNetwork. -> -> - [TIGEM Human Retina RNA-Seq (Sep16) RPKM -> log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=802) -> -> This dataset is public available, please contact [Michele -> Pinelli](mailto:banfi@tigem.it) at [Telethon Institute of Genetics and -> Medicine (TIGEM)](http://www.tigem.it) for further information. -> (Implemented by Michele Pinelli, Arthur Centeno and Rob Williams). - -> **2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=804) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level -> RMA \*\*** profiling by array entered into GeneNetwork. -> -> - [UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=803) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2016-07-26: Raw and processed data from our Hippocampus studies -> based on publication "Genetics of the hippocampal transcriptome in -> mouse: a systematic survey and online neurogenomics resource" can be -> accessed now through GEO series GSE84767.** -> -> - [Data Set Group: Hippocampus Consortium -> M430v2](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84767) -> Pubmed ID:[20582282](http://www.ncbi.nlm.nih.gov/pubmed/20582282) -> - have been assigned with a [GEO Series record -> GSE84767](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84767) -> which provides access to all of the data and is the accession that -> should be quoted in any manuscript discussing the data. - -> **2016-07-16: Gene expression data for 39 inbred mice strains for CD4+ -> T cells** profiling by array entered into GeneNetwork. -> -> - [HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Gene -> Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=801) -> - [HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Exon -> Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=804) -> -> [GEO Series: -> GSE60337](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60337). -> To determine the breadth and underpinning of changes in immunocyte -> gene expression due to genetic variation in mice, we performed, as -> part of the Immunological Genome Project, gene expression profiling -> for CD4(+) T cells and neutrophils purified from 39 inbred strains of -> the Mouse Phenome Database. - -> **2016-05-16: FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST -> (May16) log2** profiling by array entered into GeneNetwork. -> -> - [FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=799) -> -> Currently this dataset is confidential, please contact [Michal -> Pravenec](mailto:pravenec%20@%20biomed.cas.cz) Czech Academy of -> Sciences for further information. (Implemented by Michal Pravenec, -> Arthur Centeno and Rob Williams). - -> **2016-04-16: EPFL/ETHZ BXD Brown Adipose Proteome (Apr16)** profiling -> by array entered into GeneNetwork. -> -> - [EPFL/ETHZ BXD Brown Adipose, Isolated Mitochondria Proteome, Chow -> Diet (Apr16) Light SWATH -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=798) -> - [EPFL/ETHZ BXD Brown Adipose, Total Tissue Proteome, Chow Diet -> (Apr16) Light SWATH -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=797) -> -> Currently this dataset is confidential, please contact [Johan -> Auwerx](mailto:admin.auwerx@epfl.ch) Ecole Polytechnique Federale de -> Lausanne for further information. (Implemented by Johan Auwerx, Arthur -> Centeno and Rob Williams). - -> **2016-04-16: DoD TATRC Retina Affy MoGene 2.0 ST** profiling by array -> entered into GeneNetwork. -> -> - [DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA -> Exon Level -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=796) -> - [DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA -> Gene Level -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=787) -> - [DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Exon Level -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=786) -> - [DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Gene Level -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=785) -> -> Currently this dataset is confidential, please contact [Eldon -> Geisert](mailto:egeiser@emory.edu) Emory Eye Center for further -> information. (Implemented by Eldon Geisert, Arthur Centeno and Rob -> Williams). - -> **2016-04-16: VCU BXD NAc EtOH vs CIE Air M430 2.0** profiling by -> array entered into GeneNetwork. -> -> - [VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=795) -> - [VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=794) -> - [VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=793) -> - [VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=792) -> - [VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=791) -> - [VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=790) -> - [VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=789) -> - [VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=788) -> -> Currently this dataset is confidential, please contact [Michael -> Miles](mailto:mfmiles@vcu.edu) Virginia Commonwealth University for -> further information. (Implemented by Michael Miles, Arthur Centeno and -> Rob Williams). - -> **2016-02-16: UCAMC LXS Whole Brain Saline and Ethanol RNA Sequence -> FPKM** profiling by array entered into GeneNetwork. -> -> - [UCAMC LXS Whole Brain Saline RNA Sequence (Feb16) FPKM -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=784) -> - [UCAMC LXS Whole Brain Ethanol RNA Sequence (Feb16) FPKM -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=784) -> -> Currently this dataset is confidential, please contact [Richard -> Radcliffe](mailto:richard.radcliffe@ucdenver.edu) University of -> Colorado at Denver for further information. (Implemented by Richard -> Radcliffe, Arthur Centeno and Rob Williams). - -> **2016-02-16: UTHSC Hippocampus Illumina v6.1 NOS, NOE, RSS, and RSE -> data sets** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb16) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=782) -> - [UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb16) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=781) -> - [UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb16) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=780) -> -> 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](http://www.nervenet.org/papers/Ziebarth-EtOH.pdf) or the -> original paper that used this paradigm by Kerns RT, Ravindranathan A, -> Hassan S, Cage MP, York T, Williams RW, Miles MF -> ([2005](http://www.jneurosci.org/cgi/reprint/25/9/2255)) -> 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. -> -> Please contact [Rob Williams](mailto:rwilliams@uthsc.edu) University -> of Tennessee Health Science Center for further information. -> (Implemented by Lu Lu, Arthur Centeno and Rob Williams). - -> **2016-02-16: EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 -> GeneLevel Main (Feb16) RMA** profiling by array entered into -> GeneNetwork. -> -> - [EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level Main -> (Feb16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=779) -> - [EPFL/LISP BXD HFD Subcutaneous WAT Affy MTA 1.0 Gene Level Main -> (Feb16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=778) -> - [EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 Gene Level -> Main (Feb16) RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=777) -> -> The BXD genetic reference population is a