INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA

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

Original Assignment had 253 probe sets with LRS >46.

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

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

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

Experiment design

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.

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

About cases

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

Index Sample ID Strain Tissue Sex
1 R6947A BXD48 Adrenal M
2 R6948A BXD90 Adrenal M
3 R6949A BXD97 Adrenal M
4 R6950A BXD87 Adrenal M
5 R6952A BXD83 Adrenal F
6 R6953A BXD67 Adrenal M
7 R6954A BXD56 Adrenal M
8 R6955A BXD48 Adrenal F
9 R6956A BXD90 Adrenal F
10 R6957A BXD89 Adrenal M
11 R6958A BXD65 Adrenal M
12 R6959A BXD65 Adrenal F
13 R6960A BXD63 Adrenal F
14 R6961A BXD63 Adrenal M
15 R6963A BXD31 Adrenal M
16 R6964A BXD31 Adrenal F
17 R6965A BXD1 Adrenal F
18 R6966A BXD1 Adrenal F
19 R6967A BXD24 Adrenal F
20 R6968A BXD34 Adrenal M
21 R6969A BXD1 Adrenal M
22 R6971A BXD27 Adrenal F
23 R6972A BXD29 Adrenal M
24 R6973A BXD12 Adrenal F
25 R6974A BXD14 Adrenal F
26 R6975A BXD99 Adrenal F
27 R6976A BXD32 Adrenal F
28 R6977A BXD97 Adrenal F
29 R6978A BXD84 Adrenal M
30 R6979A BXD39 Adrenal M
31 R6980A BXD24 Adrenal M
32 R6981A BXD50 Adrenal F
33 R6982A BXD75 Adrenal M
34 R6983A BXD42 Adrenal M
35 R6984A BXD39 Adrenal F
36 R6985A BXD34 Adrenal F
37 R6986A BXD87 Adrenal F
38 R6987A BXD50 Adrenal M
39 R6989A BXD62 Adrenal M
40 R6990A BXD70 Adrenal M
41 R6991A BXD64 Adrenal F
42 R6992A BXD84 Adrenal F
43 R6993A BXD100 Adrenal F
44 R6994A BXD62 Adrenal F
45 R6996A BXD95 Adrenal M
46 R6998A BXD32 Adrenal M
47 R6999A BXD101 Adrenal F
48 R7000A BXD49 Adrenal M
49 R7002A BXD11 Adrenal M
50 R7003A BXD100 Adrenal M
51 R7004A BXD43 Adrenal F
52 R7005A BXD103 Adrenal M
53 R7006A BXD73 Adrenal F
54 R7008A BXD43 Adrenal M
55 R7009A BXD102 Adrenal F
56 R7010A BXD69 Adrenal F
57 R7011A BXD60 Adrenal M
58 R7012A BXD45 Adrenal F
59 R7013A BXD79 Adrenal M
60 R7014A BXD40 Adrenal M
61 R7015A BXD79 Adrenal F
62 R7016A BXD40 Adrenal F
63 R7017A BXD68 Adrenal F
64 R7018A BXD85 Adrenal F
65 R7019A BXD44 Adrenal F
66 R7020A BXD70 Adrenal F
67 R7021A BXD68 Adrenal M
68 R7023A BXD44 Adrenal M
69 R7024A BXD95 Adrenal F
70 R7025A BXD56 Adrenal F
71 R7032A BXD103 Adrenal F
72 R7034A BXD24 Adrenal F
73 R7035A BXD101 Adrenal M
74 R7036A BXD29 Adrenal F
75 R7037A BXD60 Adrenal F
76 R7038A BXD69 Adrenal M
77 R7039A BXD73 Adrenal M
78 R7040A BXD80 Adrenal M
79 R7041A BXD11 Adrenal F
80 R7042A BXD74 Adrenal F
81 R7043A BXD67 Adrenal F
82 R7044A BXD67 Adrenal M
83 R7046A C57BL/6J Adrenal F
84 R7047A D2B6F1 Adrenal F
85 R7048A B6D2F1 Adrenal M
86 R7051A BXD80 Adrenal F
87 R7053A BXD102 Adrenal M
88 R7054A BXD49 Adrenal F
89 R7055A BXD77 Adrenal F
90 R7056A BXD77 Adrenal M
91 R7057A BXD66 Adrenal M
92 R7058A BXD66 Adrenal F
93 R7059A BXD45 Adrenal F
94 R7145A BXD67 Adrenal M
95 R7147A BXD85 Adrenal M
96 R7148A DBA/2J Adrenal F
97 R7149A D2B6F1 Adrenal M
98 R7150A D2B6F1 Adrenal F
99 R7151A BXD27 Adrenal M
100 R7152A B6D2F1 Adrenal M
101 R7153A DBA/2J Adrenal M
102 R7159A C57BL/6J Adrenal F
103 R7161A C57BL/6J Adrenal M
104 R7164A B6D2F1 Adrenal F
105 R7166A B6D2F1 Adrenal M
106 R7167A DBA/2J Adrenal F
107 R7168A DBA/2J Adrenal M

About tissue

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

About platform

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.

About data processing

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.