From e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 Mon Sep 17 00:00:00 2001 From: Bonface Date: Thu, 15 Feb 2024 06:09:54 -0600 Subject: Update dataset RTF Files. --- general/datasets/IBR_M_0405_P/tissue.rtf | 977 ------------------------------- 1 file changed, 977 deletions(-) delete mode 100644 general/datasets/IBR_M_0405_P/tissue.rtf (limited to 'general/datasets/IBR_M_0405_P/tissue.rtf') diff --git a/general/datasets/IBR_M_0405_P/tissue.rtf b/general/datasets/IBR_M_0405_P/tissue.rtf deleted file mode 100644 index 841d879..0000000 --- a/general/datasets/IBR_M_0405_P/tissue.rtf +++ /dev/null @@ -1,977 +0,0 @@ -
The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai. All samples were subsequently processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence by Thomas R. Sutter, Shirlean Goodwin, and colleagues at the University of Memphis. - -

Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M).

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Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below.

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The table below summarizes information on strain, sex, age, sample name, batch result date, and source of mice.

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IdStrainSexAgeSample_nameResult dateSource
1C57BL/6JF65R0903F1Nov03UTM RW
2C57BL/6JF65R0903F1Jan04UTM RW
3C57BL/6JM66R0906F1Nov03UTM RW
4C57BL/6JM66R0906F1Jan04UTM RW
5C57BL/6JM66R0906F1Feb05UTM RW
6C57BL/6JM76R0997F1Feb05UTM RW
7D2B6F1F57R1066F1Feb05UTM RW
8D2B6F1M59R1381F1Feb05UTM RW
9DBA/2JF60R0917F1Nov03UTM RW
10DBA/2JF60R0917F1Feb05UTM RW
11DBA/2JF60R0917F2Jan04UTM RW
12DBA/2JF64R1123F1Feb05UTM RW
13DBA/2JM60R0918F1Nov03UTM RW
14DBA/2JM60R0918F1Jan04UTM RW
15DBA/2JM73R1009F1Feb05UTM RW
16B6D2F1F127R0919F1Jan04UTM JB
17B6D2F1F127R0919F2Jan04UTM JB
18B6D2F1F64R1053F1Feb05UTM RW
19B6D2F1F64R1053F1Feb05UTM RW
20B6D2F1M127R0920F1Jan04UTM JB
21B6D2F1M127R0920F2Jan04UTM JB
22B6D2F1M66R1057F1Feb05UTM RW
23BXD1M181R0956F1Feb05UTM JB
24BXD1F95R0895F1Jan04UMemphis
25BXD2F142R0907F1Feb05UAB
26BXD5F56R0744F1Feb05UMemphis
27BXD5M71R0728F1Jan04UMemphis
28BXD6F57R1711F1Feb05JAX
29BXD6F92R0901F1Feb05UMemphis
30BXD6M92R0902F1Jan04UMemphis
31BXD8F72R0167F1Jan04UAB
32BXD9F86R0908F1Feb05UMemphis
33BXD9M86R0909F1Jan04UMemphis
34BXD11F97R0745F1Feb05UAB
35BXD11M92R0666F1Feb05UMemphis
36BXD12F64R0896F1Feb05UMemphis
37BXD12M64R0897F1Jan04UMemphis
38BXD13F86R0730F1Feb05UMemphis
39BXD13F86R0748F1Jan04UMemphis
40BXD13M76R0929F1Feb05UMemphis
41BXD14M91R0912F1Jan04UMemphis
42BXD14M68R1051F1Feb05UTM RW
43BXD15F80R0928F1Feb05UMemphis
44BXD18F108R0771F1Jan04UAB
45BXD19M157R1229F1Feb05UTM JB
46BXD19F56R0236F1Jan04UAB
47BXD21F67R0740F1Jan04UAB
48BXD21F67R0740F1Feb05UAB
49BXD23F66R1035F1Feb05UTM RW
50BXD23M66R1037F1Feb05UTM RW
51BXD23F88R0815F1Jan04UAB
52BXD23F88R0815F1Feb05UAB
53BXD24F71R0914F1Feb05UMemphis
54BXD24M71R0913F1Jan04UMemphis
55BXD25F74R0373F1Jan04UTM RW
56BXD28F79R0910F1Jan04UMemphis
57BXD28M79R0911F1Feb05UMemphis
58BXD28F113R0892F1Feb05UTM RW
59BXD29F76R0693F1Jan04UMemphis
60BXD31F61R1199F1Feb05UTM RW
61BXD31M61R1141F1Feb05UTM RW
62BXD32F93R0898F1Jan04UAB
63BXD32F76R1214F1Feb05UMemphis
64BXD32M65R1478F1Feb05UMemphis
65BXD33M77R0915F1Jan04UMemphis
66BXD34F92R0900F1Feb05UMemphis
67BXD34M56R0617F1Feb05UMemphis
68BXD34M72R0916F1Jan04UMemphis
69BXD36F61R1145F1Feb05UTM RW
70BXD36M77R0926F1Jan04UMemphis
71BXD36M61R1211F1Feb05UMemphis
72BXD38M83R1208F1Feb05UMemphis
73BXD38F69R0729F1Feb05UMemphis
74BXD38M69R0731F1Jan04UMemphis
75BXD39F76R1712F1Feb05JAX
76BXD39M71R0602F1Feb05UAB
77BXD40F184R0741F1Feb05UAB
78BXD40M56R0894F1Feb05UMemphis
79BXD42F100R0742F1Feb05UAB
80BXD42M97R0936F1Jan04UMemphis
81BXD42M105R0937F1Feb05UMemphis
82BXD43M63R1047F1Feb05UTM RW
83BXD44F57R1069F1Feb05UTM RW
84BXD44M58R1072F1Feb05UTM RW
85BXD45F58R1398F1Feb05UTM RW
86BXD48F59R0946F1Feb05UTM RW
87BXD48M64R0970F1Feb05UTM RW
88BXD51F63R1430F1Feb05UTM RW
89BXD51M65R1001F1Feb05UTM RW
90BXD60F64R0976F1Feb05UTM RW
91BXD60M59R1075F1Feb05UTM RW
92BXD62F59R1033F1Feb05UTM RW
93BXD62M58R1027F1Feb05UTM RW
94BXD69F60R1438F1Feb05UTM RW
95BXD69M64R1193F1Feb05UTM RW
96BXD73F60R1275F1Feb05UTM RW
97BXD73M76R1442F1Feb05UTM RW
98BXD77M61R1426F1Feb05UTM RW
99BXD86F77R1414F1Feb05UTM RW
100BXD86M77R1418F1Feb05UTM RW
101BXD87F89R1713F1Feb05UTM RW
102BXD87M84R1709F1Feb05UTM RW
103BXD90M61R1452FFeb05UTM RW
104BXD92F58R1299F1Feb05UTM RW
105BXD92M59R1307F1Feb05UTM RW
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