recombinant inbred panel -> descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains -> of mice, which segregate for about 5 million sequence variants. -> Recently, some these variants have been established with effects on -> general metabolic phenotypes such as glucose response and bone -> strength. In this study, we examined both genetic variants across 40 -> strains of BXD and the two founder lines, in addition to a major -> environmental influence—long term feeding with chow diet (CD) or high -> fat diet (HFD)—to see how metabolic gene expression varies by genotype -> and environment, and gene-by-environment interactions. The basic heart -> phenotypes quantified in these cohorts were not affected by HFD -> feeding (e.g. blood pressure and heart rate). -> -> Currently this dataset is confidential, please contact [Johan -> Auwerx](mailto:admin.auwerx@epfl.ch) Ecole Polytechnique Federale de -> Lausanne for further information. (Implemented by Johan Auwerx, Arthur -> Centeno and Rob Williams). - -> **2015-12-09: INIA LCM (11 Regions) RNA-seq Transcript Level (Dec15)** -> profiling by array entered into GeneNetwork. -> -> - [INIA LCM (11 Regions) CIE/AIR/BAS RNA-seq Transcript Level -> (Dec15)](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=776) -> - [INIA LCM (11 Regions) BASELINE RNA-seq Transcript Level -> (Dec15)](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=775) -> - [INIA LCM (11 Regions) CIE/AIR RNA-seq Transcript Level -> (Dec15)](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=772) -> -> This dataset is now public, please contact [Megan -> Mulligan](mailto:mmulliga@uthsc.edu) University of Tennessee Health -> Science Center for further information. (Implemented by Megan -> Mulligan, Arthur Centeno and Rob Williams). - -> **2015-12-07: UTHSC Affy MoGene 1.0 ST Spleen** profiling by array -> entered into GeneNetwork. -> -> - [UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA -> Set2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=774) -> - [UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA -> Set1](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=773) -> -> This is a preliminary release with known errors 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. 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").This -> dataset is now public, please contact [Robert -> Williams](mailto:rwilliams@uthsc.edu) University of Tennessee Health -> Science Center for further information. (Implemented by Lu Lu, Arthur -> Centeno and Rob Williams). - -> **2015-11-10: Hippocampus Mouse Transcriptome Assay 1.0 GeneLevel Main -> (Nov15) RMA** profiling by array entered into GeneNetwork. -> -> - [Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Main (Nov15) -> RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=771) -> -> Please contact [Megan Mulligan](mailto:mmulliga@uthsc.edu) University -> of Tennessee Health Science Center for further information. -> (Implemented by Megan Mulligan, Arthur Centeno and Rob Williams). - -> **2015-10-13: UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) -> RankInv** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=817) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2015-10-14: UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) -> RankInv** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=816) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2015-10-15: UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) -> RankInv** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=815) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2015-10-16: UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) -> RankInv** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) -> RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=814) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. - -> **2015-09-14: The Genotype-Tissue Expression (GTEx)** is providing a -> comprehensive atlas of gene expression and regulation across 53 human -> tissues. The latest GTEx data release (**dbGaP release -> phs000424.v5.p1**) is now available on GeneNetwork. -> -> - [All 53 Tissues, RNA-Seq GTEx dbGaP release -> phs000424.v5.p1](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=770) -> -> Note: Please disregard confusing legend provided in Study tab of the -> study page which claims that study contains 552 subjects with -> genotypes - those totals are counts of subjects with all molecular -> data types, not just molecular genotypes. -> -> More detailed representation of subject counts in molecular datasets -> (including genotypes) may be found in 'Molecular Data' tab at [Common -> Fund (CF) Genotype-Tissue Expression Project (GTEx) dbGaP Study -> Accession: -> phs000424.v5.p1](http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/molecular.cgi?study_id=phs000424.v5.p1). - -> **2015-05-30: UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST -> (Jun15) Exon Level RMA** profiling by array entered into GeneNetwork. -> -> - [UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) Exon -> Level -> RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=805) -> -> This dataset is publicly available in most cases. For more information -> on how to access the data please refer to the link above. + **2019-Sep-24: BXD Genotypes file: Sequence-based improvements coming + soon** + + The BXD sequencing consortium has generated full genome sequence for + 152 extant BXD strains. Dr. David Ashbrook has extracted the most + informative 40,000 SNPs from sequence data, and compared + sequence-based genotypes with those based on array platforms (see + entries below). In general there is excellent concordance for all but + a handful of the BXD strains that are in widespread use (BXD1 to + BXD102). However, there are some problems and mixups that we list + below. We are currently working on harmonizing data when possible, and + understanding and fixing errors, when not. + + This evaluation of genotypes is based on data extracted from whole-genome sequencing of BXD male spleen samples obtained in January 2017 from the Jackson Laboratory whenever possible, and from the UTHSC colony in all other cases. All animals were born between January and December 2016. + + #### 1. BXD65b (sourced from JAX). The sequence-based genotypes correlate better to array-based 2017 genotypes of BXD65 and BXD65a than with the BXD65b array-based genotypes. It is possible that there are two somewhat distinct sub-strains now called BXD65b—one at JAX and one at UTHSC. **Recommended Action:**Sourcing BXD65b animals from JAX. {style="margin-left:40px"}** + + #### 2. BXD53 array-based genotypes do not correlate well with sequence-based genotypes for BXD53/2. BXD53 was rederived a second time by JAX and is now referred to formally at BXD53/2RwwJ (Stock 017749). The likely reason for the discrepancy is that we sequenced BXD53/2RwwJ (Stock 017749) rather than the older BXD53 (sourced from UTHSC) for array-based genotyping. BXD53 sequence-based genotypes correlate well with eQTL data for BXD53. **Recommended Action:**If using BXD53/2RwwJ, please obtain current sequence-based genotypes from David Ashbrook. {style="margin-left:40px"}** + + #### 3. BXD68 animals at UTHSC used from about 2012 to 2017 were BXD34 animals. Genotypes in the 2017 