From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001 From: Bonface Date: Tue, 13 Feb 2024 23:52:26 -0600 Subject: Update dataset RTF Files. --- .../datasets/INIA_Adrenal_RMA_Ex_0612/cases.rtf | 771 --------------------- .../INIA_Adrenal_RMA_Ex_0612/experiment-design.rtf | 3 - .../datasets/INIA_Adrenal_RMA_Ex_0612/platform.rtf | 1 - .../INIA_Adrenal_RMA_Ex_0612/processing.rtf | 1 - .../datasets/INIA_Adrenal_RMA_Ex_0612/summary.rtf | 17 - .../datasets/INIA_Adrenal_RMA_Ex_0612/tissue.rtf | 1 - 6 files changed, 794 deletions(-) delete mode 100644 general/datasets/INIA_Adrenal_RMA_Ex_0612/cases.rtf delete mode 100644 general/datasets/INIA_Adrenal_RMA_Ex_0612/experiment-design.rtf delete mode 100644 general/datasets/INIA_Adrenal_RMA_Ex_0612/platform.rtf delete mode 100644 general/datasets/INIA_Adrenal_RMA_Ex_0612/processing.rtf delete mode 100644 general/datasets/INIA_Adrenal_RMA_Ex_0612/summary.rtf delete mode 100644 general/datasets/INIA_Adrenal_RMA_Ex_0612/tissue.rtf (limited to 'general/datasets/INIA_Adrenal_RMA_Ex_0612') diff --git a/general/datasets/INIA_Adrenal_RMA_Ex_0612/cases.rtf b/general/datasets/INIA_Adrenal_RMA_Ex_0612/cases.rtf deleted file mode 100644 index f0b204b..0000000 --- a/general/datasets/INIA_Adrenal_RMA_Ex_0612/cases.rtf +++ /dev/null @@ -1,771 +0,0 @@ -

Young adult mice raised in specific pathogen-free vivarium at UTHSC.
-Table 1. Final strain correction by Khyobeni Mozhui on Mar 28, 2013.

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IndexSample IDStrainTissueSex
1R6947ABXD48AdrenalM
2R6948ABXD90AdrenalM
3R6949ABXD97AdrenalM
4R6950ABXD87AdrenalM
5R6952ABXD83AdrenalF
6R6953ABXD67AdrenalM
7R6954ABXD56AdrenalM
8R6955ABXD48AdrenalF
9R6956ABXD90AdrenalF
10R6957ABXD89AdrenalM
11R6958ABXD65AdrenalM
12R6959ABXD65AdrenalF
13R6960ABXD63AdrenalF
14R6961ABXD63AdrenalM
15R6963ABXD31AdrenalM
16R6964ABXD31AdrenalF
17R6965ABXD1AdrenalF
18R6966ABXD1AdrenalF
19R6967ABXD24AdrenalF
20R6968ABXD34AdrenalM
21R6969ABXD1AdrenalM
22R6971ABXD27AdrenalF
23R6972ABXD29AdrenalM
24R6973ABXD12AdrenalF
25R6974ABXD14AdrenalF
26R6975ABXD99AdrenalF
27R6976ABXD32AdrenalF
28R6977ABXD97AdrenalF
29R6978ABXD84AdrenalM
30R6979ABXD39AdrenalM
31R6980ABXD24AdrenalM
32R6981ABXD50AdrenalF
33R6982ABXD75AdrenalM
34R6983ABXD42AdrenalM
35R6984ABXD39AdrenalF
36R6985ABXD34AdrenalF
37R6986ABXD87AdrenalF
38R6987ABXD50AdrenalM
39R6989ABXD62AdrenalM
40R6990ABXD70AdrenalM
41R6991ABXD64AdrenalF
42R6992ABXD84AdrenalF
43R6993ABXD100AdrenalF
44R6994ABXD62AdrenalF
45R6996ABXD95AdrenalM
46R6998ABXD32AdrenalM
47R6999ABXD101AdrenalF
48R7000ABXD49AdrenalM
49R7002ABXD11AdrenalM
50R7003ABXD100AdrenalM
51R7004ABXD43AdrenalF
52R7005ABXD103AdrenalM
53R7006ABXD73AdrenalF
54R7008ABXD43AdrenalM
55R7009ABXD102AdrenalF
56R7010ABXD69AdrenalF
57R7011ABXD60AdrenalM
58R7012ABXD45AdrenalF
59R7013ABXD79AdrenalM
60R7014ABXD40AdrenalM
61R7015ABXD79AdrenalF
62R7016ABXD40AdrenalF
63R7017ABXD68AdrenalF
64R7018ABXD85AdrenalF
65R7019ABXD44AdrenalF
66R7020ABXD70AdrenalF
67R7021ABXD68AdrenalM
68R7023ABXD44AdrenalM
69R7024ABXD95AdrenalF
70R7025ABXD56AdrenalF
71R7032ABXD103AdrenalF
72R7034ABXD24AdrenalF
73R7035ABXD101AdrenalM
74R7036ABXD29AdrenalF
75R7037ABXD60AdrenalF
76R7038ABXD69AdrenalM
77R7039ABXD73AdrenalM
78R7040ABXD80AdrenalM
79R7041ABXD11AdrenalF
80R7042ABXD74AdrenalF
81R7043ABXD67AdrenalF
82R7044ABXD67AdrenalM
83R7046AC57BL/6JAdrenalF
84R7047AD2B6F1AdrenalF
85R7048AB6D2F1AdrenalM
86R7051ABXD80AdrenalF
87R7053ABXD102AdrenalM
88R7054ABXD49AdrenalF
89R7055ABXD77AdrenalF
90R7056ABXD77AdrenalM
91R7057ABXD66AdrenalM
92R7058ABXD66AdrenalF
93R7059ABXD45AdrenalF
94R7145ABXD67AdrenalM
95R7147ABXD85AdrenalM
96R7148ADBA/2JAdrenalF
97R7149AD2B6F1AdrenalM
98R7150AD2B6F1AdrenalF
99R7151ABXD27AdrenalM
100R7152AB6D2F1AdrenalM
101R7153ADBA/2JAdrenalM
102R7159AC57BL/6JAdrenalF
103R7161AC57BL/6JAdrenalM
104R7164AB6D2F1AdrenalF
105R7166AB6D2F1AdrenalM
106R7167ADBA/2JAdrenalF
107R7168ADBA/2JAdrenalM
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diff --git a/general/datasets/INIA_Adrenal_RMA_Ex_0612/experiment-design.rtf b/general/datasets/INIA_Adrenal_RMA_Ex_0612/experiment-design.rtf deleted file mode 100644 index b069873..0000000 --- a/general/datasets/INIA_Adrenal_RMA_Ex_0612/experiment-design.rtf +++ /dev/null @@ -1,3 +0,0 @@ -

