INIA M430 brain RMA Database (January/06 Freeze)

Accession number: GN102

    Summary:

HIGHLY SELECTIVE DATA SET: This January 2006 data freeze provides estimates of mRNA expression in adult forebrain and midbrain from 43 lines of mice including C57BL/6J, DBA/2J, reciprocal F1 hybrids, and 39 BXD recombinant inbred strains. Data were generated at UTHSC and the University of Memphis with support from grants from the NIAAA Integrative Neuroscience Initiative on Alcoholism (INIA). Samples were hybridized in small pools (n = 3) to a total of 121 Affymetrix M430A and B array pairs. This data set only includes the highest quality subset of 76 arrays that have been quantile normalized at both probe and probe set levels. This data set was initially processed using the RMA protocol. Data were renormalized after generating the RMA values using a second quantile normalization step and a round of correction for group and batch effects. To simplify comparisons among transforms, final RMA values of each array have been adjusted to an average of 8 units and a standard deviation of 2 units. A total of 355 probe sets have LRS values above 50.

    About the cases used to generate this set of data:

We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage for D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from Celera. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues

All stock was obtained originally from The Jackson Laboratory between 1999 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu).

    About the tissue used to generate this set of data:

The INIA M430 brain Database (Jan06) consists of 78 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 or retina, 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 was to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. While we achieved this goal technically, not all of the replicates were of sufficient quality to be included in this highly selected set. This data set is now complete and includes more than 20 replicates. Despite the lack of replicates for about 20 strains we still recommend this data set strongly over earliers data sets that included more arrays, many of which are suboptimal.

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. Two more batches were run; the final in December 2005 (16 arrays pairs). Batch effects were corrected at the individual probe level as described below.

The table below summarizes information on strain, sex, age, sample name, batch result date, the grouping to which an arrays data set belongs based on expression similarity, and source of mice.

