UCHSC BXD Whole Brain M430 2.0 November 2006 RMA modify this page

    Summary:

This November 2006 data freeze provides estimates of mRNA expression in whole brains of BXD recombinant inbred mice measured using Affymetrix MOE 430 version 2 micorarrays. Data were generated at the University of Colorado at Denver and Health Science Center (UCDHSC). Single whole brain samples were hybridized to 248 individual arrays. Data were processed using the RMA protocol followed by a secondary quantile normalization at the probe set level and a scale and location adjustment to ensure an average expression level of 8 units and a standard deviation of 2 units for easy comparison to other transforms.

    About the cases used to generate this set of data:

This data set includes estimates of gene expression for 50 genetically uniform lines of mice: C57BL/6J (B6 or simply B), DBA/2J (D2 or D), 30 BXD recombinant inbred (RI) strain derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations, and 18 other inbred strains of mice available from the Jackson Laboratory. All mice used were naïve males from 70-90 days old. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. Another significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.

In this mRNA expression database we generally used stock obtained directly from The Jackson Laboratory between 2003 and 2005.

    About the tissue used to generate these data:

Naïve male mice were euthanized by CO2 exposure, and whole brains were removed and frozen on dry ice. Brains were stored at -70 deg C until used. The RNeasy Midi kit for lipid-rich tissues (Qiagen, Valencia, CA) was used to extract total RNA, and the RNeasy Mini kit (Qiagen) was used for cleanup. Biotin-labeled cRNA was obtained by in vitro transcription of the double-stranded cDNA that was originally synthesized from the total RNA. Each whole brain sample of biotin-labeled cRNA was fragmented and hybridized to a separate oligonucleotide array. After hybridization, the chips were stained with streptavidin-phycoerythrin conjugate and scanned using an Affymetrix GeneArray scanner.