array-based file HAVE or HAVE NOT been corrected. We have corrected this error in some phenotype data sets. BXD68 from The Jackson Laboratory are genuine BXD68. We sequenced BXD68 DNA from JAX. **Recommended Action: **None unless you have used BXD68 animals obtained from UTHSC between 2012 and 2017. If so, these animals should be relabeled BXD34. {style="margin-left:40px"}** + + #### 4. BXD81 sequence-based genotypes correlate well with the new array-based genotypes (r = 0.81) but less well with old array-based genotypes (r = 0.66). This is presumably due to more complete inbreeding. The new sequence-based genotypes are for BXD81 sources from JAX. **Recommended Action: **None {style="margin-left:40px"}** + + #### 5. BXD88 sequence-based genotypes do not correlate well with either of the two array-based genotype files (r = 0.50 and 0.54). Like BXD53, BXD88 was rederived a second time by JAX and is now referred to formally at BXD88/2RwwJ (Stock 007110). BXD88 was admixed at some point in the last decade that has since been rederived. BXD88/2RwwJ is only available at JAX. **Recommended Action:**Sourcing BXD88/2RwwJ from JAX; do not treat as equivalent to old BXD88. {style="margin-left:40px"}** + + #### 6. BXD100 (JAX stock 007143) sequence-based genotypes correlates well with the older array-based genotypes (r = 0.96) but not so well with newer 2017 array data (r = 0.55). This suggests some admixture in the last decade at UTHSC that has since been fixed. **Recommended Action:**If you used BXD100s between 2006 and 2014, we recommend using genotypes from the older array-based file for this strain. If you are using new BXD100 animals sourced from JAX, then use the newer 2017 array-based genotypes or the sequence-based genotypes. {style="margin-left:40px"}** + + #### 7. BXD151 (UTHSC stock) sequence-based genotypes do not correlate with the array-based genotypes at all (r = -0.79 and -0.06). BXD151 sequence-based genotypes correlate very well with older array-based sequence for the now (formally) extinct BXD128a (r = 0.97 and 0.99 with the two array-based files). We need to check sequence of BXD151/RwwJ (JAX 029868). **Recommended Action:**None. It appears likely that BXD151 may be equivalent to what we used to call BXD128a. BXD128a is no longer officially available and we will retain the name BXD151. {style="margin-left:40px"}** + + #### 8. BXD155 (UTHSC stock) sequence-based genotypes do not correlate with arrays (r = 0.21 and 0.18). BXD155 has an excellent correlation with previous array-based genotypes for strain BXD152 (r = 0.95 and 0.95 with arrays, 0.99 with sequence). Likely reading error or strain swap at UTHSC. BXD152 (Stock 029869, non-agouti black coat color) can be obtained from JAX, but BXD155 (gray coat color) is not yet available from JAX. **Recommended Action:**Check with David Ashbrook or Rob Williams on whether this issue has been resolved. It seems likely that the BXD155 sample that we sequenced was actually at BXD152. {style="margin-left:40px"}** + + #### 9. BXD162 (UTHSC stock) sequence-based genotypes correlate poorly well with new array genotypes (r = 0.65 and 0.69). This strain also has a reasonable correlation with BXD170 in older array genotypes (r = 0.7). Possible admixture. BXD162 is not yet available from JAX. **Recommended Action:**Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. {style="margin-left:40px"}** + + #### 10. BXD194 (UTHSC stock) sequence-based genotypes correlated with BXD87 (JAX stock) sequence-based genotypes. Probably a sample error at UTHSC when preparing samples for sequencing. We need to check the JAX BXD194/RwwJ (Stock 030878). **Recommended Action:**Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. {style="margin-left:40px"}** + + **2018-12-19: BXD Genotypes file status (December 2018)** + + In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, + and Danny Arends released new genotype files for many of the original + BXD strains (BXD1 through BXD102), and for all of the new strains + (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs + using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de + Villena (University of North Carolina) and Gary Churchill (The Jackson + Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with + financial support from the University of Tennessee Center for + Integrative and Translational Genomics. + + **Update**The new genotypes are now available in GeneNetwork as the + [2019 Genotype + file](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600). + All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly + and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 + GigaMUGA and many other markers we have typed, only about 6800 are + useful (informative) in defining recombination events in the current + set of BXDs. These informative markers either define unique + recombination patterns across the 198 BXD strains (including extinct + strains) or they define the proximal and distal ends of regions that + do not contain any known recombinations in the BXD family. + + This file provides consensus genotypes for 198 BXD strains and for the + two progenitor strains and the reciprocal F1s. Of the 198 BXD strains, + 191 are independent, whereas 7 are substrains (e.g., BXD48 and + BXD48a). This file provides approximate locations of 10300 + recombinations, an average of 52 per strain. Genotypes were generated + using Affymetrix, MUGA, MegaMUGA, and GigaMUGA Illumina platforms. + Microsatellites and eQTL genotypes were generated by the Williams/Lu + laboratory. Unknown genotypes were imputed as B or D, or were called + as H (heterozygous) if the genotype was uncertain. Genotypes were + manually curated by RW Williams. Genotypes were smoothed to remove + unlikely recombination events. Almost all recombinations are supported + by multiple markers, although only one or two representative markers + may be provided in this file. The original parent file + (BXD\_El\_Grande\_Master\_Used\_to\_Proof\_Final\_Genotypes\_2016.xlxs) + contains data for approximately 37000 markers. A subset of the most + informative 7300 markers are included here. Genotypes for Chr Y and + Chr M are provisional. + + The file does not include any markers for Chr Y or the mitochondrion. + + As of December 2018 GeneNetwork uses mm10 coordinates for mapping + functions. + + (Updated Dec 19, 2018 by RW Williams) + + **2018-09-12: GeneNetwork 1 will be supported in 2018 but GeneNetwork + 2 will become the main production server** + + [GeneNetwork 2](http://gn2.genenetwork.org) is ready for testing and + research projects. GeneNetwork 1 (GN1) and GeneNetwork 2 (GN2) share + the a single database, but they use different code and algorithms for + mapping and data analysis. There are some benefits of using GN2, + including more powerful linear mixed model mapping methods that + account for kinship structure. + + The interface of GN2 is still a work in progress. Please send any + suggestion, requests, or bug reports to rwilliams@uthsc.edu. + + **2018-09-12: Notes on new BXD names**. + + 1. [BXD73](http://jaxmice.jax.org/strain/007117), + [BXD73a](http://jaxmice.jax.org/strain/007124) (original known as + *BXD80*), and [BXD73b](http://jaxmice.jax.org/strain/007146) + (originally known as *BXD103*) are genetically very