Id Strain Sex Age Sample Batch Final Grouping Source 1 B6D2F1 F 127 R0919F1 2 e_2 UTM JB 2 B6D2F1 F 127 R0919F2 2 e_2 UTM JB 3 B6D2F1 F 64 R1053F1 3 g_3 UTM RW 4 B6D2F1 F 64 R1053F1 3 e_3 UTM RW 5 B6D2F1 M 66 R1057F1 3 e_3 UTM RW 6 D2B6F1 F 57 R1066F1 3 e_3 UTM RW 7 C57BL/6J F 65 R0903F1 1 se_1 UTM RW 8 C57BL/6J F 65 R0903F1 2 e_2 UTM RW 9 C57BL/6J M 66 R0906F1 1 e_1 UTM RW 10 C57BL/6J M 76 R0997F1 3 g_3 UTM RW 11 DBA/2J F 60 R0917F1 1 e_1 UTM RW 12 DBA/2J F 64 R1123F1 3 g_3 UTM RW 13 DBA/2J M 60 R0918F1 2 sgA_2 UTM RW 14 DBA/2J M 73 R1009F1 3 w_3 UTM RW 15 BXD1 M 181 R0956F1 3 e_3 UTM JB 16 BXD2 F 142 R0907F1 3 e_3 UAB 17 BXD5 F 56 R0744F1 3 o_3 UMemphis 18 BXD5 M 71 R0728F1 2 e_2 UMemphis 19 BXD6 F 57 R1711F1 3 g_3 JAX 20 BXD8 M 71 R2664F1 4 se_4 JAX 21 BXD11 F 97 R0745F1 3 gA_3 UAB 22 BXD12 F 64 R0896F1 3 o_3 UMemphis 23 BXD12 M 64 R0897F1 2 e_2 UMemphis 24 BXD13 F 86 R0748F1 2 e_2 UMemphis 25 BXD13 F 86 R0730F1 3 e_3 UMemphis 26 BXD13 M 76 R0929F1 3 e_3 UMemphis 27 BXD14 M 68 R1051F1 3 e_3 UTM RW 28 BXD15 F 80 R0928F1 3 e_3 UMemphis 29 BXD18 F 108 R0771F1 2 e_2 UAB 30 BXD19 M 157 R1229F1 3 gA_3 UTM JB 31 BXD21 F 67 R0740F1 3 gA_3 UAB 32 BXD23 F 88 R0815F1 3 gA_3 UAB 33 BXD23 F 66 R1035F1 3 gA_3 UTM RW 34 BXD23 M 66 R1256F1 4 e_4 UTM RW 35 BXD23 M 66 R1037F1 3 gA_3 UTM RW 36 BXD24 F 71 R0914F1 3 e_3 UMemphis 37 BXD24 M 71 R0913F1 2 e_2 UMemphis 38 BXD25 F 74 R0373F1 2 e_2 UTM RW 39 BXD25 M 58 R2623F1 4 e_4 UTM RW 40 BXD27 M 54 R2660F1 4 e_4 UTM RW 41 BXD28 F 113 R0892F1 3 e_3 UTM RW 42 BXD28 M 79 R0911F1 3 g_3 UMemphis 43 BXD31 M 61 R1141F1 3 e_3 UTM RW 44 BXD32 F 93 R0898F1 2 e_2 UAB 46 BXD32 M 76 R1217F2 4 e_4 UMemphis 47 BXD32 M 65 R1478F1 3 e_3 UMemphis 48 BXD34 M 72 R0916F1 2 e_2 UMemphis 49 BXD34 F 92 R0900F1 3 e_3 UMemphis 50 BXD36 F 79 R2654F1 4 e_4 UTM RW 51 BXD36 F 61 R1145F1 3 e_3 UTM RW 52 BXD36 M 77 R0926F1 2 e_2 UMemphis 53 BXD38 F 69 R0729F1 3 e_3 UMemphis 54 BXD38 F 83 R1208F1 3 g_3 UMemphis 55 BXD39 F 76 R1712F1 3 e_3 JAX 57 BXD40 F 184 R0741F1 3 e_3 UAB 58 BXD40 M 56 R0894F1 3 e_3 UMemphis 59 BXD42 F 100 R0742F1 3 e_3 UAB 60 BXD43 F 61 R1199F1 3 e_3 UTM RW 61 BXD43 F 59 R0980F1 4 e_4 UTM RW 62 BXD44 M 58 R1072F1 3 e_3 UTM RW 63 BXD45 F 58 R1398F1 3 o_3 UTM RW 64 BXD45 M 81 R1658F2 4 e_4 UTM RW 65 BXD48 F 59 R0946F1 3 e_3 UTM RW 66 BXD51 F 63 R1430F1 3 e_3 UTM RW 67 BXD51 M 65 R1001F1 3 e_3 UTM RW 68 BXD60 M 59 R1075F1 3 g_3 UTM RW 69 BXD62 M 58 R1027F1 3 e_3 UTM RW 70 BXD69 F 60 R1438F1 3 e_3 UTM RW 71 BXD69 M 64 R1193F1 3 o_3 UTM RW 72 BXD73 F 60 R1275F1 3 e_3 UTM RW 73 BXD73 M 76 R1442F1 3 g_3 UTM RW 74 BXD77 M 61 R1426F1 3 g_3 UTM RW 75 BXD87 F 89 R1713F1 3 e_3 UTM RW 76 BXD90 F 71 R2628F1 4 e_4 UTM RW 77 BXD90 M 61 R1452F 3 g_3 UTM RW 78 BXD92 F 58 R1299F1 3 e_3 UTM RW

The table below quality information on scale factor, background, present, absent, marginal, and control genes to which an arrays data set is from it's report file.