Strain Sample Number Scale
factor
Average
background
Absent Marginal Present Affy-bActin Affy-GAPH
BXD1 1 0.343 65.57 45.5% 4.1% 50.4% 1.33 0.74
BXD1 2 0.362 68.26 46.9% 4.5% 48.6% 1.30 0.76
BXD1 3 0.375 66.19 46.9% 4.2% 48.9% 1.27 0.77
BXD1 4 0.408 57.16 45.0% 4.0% 51.1% 1.27 0.80
BXD2 1 0.270 60.53 44.0% 4.1% 51.8% 1.52 0.87
BXD2 2 0.280 67.57 45.0% 4.2% 50.8% 1.31 0.75
BXD2 3 0.295 67.03 45.2% 4.1% 50.7% 1.34 0.76
BXD2 4 0.209 99.86 50.0% 4.7% 45.3% 1.24 0.73
BXD2 5 0.246 73.28 46.2% 4.3% 49.5% 1.34 0.73
BXD5 1 0.249 75.34 47.3% 4.4% 48.3% 1.34 0.73
BXD5 2 0.306 70.11 47.5% 4.5% 47.9% 1.31 0.77
BXD5 3 0.265 64.80 44.8% 4.3% 50.9% 1.33 0.74
BXD5 4 0.282 66.04 45.5% 4.2% 50.4% 1.41 0.76
BXD5 5 0.216 71.87 46.0% 3.9% 50.1% 3.07 1.01
BXD6 1 0.294 66.72 45.8% 4.3% 49.9% 1.38 0.75
BXD6 2 0.304 62.83 45.8% 4.2% 50.0% 1.25 0.72
BXD6 3 0.301 61.80 45.3% 4.3% 50.5% 1.27 0.76
BXD6 5 0.273 67.04 44.4% 4.2% 51.4% 1.32 0.76
BXD6 6 0.272 66.39 45.4% 4.3% 50.3% 1.32 0.75
BXD8 1 0.207 81.90 44.0% 3.9% 52.1% 1.33 0.74
BXD8 2 0.254 70.19 44.0% 3.9% 52.0% 1.32 0.72
BXD8 3 0.300 72.61 46.0% 4.0% 50.0% 1.30 0.74
BXD8 4 0.457 52.63 39.5% 3.3% 57.2% 1.14 0.79
BXD8 5 0.381 55.09 41.2% 3.4% 55.4% 1.12 0.79
BXD9 1 0.349 90.32 48.5% 4.1% 47.4% 1.38 0.78
BXD9 2 0.241 86.66 51.2% 4.8% 44.0% 1.38 0.75
BXD9 3 0.284 67.21 47.2% 4.3% 48.5% 1.33 0.78
BXD9 4 0.303 64.47 46.9% 4.5% 48.6% 1.32 0.77
BXD9 5 0.351 59.40 47.4% 4.4% 48.2% 1.41 0.80
BXD9 6 0.312 63.41 46.3% 4.4% 49.4% 1.39 0.76
BXD11 1 0.267 61.85 44.6% 4.3% 51.1% 1.36 0.75
BXD11 2 0.317 63.76 45.3% 4.3% 50.4% 1.29 0.79
BXD11 3 0.306 59.35 44.8% 4.2% 51.0% 1.33 0.79
BXD11 4 0.223 98.84 51.1% 4.6% 44.3% 1.32 0.73
BXD11 5 0.292 65.03 45.4% 4.0% 50.5% 1.38 0.78
BXD12 1 0.357 54.50 42.5% 3.7% 53.8% 1.15 0.76
BXD12 2 0.379 55.05 42.7% 3.7% 53.6% 1.15 0.76
BXD12 3 0.347 56.34 43.2% 3.9% 52.9% 1.17 0.74
BXD12 4 0.541 65.16 43.1% 3.4% 53.6% 1.08 0.79
BXD12 5 0.178 96.04 43.4% 4.0% 52.7% 1.29 0.74
BXD12 6 0.234 67.32 43.0% 3.9% 53.0% 1.31 0.75
BXD12 7 0.255 68.41 42.7% 4.2% 53.2% 1.50 0.76
BXD13 1 0.285 59.51 45.8% 4.2% 49.9% 1.22 0.75