similar. + [BXD73](http://jaxmice.jax.org/strain/007117) and *BXD80* are + genetically identical at 82264 of 100290 markers (82% identical by + descent). [BXD73](http://jaxmice.jax.org/strain/007117) keeps its + original name and JAX identifier number (JR\#7117), whereas + *BXD80* is now referred to as + [BXD73a](http://jaxmice.jax.org/strain/007124) (JR\#7124). + [BXD73](http://jaxmice.jax.org/strain/007117) and BXD103 are + genetically identical at 90917 of 100290 markers (90.6% identical + by descent). *BXD103* is now referred to as + [BXD73b](http://jaxmice.jax.org/strain/007146) (JR\#7146). + 2. [BXD48](http://jaxmice.jax.org/strain/007097) and + [BXD48a](http://jaxmice.jax.org/strain/007139) (originally known + as *BXD96*) are sister substrains, and are genetically identical + at 93485 of 100290 markers (93.2% identical by descent). + [BXD48](http://jaxmice.jax.org/strain/007097) retains its original + name and JAX identifier number (JAX JR\#7097) whereas BXD96 is now + referred to as [BXD48a](http://jaxmice.jax.org/strain/007139) + (JR\#7139). + 3. [BXD65](http://jaxmice.jax.org/strain/007110), + [BXD65a](http://jaxmice.jax.org/strain/007140) (originally known + as *BXD97*), and [BXD65b](http://jaxmice.jax.org/strain/009677) + (originally known as *BXD92*) are sister substrains. + [BXD65](http://jaxmice.jax.org/strain/007110) and *BXD97* are + genetically identical at 92225 of 100290 markers (92% identical by + descent). *BXD97* is now referred to as + [BXD65a](http://jaxmice.jax.org/strain/007140) (JR\#7140). + [BXD65](http://jaxmice.jax.org/strain/007110) and *BXD92* are + genetically identical at 6155 of 6459 markers (95.3% identical by + descent). [BXD65](http://jaxmice.jax.org/strain/007110) retains + its original name and JAX identifier (JR\#7110) whereas *BXD92* is + now referred to as [BXD65b](http://jaxmice.jax.org/strain/009677) + (JR\#9677). + + **2018-09-08: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2 and raw + data.** profiling by array entered into GeneNetwork. + + - [UConn-Rheaume Retina RGC (Sep18) scRNA-Seq + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=866) + - [UConn-Rheaume Retina RGC (Sep18) scRNA-Seq + Raw](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=865) + - [UConn-Rheaume Retina RGC (Sep18) scRNA-Seq + Siamak](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=867) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-08-23: HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog** + profiling by array entered into GeneNetwork. + + - [HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) + rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=864) + - [HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) + rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=863) + - [HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) + rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=862) + - [HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) + rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=861) + - [HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) + rlog](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=860) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-08-14: EPFL/LISP BXD HFD+CD Liver Affy Mouse Gene 1.0 ST + (Aug18) RMA** profiling by array entered into GeneNetwork. + + - [EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=859) + - [EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=858) + - [EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=857) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-08-10: NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2** profiling + by array entered into GeneNetwork. + + - [NIA Aging BXD CD Liver RNA-Seq (Aug18) + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=856) + - [NIA Aging BXD HFD Liver RNA-Seq (Aug18) + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=855) + - [NIA Aging BXD CD+HFD Liver RNA-Seq (Aug18) + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=854) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-08-07: NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) + RMA \*\*** profiling by array entered into GeneNetwork. + + - [NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=853) + - [NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=852) + - [NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=851) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-08-06: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) + RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=850) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-04-27: JAX Retina (Apr18) RNA-Seq log2-Z** profiling by array + entered into GeneNetwork. + + - [JAX Retina (Apr18) RNA-Seq + log2-Z](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=847) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-04-11: UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq** profiling + by array entered into GeneNetwork. + + - [UCSD AIL Prefrontal Cortex (Apr18) + RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=846) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-04-11: UCSD AIL Striatum (Apr18) RNA-Seq** profiling by array + entered into GeneNetwork. + + - [UCSD AIL Striatum (Apr18) + RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=845) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-04-11: UCSD AIL Hippocampus (Apr18) RNA-Seq** profiling by + array entered into GeneNetwork. + + - [UCSD AIL Hippocampus (Apr18) + RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=844) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2018-01-04: UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 \*\*** + profiling by array entered into GeneNetwork. + + - [UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=843) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-09-29: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) + RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=842) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-09-12: EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S + GeneLevel Main (Sep17) RMA \*\*** profiling by array entered into + GeneNetwork. + + - [EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main + (Sep17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=841) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-09-12: EPFL/LISP BXD CD Gastrointestinal Affy Clariom S + GeneLevel Main (Sep17) RMA \*\*** profiling by array entered into + GeneNetwork. + + - [EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main + (Sep17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=840) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-09-12: EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S + GeneLevel Main (Sep17) RMA \*\*** profiling by array entered into + GeneNetwork. + + - [EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel + Main (Sep17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=839) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction + B, HFD Cohorts (Mar 2017) log2** profiling by array entered into + GeneNetwork. + + - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD + Cohorts (Mar 2017) + log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=838) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction + B, Chow Diet Cohorts (Mar 