Id Strain Sample Final grouping Set scale factor back ground present absent marginal Affy- b- Actin Affy- Gapdh 1 B6D2F1 R0919F1 e_B2 A 14.212 46.93 0.417 0.564 0.019 1.24 0.8 1 B6D2F1 R0919F1 e_B2 B 30.349 42.21 0.233 0.748 0.019 1.24 0.74 2 B6D2F1 R0919F2 e_B2 A 5.95 53 0.468 0.511 0.021 1.17 0.73 2 B6D2F1 R0919F2 e_B2 B 14.795 47.95 0.264 0.716 0.02 1.19 0.75 3 B6D2F1 R1053F1 g_B3 A 4.445 50.82 0.536 0.447 0.017 1.92 1.69 3 B6D2F1 R1053F1 g_B3 B 16.596 51.44 0.278 0.702 0.02 1.93 1.76 4 B6D2F1 R1053F1 e_B3 A 11.196 42.4 0.457 0.523 0.02 1.84 1.32 4 B6D2F1 R1053F1 e_B3 B 16.596 51.44 0.278 0.702 0.02 1.93 1.76 5 B6D2F1 R1057F1 e_B3 A 7.332 42.21 0.505 0.475 0.02 1.64 1.2 5 B6D2F1 R1057F1 e_B3 B 16.444 40.31 0.314 0.661 0.025 1.13 1.31 6 C57BL/6J R0903F1 se_B1 A 10.15 46.46 0.418 0.562 0.019 1.13 0.76 6 C57BL/6J R0903F1 se_B1 B 20.223 47.78 0.222 0.759 0.018 1.36 0.89 7 C57BL/6J R0903F1 e_B2 A 7.406 52.47 0.473 0.507 0.02 1.01 0.74 7 C57BL/6J R0903F1 e_B2 B 20.71 46.98 0.252 0.729 0.02 1.08 0.74 8 C57BL/6J R0906F1 e_B1 A 9.407 46.55 0.439 0.54 0.022 1 0.8 8 C57BL/6J R0906F1 e_B1 B 28.77 44.52 0.21 0.77 0.019 1.04 0.74 9 C57BL/6J R0997F1 g_B3 A 8.118 55.74 0.448 0.53 0.022 0.9 1.04 9 C57BL/6J R0997F1 g_B3 B 13.24 49.64 0.316 0.661 0.023 1.41 1.11 10 D2B6F1 R1066F1 e_B3 A 8.147 46.39 0.481 0.5 0.019 0.97 1.22 10 D2B6F1 R1066F1 e_B3 B 18.835 43.24 0.285 0.695 0.021 1.11 1.29 11 DBA/2J R0917F1 e_B1 A 13.775 50.2 0.253 0.729 0.019 1.18 0.76 11 DBA/2J R0917F1 e_B1 B 22.301 47.49 0.241 0.741 0.018 1.37 0.88 12 DBA/2J R1123F1 g_B3 A 9.452 50.14 0.456 0.523 0.021 1.37 1.87 12 DBA/2J R1123F1 g_B3 B 23.467 42.27 0.25 0.729 0.021 0.91 1.9 13 DBA/2J R0918F1 sgA_B2 A 9.105 48.24 0.462 0.517 0.019 1.22 0.81 13 DBA/2J R0918F1 sgA_B2 B 25.007 46.99 0.244 0.736 0.019 1.22 0.81 14 DBA/2J R1009F1 w_B3 A 5.736 42.88 0.527 0.455 0.017 1.11 2.4 14 DBA/2J R1009F1 w_B3 B 17.739 43.75 0.291 0.69 0.019 0.91 2.36 15 BXD1 R0956F1 e_B3 A 4.923 44.74 0.519 0.46 0.021 1.5 1.09 15 