BXD13 2 0.275 67.19 44.9% 4.2% 50.9% 1.29 0.76
BXD13 3 0.277 66.05 45.7% 4.2% 50.2% 1.38 0.79
BXD13 4 0.214 82.73 48.6% 4.5% 46.9% 1.40 0.78
BXD13 5 0.237 71.73 46.0% 4.3% 49.7% 1.29 0.77
BXD13 6 0.308 57.58 47.2% 4.2% 48.6% 1.33 0.74
BXD14 2 0.372 58.42 46.8% 4.4% 48.8% 1.19 0.74
BXD14 3 0.354 57.39 45.0% 4.2% 50.8% 1.20 0.72
BXD14 4 0.296 64.96 45.7% 4.4% 49.9% 1.20 0.69
BXD14 5 0.257 66.46 44.9% 4.4% 50.8% 1.24 0.72
BXD14 6 0.418 54.03 47.4% 4.1% 48.5% 1.10 0.74
BXD15 1 0.396 58.77 43.6% 3.9% 52.5% 1.33 0.78
BXD15 2 0.270 151.42 52.7% 4.7% 42.6% 1.36 0.73
BXD15 3 0.366 70.26 44.7% 3.9% 51.4% 1.29 0.79
BXD15 4 0.407 53.40 43.6% 4.1% 52.4% 1.38 0.79
BXD16 1 0.388 48.98 43.7% 4.1% 52.2% 1.41 0.79
BXD16 2 0.353 55.48 43.7% 4.0% 52.3% 1.44 0.82
BXD16 3 0.339 61.60 45.3% 4.2% 50.5% 1.42 0.80
BXD16 4 0.240 95.15 50.4% 4.7% 44.9% 1.39 0.73
BXD16 5 0.270 70.63 46.3% 4.3% 49.4% 1.45 0.75
BXD16 6 0.281 72.99 47.0% 4.2% 48.8% 1.40 0.77
BXD18 1 0.384 59.78 45.4% 4.0% 50.6% 1.12 0.71
BXD18 2 0.288 93.67 49.5% 4.4% 46.1% 1.15 0.70
BXD18 3 0.286 89.64 45.2% 4.1% 50.8% 1.27 0.71
BXD18 4 0.294 69.85 44.0% 4.1% 51.8% 1.26 0.70
BXD18 5 0.417 59.80 47.0% 4.3% 48.7% 1.15 0.72
BXD18 6 0.373 65.30 45.9% 4.3% 49.8% 1.18 0.74
BXD19 1 0.364 59.35 46.7% 4.2% 49.1% 1.27 0.73
BXD19 2 0.419 59.77 46.8% 4.1% 49.1% 1.23 0.74
BXD19 3 0.303 62.66 46.0% 4.4% 49.6% 1.30 0.74
BXD19 4 0.280 91.00 51.8% 4.5% 43.7% 1.32 0.68
BXD19 5 0.303 66.18 47.1% 4.5% 48.4% 1.33 0.72
BXD19 6 0.389 63.61 47.5% 4.4% 48.1% 1.28 0.73
BXD21 1 0.350 75.93 44.9% 3.9% 51.3% 1.29 0.77
BXD21 2 0.338 59.00 43.8% 4.0% 52.1% 1.29 0.77
BXD21 3 0.304 59.94 44.9% 4.0% 51.2% 1.44 0.77
BXD21 4 0.235 94.44 51.0% 4.8% 44.2% 1.35 0.73
BXD21 5 0.310 64.22 46.9% 4.2% 48.9% 1.42 0.77
BXD22 1 0.363 58.10 45.3% 3.9% 50.8% 1.24 0.80
BXD22 2 0.385 55.58 44.5% 4.0% 51.5% 1.28 0.80
BXD22 3 0.345 61.03 46.8% 4.3% 48.9% 1.35 0.81
BXD22 4 0.242 85.36 53.6% 4.8% 41.6% 1.35 0.75
BXD22 5 0.316 62.02 47.3% 4.5% 48.2% 1.40 0.77
BXD22 6 0.325 66.38 47.5% 4.3% 48.2% 1.29 0.78
BXD23 1 0.276 75.99 45.3% 4.1% 50.6% 1.27 0.75
BXD23 2 0.333 81.76 47.9% 4.0% 48.1% 1.28 0.78