2017) log2** profiling by array entered into + GeneNetwork. + + - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow + Diet Cohorts (Mar 2017) + log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=837) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction + A, HFD Cohorts (Mar 2017) log2** profiling by array entered into + GeneNetwork. + + - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD + Cohorts (Mar 2017) + log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=836) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction + A, Chow Diet Cohorts (Mar 2017) log2** profiling by array entered into + GeneNetwork. + + - [UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, Chow + Diet Cohorts (Mar 2017) + log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=835) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-04-27: INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) + RMA** profiling by array entered into GeneNetwork. + + - [INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=834) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-05-05: INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) + RMA \*\*** profiling by array entered into GeneNetwork. + + - [INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=833) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-05-05: INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel + (Apr17) RMA \*\*** profiling by array entered into GeneNetwork. + + - [INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) + RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=832) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-05-05: INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel + (Mar18) RMA** profiling by array entered into GeneNetwork. + + - [INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel (Mar18) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=831) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-04-28: INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) + RMA** profiling by array entered into GeneNetwork. + + - [INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=830) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-25: UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level + (Mar17) RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) + RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=829) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-26: UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) + RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=828) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-27: UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level + (Mar17) RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=827) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-28: UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) + RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=826) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-29: UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level + (Mar17) RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) + RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=825) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-24: UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA + \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=824) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-02: UCLA CXB Liver Affy M430 2.0 (Jan16) RMA** profiling by + array entered into GeneNetwork. + + - [UCLA CXB Liver Affy M430 2.0 (Jan16) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=823) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-02: UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA** profiling + by array entered into GeneNetwork. + + - [UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=822) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-02: UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA** profiling by + array entered into GeneNetwork. + + - [UCLA CXB Aorta Affy M430 2.0 (Jan16) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=821) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-02: UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA** profiling + by array entered into GeneNetwork. + + - [UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=820) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-02: UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA** profiling by + array entered into GeneNetwork. + + - [UCLA BXD Aorta Affy M430 2.0 (Jan16) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=819) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-03-02: UCLA BXD Liver Affy M430 2.0 (Jan16) RMA** profiling by + array entered into GeneNetwork. + + - [UCLA BXD Liver Affy M430 2.0 (Jan16) + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=818) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-02-04: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 + Z-score** profiling by array entered into GeneNetwork. + + - [UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 + Z-score](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=813) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-02-04: UCSD CFW Striatum (Jan17) RNA-Seq Log2 Z-score** + profiling by array entered into GeneNetwork. + + - [UCSD CFW Striatum (Jan17) RNA-Seq Log2 + Z-score](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=812) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-02-04: UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 Z-score** + profiling by array entered into GeneNetwork. + + - [UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 + Z-score](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=811) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-01-17: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq** profiling + by array entered into GeneNetwork. + + - [UCSD CFW Prefrontal Cortex (Jan17) + RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=810) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-01-17: UCSD CFW Striatum (Jan17) RNA-Seq** profiling by array + entered into GeneNetwork. + + - [UCSD CFW Striatum (Jan17) + RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=809) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2017-01-17: UCSD CFW Hippocampus (Jan17) RNA-Seq** profiling by + array entered into GeneNetwork. + + - [UCSD CFW Hippocampus (Jan17) + RNA-Seq](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=808) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2016-11-28: EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) + RMA Exon Level** profiling by array entered into GeneNetwork. + + - [EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon + Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=849) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2016-11-28: EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) + RMA Exon Level** profiling by array entered into GeneNetwork. + + - [EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon + Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=848) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2016-11-04: UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA \*\*** + profiling by array entered into