BXD1 R0956F1 e_B3 B 15.937 39.5 0.31 0.665 0.025 1.47 1.21 16 BXD2 R0907F1 e_B3 A 6.191 45.77 0.48 0.498 0.022 1.37 1.23 16 BXD2 R0907F1 e_B3 B 16.15 43.78 0.3 0.677 0.023 1.74 1.37 17 BXD5 R0744F1 o_B3 A 10.448 60.78 0.403 0.576 0.021 1.23 1.38 17 BXD5 R0744F1 o_B3 B 28.054 44.72 0.236 0.746 0.018 1.43 1.68 18 BXD5 R0728F1 e_B2 A 7.884 53.56 0.43 0.549 0.021 1.12 0.71 18 BXD5 R0728F1 e_B2 B 18.92 42.5 0.245 0.735 0.019 1 0.76 19 BXD6 R1711F1 g_B3 A 7.1 46.57 0.498 0.481 0.02 1.97 1.66 19 BXD6 R1711F1 g_B3 B 12.465 46.02 0.319 0.66 0.022 2.06 1.78 20 BXD8 R2664F1 se_B4 A 2.126 45.64 0.594 0.39 0.016 1.73 1 20 BXD8 R2664F1 se_B4 B 7.133 41.85 0.377 0.603 0.02 1.95 0.99 21 BXD11 R0745F1 gA_B3 A 6.242 40.99 0.501 0.48 0.019 1.4 1.24 21 BXD11 R0745F1 gA_B3 B 18.681 41.11 0.278 0.702 0.02 1.28 1.27 22 BXD12 R0896F1 o_B3 A 8.237 51.23 0.433 0.546 0.021 1.72 1.28 22 BXD12 R0896F1 o_B3 B 19.781 43.61 0.264 0.714 0.022 1.44 1.45 23 BXD12 R0897F1 e_B2 A 10.713 46.56 0.421 0.56 0.019 1.23 0.75 23 BXD12 R0897F1 e_B2 B 20.093 50.31 0.236 0.744 0.02 1.25 0.76 24 BXD13 R0748F1 e_B2 A 7.149 57.35 0.435 0.543 0.022 1.02 0.74 24 BXD13 R0748F1 e_B2 B 12.77 56.44 0.248 0.734 0.019 1.05 0.8 25 BXD13 R0730F1 e_B3 A 6.076 44.57 0.49 0.488 0.022 1.26 1.45 25 BXD13 R0730F1 e_B3 B 15.7 44.24 0.293 0.687 0.02 1.31 1.52 26 BXD13 R0929F1 e_B3 A 5.493 47.46 0.507 0.472 0.021 1.65 1.35 26 BXD13 R0929F1 e_B3 B 14.739 46.05 0.301 0.677 0.023 0.93 1.62 27 BXD14 R1051F1 e_B3 A 6.393 45.19 0.49 0.489 0.021 1.22 1.26 27 BXD14 R1051F1 e_B3 B 15.488 41.14 0.325 0.653 0.022 1.12 1.38 28 BXD15 R0928F1 e_B3 A 5.646 39.95 0.524 0.456 0.02 1.95 1.34 28 BXD15 R0928F1 e_B3 B 19.344 37.65 0.296 0.682 0.023 1.33 1.42 29 BXD18 R0771F1 e_B2 A 4.168 54.8 0.503 0.477 0.02 1.13 0.77 29 BXD18 R0771F1 e_B2 B 9.679 54.7 0.277 0.702 0.02 1.4 0.76 30 BXD19 R1229F1 gA_B3 A 6.991 39.65 0.49 0.491 0.02 1.92 1.29 30 BXD19 R1229F1 gA_B3 B 20.945 40.5 0.277 0.702 0.021 1.54 1.22 31 BXD21 R0740F1 gA_B3 A 6.229 