BXD23 3 0.275 102.46 47.4% 3.9% 48.8% 1.30 0.77
BXD23 4 0.178 115.83 50.2% 4.7% 45.2% 1.38 0.73
BXD23 5 0.258 92.38 47.6% 4.2% 48.2% 1.32 0.77
BXD23 6 0.256 88.23 46.3% 4.1% 49.5% 1.31 0.74
BXD24 1 0.348 71.69 44.9% 4.1% 51.1% 1.25 0.74
BXD24 2 0.324 74.05 44.3% 4.0% 51.7% 1.23 0.80
BXD24 3 0.401 64.08 45.6% 4.0% 50.4% 1.08 0.74
BXD24 4 0.246 82.84 45.7% 4.3% 50.0% 1.20 0.75
BXD24 6 0.389 54.28 44.3% 4.2% 51.5% 1.20 0.67
BXD27 1 0.507 50.08 43.6% 3.9% 52.5% 1.48 0.81
BXD27 2 0.468 51.29 44.0% 3.7% 52.3% 1.44 0.90
BXD27 3 0.526 49.67 43.5% 3.9% 52.6% 1.29 0.94
BXD27 4 0.537 48.92 43.5% 3.8% 52.8% 1.46 0.91
BXD28 1 0.284 51.58 44.6% 4.2% 51.2% 1.26 0.80
BXD28 2 0.322 50.16 44.9% 4.3% 50.8% 1.21 0.76
BXD28 3 0.397 50.97 45.9% 4.2% 49.9% 1.14 0.78
BXD28 4 0.330 74.26 51.4% 4.6% 44.0% 1.26 0.72
BXD28 5 0.284 52.34 44.3% 4.4% 51.3% 1.32 0.73
BXD28 6 0.349 57.14 47.8% 4.5% 47.7% 1.30 0.79
BXD29 1 0.422 58.68 44.0% 3.7% 52.3% 1.42 0.86
BXD29 3 0.400 58.72 43.1% 3.8% 53.2% 1.31 0.89
BXD29 5 0.365 61.79 46.9% 4.3% 48.8% 1.38 0.91
BXD31 1 0.379 51.10 45.8% 4.3% 50.0% 1.13 0.75
BXD31 2 0.333 48.64 43.7% 4.1% 52.2% 1.22 0.71
BXD31 3 0.519 47.71 48.2% 4.3% 47.5% 1.13 0.72
BXD31 4 0.243 75.24 48.6% 4.8% 46.6% 1.23 0.71
BXD31 5 0.325 53.19 46.9% 4.6% 48.6% 1.22 0.75
BXD31 6 0.320 46.98 44.5% 4.3% 51.2% 1.24 0.74
BXD32 1 0.256 70.43 45.4% 3.9% 50.8% 1.83 0.87
BXD32 2 0.288 67.44 44.5% 4.1% 51.4% 1.34 0.77
BXD32 3 0.361 58.13 44.4% 4.0% 51.6% 1.36 0.77
BXD32 4 0.367 61.39 44.7% 4.1% 51.2% 1.40 0.78
BXD32 5 0.324 68.04 45.6% 4.3% 50.1% 1.39 0.75
BXD32 6 0.266 95.49 50.8% 4.5% 44.6% 1.41 0.73
BXD33 1 0.344 61.65 44.9% 3.9% 51.2% 1.38 0.82
BXD33 2 0.356 61.04 44.7% 4.1% 51.2% 1.44 0.79
BXD33 4 0.385 59.92 44.1% 3.9% 52.0% 1.38 0.82
BXD34 1 0.297 91.13 52.1% 4.6% 43.3% 1.34 0.70
BXD34 2 0.508 51.79 44.8% 3.9% 51.3% 1.42 0.76
BXD34 3 0.284 85.33 50.7% 4.6% 44.7% 1.51 0.72
BXD34 4 0.297 61.95 44.9% 4.1% 51.0% 1.36 0.77
BXD34 5 0.516 56.02 46.3% 4.0% 49.7% 1.33 0.74
BXD34 6 0.545 54.46 45.2% 3.8% 51.0% 1.49 0.87
BXD36 1 0.435 62.74 48.1% 4.0% 47.8% 1.36 0.73
BXD36 2 0.333 71.24 48.8% 4.3% 46.8% 1.44 0.72