GeneNetwork. + + - [UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=806) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2016-10-02: BXD Genotypes file status (October 2016)** + + In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, + and Danny Arends released new genotype files for many of the original + BXD strains (BXD1 through BXD102), and for all of the new strains + (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs + using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de + Villena (University of North Carolina) and Gary Churchill (The Jackson + Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with + financial support from the University of Tennessee Center for + Integrative and Translational Genomics. + + The new genotypes are now available in GeneNetwork as the [2017 + Genotype + file](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600). + All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly + and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 + GigaMUGA and many other markers we have typed, only about 6800 are + useful (informative) in defining recombination events in the current + set of BXDs. These informative markers either define unique + recombination patterns across the 198 BXD strains (including extinct + strains) or they define the proximal and distal ends of regions that + do not contain any known recombinations in the BXD family. + + The file does not include any markers for Chr Y or the mitochondrion. + + As of October 2016 GeneNetwork still uses mm9 coordinates for mapping + functions. + + (Updated Oct 2, 2016 by RW Williams) + + **2016-09-29: TIGEM Human Retina RNA-Seq (Sep16) RPKM log2** profiling + by array entered into GeneNetwork. + + - [TIGEM Human Retina RNA-Seq (Sep16) RPKM + log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=802) + + This dataset is public available, please contact [Michele + Pinelli](mailto:banfi@tigem.it) at [Telethon Institute of Genetics and + Medicine (TIGEM)](http://www.tigem.it) for further information. + (Implemented by Michele Pinelli, Arthur Centeno and Rob Williams). + + **2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level + RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=804) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level + RMA \*\*** profiling by array entered into GeneNetwork. + + - [UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=803) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2016-07-26: Raw and processed data from our Hippocampus studies + based on publication "Genetics of the hippocampal transcriptome in + mouse: a systematic survey and online neurogenomics resource" can be + accessed now through GEO series GSE84767.** + + - [Data Set Group: Hippocampus Consortium + M430v2](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84767) + Pubmed ID:[20582282](http://www.ncbi.nlm.nih.gov/pubmed/20582282) + - have been assigned with a [GEO Series record + GSE84767](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84767) + which provides access to all of the data and is the accession that + should be quoted in any manuscript discussing the data. + + **2016-07-16: Gene expression data for 39 inbred mice strains for CD4+ + T cells** profiling by array entered into GeneNetwork. + + - [HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Gene + Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=801) + - [HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Exon + Level](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=804) + + [GEO Series: + GSE60337](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60337). + To determine the breadth and underpinning of changes in immunocyte + gene expression due to genetic variation in mice, we performed, as + part of the Immunological Genome Project, gene expression profiling + for CD4(+) T cells and neutrophils purified from 39 inbred strains of + the Mouse Phenome Database. + + **2016-05-16: FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST + (May16) log2** profiling by array entered into GeneNetwork. + + - [FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=799) + + Currently this dataset is confidential, please contact [Michal + Pravenec](mailto:pravenec%20@%20biomed.cas.cz) Czech Academy of + Sciences for further information. (Implemented by Michal Pravenec, + Arthur Centeno and Rob Williams). + + **2016-04-16: EPFL/ETHZ BXD Brown Adipose Proteome (Apr16)** profiling + by array entered into GeneNetwork. + + - [EPFL/ETHZ BXD Brown Adipose, Isolated Mitochondria Proteome, Chow + Diet (Apr16) Light SWATH + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=798) + - [EPFL/ETHZ BXD Brown Adipose, Total Tissue Proteome, Chow Diet + (Apr16) Light SWATH + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=797) + + Currently this dataset is confidential, please contact [Johan + Auwerx](mailto:admin.auwerx@epfl.ch) Ecole Polytechnique Federale de + Lausanne for further information. (Implemented by Johan Auwerx, Arthur + Centeno and Rob Williams). + + **2016-04-16: DoD TATRC Retina Affy MoGene 2.0 ST** profiling by array + entered into GeneNetwork. + + - [DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA + Exon Level + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=796) + - [DoD Retina Blast vs Normal Retina Affy MoGene 2.0 ST (Apr16) RMA + Gene Level + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=787) + - [DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Exon Level + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=786) + - [DoD Retina After Blast Affy MoGene 2.0 ST (Mar16) RMA Gene Level + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=785) + + Currently this dataset is confidential, please contact [Eldon + Geisert](mailto:egeiser@emory.edu) Emory Eye Center for further + information. (Implemented by Eldon Geisert, Arthur Centeno and Rob + Williams). + + **2016-04-16: VCU BXD NAc EtOH vs CIE Air M430 2.0** profiling by + array entered into GeneNetwork. + + - [VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=795) + - [VCU BXD NAc CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=794) + - [VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=793) + - [VCU BXD NAc CIE Air Masked ComBat M430 2.0 (Apr16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=792) + - [VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=791) + - [VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=790) + - [VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=789) + - [VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=788) + + Currently this dataset is confidential, please contact [Michael + Miles](mailto:mfmiles@vcu.edu) Virginia Commonwealth University for + further information. (Implemented by Michael Miles, Arthur Centeno and + Rob Williams). + + **2016-02-16: UCAMC LXS Whole Brain Saline and Ethanol RNA Sequence + FPKM** profiling by array entered into GeneNetwork. + + - [UCAMC LXS Whole Brain Saline RNA Sequence (Feb16) FPKM + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=784) + - [UCAMC LXS Whole Brain Ethanol RNA Sequence (Feb16) FPKM + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=784) + + Currently this dataset is confidential, please contact [Richard + Radcliffe](mailto:richard.radcliffe@ucdenver.edu) University of + Colorado at Denver for further information. (Implemented by