42.24 0.483 0.495 0.022 1.31 1.25 31 BXD21 R0740F1 gA_B3 B 16.584 41.88 0.306 0.673 0.021 1.43 1.23 32 BXD23 R0815F1 gA_B3 A 4.753 48.12 0.521 0.46 0.019 1.4 1.06 32 BXD23 R0815F1 gA_B3 B 11.555 39.41 0.353 0.626 0.022 1.44 1.1 33 BXD23 R1035F1 gA_B3 A 6.281 39.58 0.503 0.476 0.02 1.31 1.6 33 BXD23 R1035F1 gA_B3 B 22.536 34.86 0.292 0.686 0.021 1.31 1.67 34 BXD23 R1256F1 e_B4 A 2.233 46.66 0.575 0.408 0.017 1.8 1.13 34 BXD23 R1256F1 e_B4 B 4.862 43.16 0.399 0.58 0.021 1.73 1.01 35 BXD23 R1037F1 gA_B3 A 5.37 41.47 0.519 0.462 0.019 1.35 1.25 35 BXD23 R1037F1 gA_B3 B 18.483 37.49 0.305 0.671 0.024 1.24 1.28 36 BXD24 R0914F1 e_B3 A 6.212 51.11 0.497 0.482 0.021 1.09 1.53 36 BXD24 R0914F1 e_B3 B 19.649 36.07 0.309 0.671 0.021 1.4 1.76 37 BXD24 R0913F1 e_B2 A 9.002 49.85 0.437 0.543 0.02 1.24 0.71 37 BXD24 R0913F1 e_B2 B 14.375 51.49 0.246 0.734 0.02 1.36 0.79 38 BXD25 R0373F1 e_B2 A 6.222 56.95 0.457 0.522 0.022 1.37 0.75 38 BXD25 R0373F1 e_B2 B 8.337 50.91 0.291 0.685 0.024 1.19 0.77 39 BXD25 R2623F1 e_B4 A 1.985 45.8 0.588 0.395 0.016 1.6 1 39 BXD25 R2623F1 e_B4 B 7.555 40 0.374 0.607 0.019 1.78 1.03 40 BXD27 R2660F1 e_B4 A 2.688 51.77 0.582 0.403 0.016 1.4 0.84 40 BXD27 R2660F1 e_B4 B 5.735 54.08 0.392 0.588 0.02 1.51 0.78 41 BXD28 R0892F1 e_B3 A 4.143 47.2 0.537 0.442 0.021 1.05 1.08 41 BXD28 R0892F1 e_B3 B 16.413 45.83 0.297 0.682 0.021 1.04 1.23 42 BXD28 R0911F1 g_B3 A 5.811 43.06 0.517 0.465 0.018 1.19 1.43 42 BXD28 R0911F1 g_B3 B 16.22 41.15 0.3 0.678 0.022 0.85 1.65 43 BXD31 R1141F1 e_B3 A 3.607 42.59 0.547 0.435 0.019 1 1.15 43 BXD31 R1141F1 e_B3 B 11.826 41.26 0.329 0.65 0.021 1.04 1.27 44 BXD32 R0898F1 e_B2 A 9.574 45.43 0.447 0.532 0.022 1.3 0.7 44 BXD32 R0898F1 e_B2 B 28.57 42.93 0.23 0.752 0.019 1.42 0.69 45 BXD32 R1214F1 w_B3 A 5.506 41.54 0.527 0.454 0.019 1.4 2.12 46 BXD32 R1217F2 e_B4 A 1.861 68.71 0.581 0.404 0.015 1.62 0.89 46 BXD32 R1217F2 e_B4 B 5.388 55.49 0.376 0.602 0.022 1.94 0.83 47 BXD32 R1478F1 e_B3 A 5.452 42.1 0.52 0.46 0.019 