Normative expression in the adrenals (whole organ) of young adult mice. In general, a sex-balanced samples (one array from male cases, one array from female cases) for BXD and parental strains.

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Part of a systematic genetic analysis of the hypothalamus-pituitary-adrenal axis in the BXD family of strains.

diff --git a/general/datasets/INIA_Adrenal_RMA_Ex_0612/platform.rtf b/general/datasets/INIA_Adrenal_RMA_Ex_0612/platform.rtf deleted file mode 100644 index 7057d48..0000000 --- a/general/datasets/INIA_Adrenal_RMA_Ex_0612/platform.rtf +++ /dev/null @@ -1 +0,0 @@ -

The GeneChip® Mouse Gene 1.0 ST Array is the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each of the 28,853 genes is represented on the array by approximately 27 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3'-based expression array designs. The small format of the array makes it a cost-effective expression profiling solution for new microarray users. Sense DNA targets are generated from as little as 100ng of total RNA. The Gene 1.0 ST Array is part of a complete solution for gene expression analysis that includes Whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software. The array contains the most up-to-date content of well-annotated genes, and data is analyzed using a simple workflow. The Gene 1.0 ST Array uses a subset of probes from the Mouse Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, "gene-level" analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene.

diff --git a/general/datasets/INIA_Adrenal_RMA_Ex_0612/processing.rtf b/general/datasets/INIA_Adrenal_RMA_Ex_0612/processing.rtf deleted file mode 100644 index 55aad2e..0000000 --- a/general/datasets/INIA_Adrenal_RMA_Ex_0612/processing.rtf +++ /dev/null @@ -1 +0,0 @@ -

Conventional Affymetrix gene level probe summarization (RMA) followed by log2 transformation and standard GeneNetwork variance stabilization (2z +8). The z scores are multiplied by 2 and we then add a value of 8 to all values. This eliminates negative values and results in a scale of expression for which 1 unit is roughly equivalent to a two fold absolute difference in mRNA concentration.

diff --git a/general/datasets/INIA_Adrenal_RMA_Ex_0612/summary.rtf b/general/datasets/INIA_Adrenal_RMA_Ex_0612/summary.rtf deleted file mode 100644 index 9858a55..0000000 --- a/general/datasets/INIA_Adrenal_RMA_Ex_0612/summary.rtf +++ /dev/null @@ -1,17 +0,0 @@ -

Preliminary data WITH ERRORS of strain assignment as of July 20, 2012.

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Original Assignment had 253 probe sets with LRS >46.

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Corrections on Adrenal Data on July 25, 2012:
-R6963A(BXD31).....it should be BXD34
-R7018A(BXD85).....it should be BXD95
-R7152A(C57BL/6J)...it should be B6D2F1
-R7020A(BXD70).......it should be BXD65

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229 probe sets with LRS >46 after the corrections above from S. Roy of July 25, July 26 AM.

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More corrections from S. Roy (5 PM July 26)
-R6965A(BXD42).........should be BXD2
-R6973A(BXD12).........should be BXD8
-R6985A(BXD34).........should be BXD8
-R7151A(BXD99)..........should be BXD42

diff --git a/general/datasets/INIA_Adrenal_RMA_Ex_0612/tissue.rtf b/general/datasets/INIA_Adrenal_RMA_Ex_0612/tissue.rtf deleted file mode 100644 index 54000a9..0000000 --- a/general/datasets/INIA_Adrenal_RMA_Ex_0612/tissue.rtf +++ /dev/null @@ -1 +0,0 @@ -

Whole adrenal gland. Dissections by Khyobeni Mozhui, Jesse Ingels, and Adrienne Adler at UTHSC.

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