Richard + Radcliffe, Arthur Centeno and Rob Williams). + + **2016-02-16: UTHSC Hippocampus Illumina v6.1 NOS, NOE, RSS, and RSE + data sets** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb16) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=782) + - [UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb16) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=781) + - [UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb16) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=780) + + 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](http://www.nervenet.org/papers/Ziebarth-EtOH.pdf) or the + original paper that used this paradigm by Kerns RT, Ravindranathan A, + Hassan S, Cage MP, York T, Williams RW, Miles MF + ([2005](http://www.jneurosci.org/cgi/reprint/25/9/2255)) + 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. + + Please contact [Rob Williams](mailto:rwilliams@uthsc.edu) University + of Tennessee Health Science Center for further information. + (Implemented by Lu Lu, Arthur Centeno and Rob Williams). + + **2016-02-16: EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 + GeneLevel Main (Feb16) RMA** profiling by array entered into + GeneNetwork. + + - [EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level Main + (Feb16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=779) + - [EPFL/LISP BXD HFD Subcutaneous WAT Affy MTA 1.0 Gene Level Main + (Feb16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=778) + - [EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 Gene Level + Main (Feb16) RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=777) + + The BXD genetic reference population is a recombinant inbred panel + descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains + of mice, which segregate for about 5 million sequence variants. + Recently, some these variants have been established with effects on + general metabolic phenotypes such as glucose response and bone + strength. In this study, we examined both genetic variants across 40 + strains of BXD and the two founder lines, in addition to a major + environmental influence—long term feeding with chow diet (CD) or high + fat diet (HFD)—to see how metabolic gene expression varies by genotype + and environment, and gene-by-environment interactions. The basic heart + phenotypes quantified in these cohorts were not affected by HFD + feeding (e.g. blood pressure and heart rate). + + Currently this dataset is confidential, please contact [Johan + Auwerx](mailto:admin.auwerx@epfl.ch) Ecole Polytechnique Federale de + Lausanne for further information. (Implemented by Johan Auwerx, Arthur + Centeno and Rob Williams). + + **2015-12-09: INIA LCM (11 Regions) RNA-seq Transcript Level (Dec15)** + profiling by array entered into GeneNetwork. + + - [INIA LCM (11 Regions) CIE/AIR/BAS RNA-seq Transcript Level + (Dec15)](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=776) + - [INIA LCM (11 Regions) BASELINE RNA-seq Transcript Level + (Dec15)](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=775) + - [INIA LCM (11 Regions) CIE/AIR RNA-seq Transcript Level + (Dec15)](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=772) + + This dataset is now public, please contact [Megan + Mulligan](mailto:mmulliga@uthsc.edu) University of Tennessee Health + Science Center for further information. (Implemented by Megan + Mulligan, Arthur Centeno and Rob Williams). + + **2015-12-07: UTHSC Affy MoGene 1.0 ST Spleen** profiling by array + entered into GeneNetwork. + + - [UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA + Set2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=774) + - [UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA + Set1](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=773) + + This is a preliminary release with known errors 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. 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").This + dataset is now public, please contact [Robert + Williams](mailto:rwilliams@uthsc.edu) University of Tennessee Health + Science Center for further information. (Implemented by Lu Lu, Arthur + Centeno and Rob Williams). + + **2015-11-10: Hippocampus Mouse Transcriptome Assay 1.0 GeneLevel Main + (Nov15) RMA** profiling by array entered into GeneNetwork. + + - [Hippocampus Mouse Transcriptome Assay 1.0 Gene Level Main (Nov15) + RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=771) + + Please contact [Megan Mulligan](mailto:mmulliga@uthsc.edu) University + of Tennessee Health Science Center for further information. + (Implemented by Megan Mulligan, Arthur Centeno and Rob Williams). + + **2015-10-13: UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) + RankInv** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=817) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2015-10-14: UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) + RankInv** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=816) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2015-10-15: UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) + RankInv** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=815) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2015-10-16: UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) + RankInv** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) + RankInv](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=814) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. + + **2015-09-14: The Genotype-Tissue Expression (GTEx)** is providing a + comprehensive atlas of gene expression and regulation across 53 human + tissues. The latest GTEx data release (**dbGaP release + phs000424.v5.p1**) is now available on GeneNetwork. + + - [All 53 Tissues, RNA-Seq GTEx dbGaP release + phs000424.v5.p1](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=770) + + Note: Please disregard confusing legend provided in Study tab of the + study page which claims that study contains 552 subjects with + genotypes - those totals are counts of subjects with all molecular + data types, not just molecular genotypes. + + More detailed representation of subject counts in molecular datasets + (including genotypes) may be found in 'Molecular Data' tab at [Common + Fund (CF) Genotype-Tissue Expression Project (GTEx) dbGaP Study + Accession: + phs000424.v5.p1](http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/molecular.cgi?study_id=phs000424.v5.p1). + + **2015-05-30: UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST + (Jun15) Exon Level RMA** profiling by array entered into GeneNetwork. + + - [UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) Exon + Level + RMA](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=805) + + This dataset is publicly available in most cases. For more information + on how to access the data please refer to the link above. * * * * * [See More News](#)\ -> > **2014-10-21: HZI Lung Flu Infected BXD (Nov16) RNA-Seq \*\*** -> > profiling by array entered into GeneNetwork. -> > -> > - [HZI Lung Flu Infected BXD (Nov16) RNA-Seq -> > \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=807) -> > -> > This dataset is publicly available in most cases. For more -> > information on how to access the data please refer to the link -> > above. -> -> **2014-10-10: BXD