1.36 1.68 47 BXD32 R1478F1 e_B3 B 14.805 38.7 0.332 0.647 0.021 1.53 1.84 48 BXD34 R0916F1 e_B2 A 5.377 55.95 0.446 0.534 0.021 1.12 0.75 48 BXD34 R0916F1 e_B2 B 13.775 50.2 0.253 0.729 0.019 1.18 0.76 49 BXD34 R0900F1 e_B3 A 7.206 45.6 0.484 0.495 0.021 1.11 1.15 49 BXD34 R0900F1 e_B3 B 14.661 52.1 0.494 0.497 0.021 1.11 1.15 50 BXD36 R2654F1 e_B4 A 2.646 53.84 0.559 0.424 0.017 1.89 1.27 50 BXD36 R2654F1 e_B4 B 7.062 54.84 0.334 0.647 0.019 1.91 1.24 51 BXD36 R1145F1 e_B3 A 5.229 41.48 0.515 0.466 0.019 0.97 1.12 51 BXD36 R1145F1 e_B3 B 12.661 40.04 0.334 0.644 0.022 1.04 1.13 52 BXD36 R0926F1 e_B2 A 5.841 55.5 0.438 0.541 0.021 1.26 0.74 52 BXD36 R0926F1 e_B2 B 13.353 53.81 0.263 0.716 0.021 1.23 0.76 53 BXD38 R0729F1 e_B3 A 5.472 83.41 0.469 0.512 0.019 0.92 1.09 53 BXD38 R0729F1 e_B3 B 10.88 67.39 0.299 0.679 0.022 1.06 1.2 54 BXD38 R1208F1 g_B3 A 3.532 43.38 0.544 0.438 0.018 1.15 1.27 54 BXD38 R1208F1 g_B3 B 15.234 43.65 0.311 0.667 0.023 1.08 1.38 55 BXD39 R1712F1 e_B3 A 7.514 44.54 0.49 0.489 0.021 1.69 1.42 55 BXD39 R1712F1 e_B3 B 12.624 44.61 0.318 0.661 0.021 1.34 1.55 56 BXD39 R0602F1 w_B3 B 20.231 37.07 0.301 0.68 0.02 1.07 2.33 57 BXD40 R0741F1 e_B3 A 5.234 45.68 0.51 0.469 0.02 1.69 1.17 57 BXD40 R0741F1 e_B3 B 12.242 46.89 0.323 0.656 0.021 1.12 1.23 58 BXD40 R0894F1 e_B3 A 5.326 44.9 0.52 0.459 0.021 1.26 1.21 58 BXD40 R0894F1 e_B3 B 10.339 41.24 0.352 0.625 0.024 0.81 1.4 59 BXD42 R0742F1 e_B3 A 5.542 43.66 0.522 0.458 0.021 1.72 1.17 59 BXD42 R0742F1 e_B3 B 15.095 41.37 0.319 0.66 0.022 1.27 1.24 60 BXD43 R1199F1 e_B3 A 6.171 41.28 0.523 0.458 0.019 1.06 1.23 60 BXD43 R1199F1 e_B3 B 16.534 40.32 0.291 0.685 0.024 0.99 1.54 61 BXD43 R0980F1 e_B4 A 1.592 63.75 0.591 0.392 0.017 1.76 0.95 61 BXD43 R0980F1 e_B4 B 5.815 48.89 0.378 0.601 0.021 2.06 0.97 62 BXD44 R1072F1 e_B3 A 7.858 41.12 0.476 0.502 0.022 1.52 1.74 62 BXD44 R1072F1 e_B3 B 23.065 41.32 0.264 0.717 0.019 1.25 1.84 63 BXD45 R1398F1 o_B3 A 13.911 45.87 0.384 0.595 0.021 