BXD36 3 0.320 72.97 48.3% 4.3% 47.4% 1.38 0.74
BXD36 4 0.391 73.58 49.5% 4.2% 46.3% 1.25 0.75
BXD38 1 0.303 87.68 39.2% 3.3% 57.5% 1.08 0.82
BXD38 2 0.343 61.39 39.7% 3.2% 57.1% 1.12 0.82
BXD38 3 0.453 67.19 41.2% 3.4% 55.4% 1.11 0.83
BXD38 4 0.424 64.36 41.6% 3.5% 55.0% 1.11 0.82
BXD39 1 0.357 64.36 47.3% 4.3% 48.3% 1.33 0.78
BXD39 2 0.332 60.23 46.5% 4.2% 49.3% 1.41 0.80
BXD39 3 0.331 65.27 46.2% 4.2% 49.6% 1.32 0.75
BXD39 4 0.362 62.60 45.5% 4.0% 50.5% 1.28 0.80
BXD39 5 0.347 58.97 46.1% 4.3% 49.7% 1.29 0.79
BXD39 6 0.327 63.12 46.2% 4.3% 49.6% 1.29 0.77
BXD40 1 0.371 60.01 45.2% 4.1% 50.7% 1.32 0.77
BXD40 2 0.245 84.69 49.1% 4.5% 46.4% 1.33 0.72
BXD40 3 0.324 64.17 46.8% 4.3% 48.8% 1.34 0.73
BXD40 4 0.280 63.97 45.1% 4.2% 50.7% 1.48 0.74
BXD40 5 0.271 69.40 45.9% 4.3% 49.8% 1.33 0.74
BXD40 6 0.307 59.99 45.5% 4.2% 50.4% 1.37 0.76
BXD42 1 0.424 53.91 45.1% 4.1% 50.8% 1.54 0.83
BXD42 2 0.216 92.34 46.7% 4.3% 49.1% 1.44 0.76
BXD42 3 0.249 84.52 45.7% 4.1% 50.2% 1.52 0.80
BXD42 5 0.236 85.29 46.2% 4.0% 49.8% 1.38 0.77
DBA/2J 1 0.313 79.69 46.8% 4.2% 49.0% 1.24 0.72
DBA/2J 2 0.294 82.27 46.5% 4.2% 49.3% 1.27 0.73
DBA/2J 3 0.349 78.58 47.8% 4.3% 47.8% 1.31 0.73
DBA/2J 4 0.389 72.02 48.0% 4.3% 47.7% 1.21 0.77
DBA/2J 5 0.362 66.73 46.5% 4.4% 49.1% 1.23 0.75
DBA/2J 6 0.341 79.88 46.7% 4.0% 49.4% 1.33 0.74
C57BL/6J 1 0.294 82.84 46.7% 4.1% 49.2% 1.23 0.76
C57BL/6J 2 0.242 80.40 43.1% 4.1% 52.8% 1.29 0.76
C57BL/6J 3 0.250 110.90 47.8% 4.0% 48.2% 1.32 0.76
C57BL/6J 4 0.289 101.88 47.5% 4.1% 48.4% 1.18 0.75
C57BL/6J 5 0.299 114.59 48.7% 4.1% 47.3% 1.13 0.74
C57BL/6J 6 0.251 105.90 45.8% 3.8% 50.4% 1.30 0.76
129P3/J 1 0.496 59.26 41.9% 3.5% 54.5% 1.28 0.79
129P3/J 2 0.550 50.83 42.0% 3.7% 54.3% 1.16 0.78
129P3/J 3 0.443 56.08 43.0% 3.8% 53.3% 1.22 0.73
129P3/J 4 0.521 58.92 44.8% 3.8% 51.4% 1.30 0.74
129P3/J 5 0.503 58.26 44.9% 3.8% 51.3% 1.32 0.74
129S1/SvImJ 1 0.311 66.76 47.8% 3.9% 48.3% 2.04 0.97
129S1/SvImJ 2 0.262 57.63 44.5% 3.9% 51.6% 1.61 0.81
129S1/SvImJ 3 0.322 62.67 45.3% 3.8% 50.9% 1.70 0.83
129S1/SvImJ 4 0.185 119.02 50.2% 4.4% 45.5% 1.66 0.75