Elicited Peritoneal Neutrophils Gene Expression** -> profiling by array entered into GeneNetwork. -> -> - [UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) -> RMA -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=595) -> - [UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) -> RMA Exon Level -> \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=596) -> -> Currently this dataset is confidential, please contact [Marko -> Radic](mailto:mradic@uthsc.edu) University of Tennessee Health Science -> Center for further information. (Implemented by Marko Radic, Indira -> Neeli, Teruki Hagiwara, Arthur Centeno and Rob Williams). - -> **2014-08-29: Mouse Diversity Panel Hippocampus Antidepressant** -> profiling by array entered into GeneNetwork. -> -> - UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA -> \*\* -> -> Currently this dataset is confidential, please contact [Brooke -> Miller](mailto:brookemiller@ufl.edu) University of Florida for further -> information. (Implemented by Brooke Miller, Arthur Centeno and Rob -> Williams). - -> **2014-08-10: RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) Log2** -> profiling by array entered into GeneNetwork. -> -> - [RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=717) -> - [RTI RCMRC BXD Fecal Metabolites HFD (Aug14) -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=716) -> - [RTI RCMRC BXD Fecal Metabolites CD (Aug14) -> Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=715) -> -> The goal of this project is to study expression of a large set of -> defined and undefined metabolites in fecal samples from a genetically -> diverse set of BXD mouse strains (females) raised either on a high fat -> diet or low fat diet. Samples were taken from animals at sacrifices -> directly from the large intestine. -> -> Aim: Effect of genetics and diet on fecal metabolomics\ -> Use UPLC-MS Broad Spectrum Metabolomics to study:Mice fecal samples -> To capture the most signal, all samples were analyzed under positive -> and negative ion mode using a reversed-phase separation. Please -> contact [Robert Clark](mailto:rclark@rti.org) RTI International for -> further information. (Implemented by Robert Clark, Arthur Centeno and -> Rob Williams). - -> **2014-05-02: BXD Liver, Soluble Proteins CD and Hi-Fat Gene -> Expression** profiling by array entered into GeneNetwork. -> -> - EPFL/ETHZ BXD Liver, Soluble Proteins CD (May14) SWATH \*\* -> - EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH \*\* -> -> Currently this dataset is confidential, please contact [Johan -> Auwerx](mailto:admin.auwerx@epfl.ch) Ecole Polytechnique Federale de -> Lausanne for further information. (Implemented by Johan Auwerx, Evan -> Williams, Arthur Centeno and Rob Williams). - -> **2014-04-03: UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene -> Level (Apr14) RMA** profiling by array entered into GeneNetwork. -> -> - UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level -> (Apr14) RMA \*\* -> -> Currently this dataset is confidential, please contact [Dennis D -> Black](mailto:dblack@uthsc.edu) UT Le Bonheur Pediatric Specialists -> for further information. (Implemented by Dennis D Black, Arthur -> Centeno and Rob Williams). - -> **2014-03-07: The Genotype-Tissue Expression (GTEx)** is providing a -> comprehensive atlas of gene expression and regulation across multiple -> human tissues. The latest GTEx data release (dbGaP release -> phs000424.v4.p1) is now available on + **2014-10-21: HZI Lung Flu Infected BXD (Nov16) RNA-Seq \*\*** + profiling by array entered into GeneNetwork. + + - [HZI Lung Flu Infected BXD (Nov16) RNA-Seq + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=807) + + This dataset is publicly available in most cases. For more + information on how to access the data please refer to the link + above. + + **2014-10-10: BXD Elicited Peritoneal Neutrophils Gene Expression** + profiling by array entered into GeneNetwork. + + - [UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) + RMA + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=595) + - [UTHSC Elicited Peritoneal Neutrophils Affy MoGene 2.0 ST (Oct14) + RMA Exon Level + \*\*](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=596) + + Currently this dataset is confidential, please contact [Marko + Radic](mailto:mradic@uthsc.edu) University of Tennessee Health Science + Center for further information. (Implemented by Marko Radic, Indira + Neeli, Teruki Hagiwara, Arthur Centeno and Rob Williams). + + **2014-08-29: Mouse Diversity Panel Hippocampus Antidepressant** + profiling by array entered into GeneNetwork. + + - UFL MDP Hippocampus Antidepressant Affy Mouse 430 2.0 (Aug14) RMA + \*\* + + Currently this dataset is confidential, please contact [Brooke + Miller](mailto:brookemiller@ufl.edu) University of Florida for further + information. (Implemented by Brooke Miller, Arthur Centeno and Rob + Williams). + + **2014-08-10: RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) Log2** + profiling by array entered into GeneNetwork. + + - [RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=717) + - [RTI RCMRC BXD Fecal Metabolites HFD (Aug14) + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=716) + - [RTI RCMRC BXD Fecal Metabolites CD (Aug14) + Log2](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=715) + + The goal of this project is to study expression of a large set of + defined and undefined metabolites in fecal samples from a genetically + diverse set of BXD mouse strains (females) raised either on a high fat + diet or low fat diet. Samples were taken from animals at sacrifices + directly from the large intestine. + + Aim: Effect of genetics and diet on fecal metabolomics\ + Use UPLC-MS Broad Spectrum Metabolomics to study:Mice fecal samples + To capture the most signal, all samples were analyzed under positive + and negative ion mode using a reversed-phase separation. Please + contact [Robert Clark](mailto:rclark@rti.org) RTI International for + further information. (Implemented by Robert Clark, Arthur Centeno and + Rob Williams). + + **2014-05-02: BXD Liver, Soluble Proteins CD and Hi-Fat Gene + Expression** profiling by array entered into GeneNetwork. + + - EPFL/ETHZ BXD Liver, Soluble Proteins CD (May14) SWATH \*\* + - EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH \*\* + + Currently this dataset is confidential, please contact [Johan + Auwerx](mailto:admin.auwerx@epfl.ch) Ecole Polytechnique Federale de + Lausanne for further information. (Implemented by Johan Auwerx, Evan + Williams, Arthur Centeno and Rob Williams). + + **2014-04-03: UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene + Level (Apr14) RMA** profiling by array entered into GeneNetwork. + + - UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level + (Apr14) RMA \*\* + + Currently this dataset is confidential, please contact [Dennis D + Black](mailto:dblack@uthsc.edu) UT Le Bonheur Pediatric Specialists + for further information. (Implemented by Dennis D Black, Arthur + Centeno and Rob Williams). + + **2014-03-07: The Genotype-Tissue Expression (GTEx)** is providing a + comprehensive atlas of gene expression and regulation across multiple + human tissues. The latest GTEx data release (dbGaP release + phs000424.v4.p1) is now available on |