1.24 1.7 63 BXD45 R1398F1 o_B3 B 40.07 47.47 0.178 0.805 0.017 1.21 1.68 64 BXD45 R1658F2 e_B4 A 2.368 56.29 0.573 0.408 0.019 1.42 0.84 64 BXD45 R1658F2 e_B4 B 7.006 49.52 0.372 0.608 0.02 1.45 0.8 65 BXD48 R0946F1 e_B3 A 6.565 47.79 0.487 0.493 0.021 1.68 1.27 65 BXD48 R0946F1 e_B3 B 17.499 41.87 0.292 0.687 0.021 1.54 1.35 66 BXD51 R1430F1 e_B3 A 7.042 57.48 0.46 0.519 0.022 1.17 1.29 66 BXD51 R1430F1 e_B3 B 19.373 48.26 0.259 0.72 0.021 2.07 1.48 67 BXD51 R1001F1 e_B3 A 4.689 58.81 0.501 0.48 0.019 1.88 1.31 67 BXD51 R1001F1 e_B3 B 16.032 55.59 0.266 0.715 0.019 1.31 1.64 68 BXD60 R1075F1 g_B3 A 8.189 49.9 0.465 0.513 0.022 1.39 1.34 68 BXD60 R1075F1 g_B3 B 19.219 45.14 0.277 0.705 0.018 1.77 1.41 69 BXD62 R1027F1 e_B3 A 7.447 44.42 0.491 0.488 0.021 2.03 1.23 69 BXD62 R1027F1 e_B3 B 19.391 41.09 0.285 0.696 0.019 1.05 1.44 70 BXD69 R1438F1 e_B3 A 6.297 44.19 0.512 0.469 0.019 1.77 1.5 70 BXD69 R1438F1 e_B3 B 12.335 46.58 0.311 0.667 0.021 1.25 1.62 71 BXD69 R1193F1 o_B3 A 5.749 83.56 0.414 0.564 0.022 1.49 1.58 71 BXD69 R1193F1 o_B3 B 20.513 44.28 0.261 0.718 0.021 1.14 1.58 72 BXD73 R1275F1 e_B3 A 6.478 40.91 0.499 0.481 0.02 1.05 1.52 72 BXD73 R1275F1 e_B3 B 16.931 41.6 0.299 0.681 0.02 1.62 1.53 73 BXD73 R1442F1 g_B3 A 8.584 62.86 0.428 0.552 0.02 1.78 1.69 73 BXD73 R1442F1 g_B3 B 17.378 55.71 0.26 0.72 0.02 1.17 1.83 74 BXD77 R1426F1 g_B3 A 6.306 46.27 0.501 0.481 0.018 1.77 1.49 74 BXD77 R1426F1 g_B3 B 13.365 48.96 0.309 0.67 0.022 1.26 1.63 75 BXD87 R1713F1 e_B3 A 6.243 39.43 0.515 0.466 0.018 1.38 1.34 75 BXD87 R1713F1 e_B3 B 14.997 42.78 0.305 0.673 0.022 1.71 1.58 76 BXD90 R2628F1 e_B4 A 2.096 58.74 0.572 0.412 0.016 1.57 0.82 76 BXD90 R2628F1 e_B4 B 8.913 49.12 0.332 0.646 0.023 1.88 0.85 77 BXD90 R1452F g_B3 A 7.478 52.26 0.449 0.531 0.02 1.17 1.74 77 BXD90 R1452F g_B3 B 15.469 40.59 0.312 0.668 0.02 1.7 1.74 78 BXD92 R1299F1 e_B3 A 8.264 45.38 0.478 0.503 0.019 1.4 1.37 78 BXD92 R1299F1 e_B3 B 18.369 43.4 0.29 0.689 0.021 1.91 1.6

    About the array platform :

Affymetrix Mouse Genome 430A and B array pairs: The 430A and B array pairs consist of 992936 25-nucleotide probes that collectively estimate the expression of approximately 39,000 transcripts. The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequences as the 430 2.0 series. However, we have found that roughy 75000 probes differ from those on A and B arrays and those on the 430 2.0

    About data processing:

Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.

• Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell.
• Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform.
• Step 3: We computed the Z scores for each cell value.
• Step 4: We multiplied all Z scores by 2.
• Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
• Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same.
• Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5.
• Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5.
• Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables.

Probe set data: The expression data were processed by Yanhua Qu (UTHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed. Probe set values listed in WebQTL are the averages of biological replicates within strain. A few technical replicates were averaged and treated as single samples. A 1-unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.

• Setp 1: Get CAB file for all arrays (121 arrays)
• Setp 2: Unpack CAB file using GCOS 1.4 DAT, CEL, RPT, CHP
• Setp 3: Put RPT data into spreadsheet
• Setp 4: Remaining N CEL data files were transformed to old CEL format using Transfer Tool (121 arrays)
• Setp 5: Old CEL format files transformed using RMA and PDNN (121 arrays). 430A set and 430B set arrays are processed separately using RMA and PDNN, Normalize 430A and 430B separately to Z Scores (2Z+8).
• Setp 6: Examine all scatter plots of the probe sets using DataDesk and categorized them by similarity. We are looking for batch and sub-batch structure. There are still quite obvious differences. For the INIA data we defined 5 groups that did NOT align exactly with the batches. The results are indicated in the table under the heading "Final Grouping." These are letters followed by the batch. For example "e_2" is an "e" type data set from batch 2. The prefix "s" means that an array was considered the "standard" for a particular group. For example sgA_2 is the "standard" for the gA group and was a member of batch 2. We defined groups "e" (originally "e" stood for 'excellent'), "g" (originally 'g' stood for good), "o" (OK), "w" (wide), and "gA" (good subdivision A).
• Setp 7: Delete obviously bad arrays (n of 3 were deleted, leaving 118 arrays). Array BXD8(S167) is high scale factor (A:16.797,B:35.646); BXD18(R1220) and BXD33(R2627) are high 3'/5' B_Act_Sig(64.20), GAPD_Sig(84.20) and B_Act_Sig(49.92), GAPD_Sig(84.17).
• Setp 8: Group rescale four minor groups to the same level of the largest group (please note that a group may have arrays from multiple physical batches). This group correction is done on a probe_set-by-probe_set level. The result of this rescaling is a group corrected data set.
• Setp 9: Look at the group rescaled arrays and delete any arrays that do not look good where good is usually a correlation of >0.96 with respect to other arrays. For the INIA data set of 118 arrays we deleted 40 arrays using very strict goodness criteria.
• Setp 10: Reprocess the remaining 78 good old-format CEL files and process as in Step 5. , 430A set and 430B set separately using RMA and PDNN, Normalize 430A and 430B separately to Z Scores (2Z+8).
• Setp 11: Bring the two arrays (430A and 430B) into alignment. To do this we regressed Z scores of the common set of 100 probe sets to obtain a linear regression corrections to rescale the 430B arrays to the 430A array values. Make data sets for RMA_430AB and PDNN_430AB. Normalize 430AB to Z Scores.
• Setp 12:Rank order of Probe Sets: Run all of the arrays through a second quantile normalization. This involves computing the average of all probe sets across all arrays. These averages are then rank ordered. We also rank order each of the individual array data sets. Probe sets for each individual array are then assigned a new expression value based on 1. Its rank within the particular array and 2. the value of that particular rank taken from the AVERAGE data. This forces every array to have exactly the same distribution as the average data. The result of this process is colinear expression of all arrays.
• Setp 13: We normalize the means of each of these groups to a common value set to the largest group (group e now with 37 members). If the mean for probe set 100001 is 8 in group e whereas group g a mean 8.5, then we just have a correction factor of 8/8.5 for probe set 100001 in the group g. The intent of this step is to correct for group effect on a probe set by probe set level.
• Setp 14: Verify that all arrays have correlations >0.98 using RMA transform. Two arrays discovered that escaped deletion. Delete these arrays (BXD32-R1214, BXD39-R0602)
• Setp 15: Finally, we compute the arithmetic mean of the values for the set of 76 final arrays for each strain.

This data set include further normalization to produce final estimates of expression that can be compared directly to the other transforms (average of 8 units and stabilized standard deviation of 2 units within each array). Please seee Bolstad and colleagues (2003) for a helpful comparison of RMA and two other common methods of processing Affymetrix array data sets.

    About the chromosome and megabase position values:

The chromosomal locations of probe sets included on the microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.

    Data source acknowledgment:

Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core.

    Information about this text file:

This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005.