A/J 1 0.453 51.85 42.6% 3.6% 53.8% 1.20 0.73
A/J 2 0.396 56.61 45.9% 3.9% 50.2% 1.21 0.76
A/J 3 0.421 62.34 47.0% 4.1% 48.8% 1.29 0.72
A/J 4 0.508 61.52 48.2% 4.1% 47.7% 1.22 0.74
AKR/J 1 0.331 54.70 41.7% 3.9% 54.4% 1.22 0.74
AKR/J 2 0.464 55.46 44.1% 3.7% 52.1% 1.30 0.76
AKR/J 4 0.444 53.62 47.6% 4.0% 48.4% 1.23 0.71
AKR/J 5 0.439 58.62 47.4% 4.3% 48.3% 1.23 0.70
BALB/cByJ 1 0.336 75.49 50.0% 4.1% 45.9% 1.54 0.82
BALB/cByJ 2 0.280 67.93 47.1% 4.3% 48.7% 1.43 0.76
BALB/cByJ 3 0.312 73.77 47.7% 4.1% 48.2% 1.79 0.92
BALB/cByJ 4 0.262 79.97 46.1% 4.1% 49.8% 1.38 0.79
BALB/cByJ 5 0.276 81.32 46.3% 4.1% 49.6% 1.34 0.79
BALB/cJ 1 0.591 54.25 43.2% 3.5% 53.3% 1.15 0.80
BALB/cJ 2 0.346 50.36 39.9% 3.3% 56.8% 1.20 0.77
BALB/cJ 3 0.333 52.79 40.4% 3.7% 55.9% 1.25 0.77
BALB/cJ 5 0.495 54.78 45.0% 3.7% 51.3% 1.15 0.72
BTBR T+tf/J 3 0.315 62.83 46.4% 4.1% 49.5% 1.38 0.78
BTBR T+tf/J 4 0.243 90.12 51.6% 4.8% 43.6% 1.31 0.75
BTBR T+tf/J 5 0.294 71.21 46.6% 4.3% 49.0% 1.41 0.77
BTBR T+tf/J 6 0.268 67.53 46.6% 4.2% 49.2% 1.32 0.75
BTBR T+tf/J 1 0.370 55.40 45.7% 4.1% 50.2% 1.41 0.75
BTBR T+tf/J 2 0.488 50.89 47.2% 4.2% 48.6% 1.36 0.75
C3H/HeJ 1 0.511 59.20 43.3% 3.4% 53.3% 1.17 0.83
C3H/HeJ 2 0.405 79.49 41.3% 3.3% 55.5% 1.18 0.83
C3H/HeJ 3 0.454 59.47 41.7% 3.5% 54.9% 1.16 0.81
C3H/HeJ 4 0.448 56.28 41.5% 3.5% 55.0% 1.16 0.79
C3H/HeJ 5 0.389 50.17 41.1% 3.6% 55.2% 1.24 0.79
C58/J 1 0.336 56.66 46.0% 4.2% 49.8% 1.29 0.73
C58/J 2 0.372 58.61 46.7% 4.3% 49.0% 1.21 0.71
C58/J 3 0.366 64.58 46.8% 4.2% 49.0% 1.20 0.72
C58/J 4 0.371 52.72 45.3% 4.1% 50.6% 1.24 0.72
CAST/EiJ 1 0.467 55.74 47.1% 3.8% 49.1% 1.39 0.79
CAST/EiJ 2 0.545 50.29 46.8% 3.8% 49.4% 1.34 0.84
CAST/EiJ 3 0.469 55.08 47.4% 4.0% 48.5% 1.32 0.76
CAST/EiJ 4 0.390 83.05 53.0% 4.4% 42.6% 1.36 0.72
CBA/J 1 0.292 67.25 44.9% 4.0% 51.2% 1.22 0.76
CBA/J 2 0.347 61.99 46.4% 4.0% 49.7% 1.25 0.82
CBA/J 3 0.305 62.16 46.3% 4.3% 49.4% 1.31 0.75
CBA/J 4 0.303 64.82 46.5% 4.0% 49.5% 1.34 0.76
CBA/J 5 0.313 64.15 45.3% 4.1% 50.7% 1.37 0.78
CBA/J 6 0.365 56.84 45.6% 4.1% 50.4% 1.31 0.76
FVB/NJ 1 0.497 63.99 44.2% 3.5% 52.3% 1.33 0.79
FVB/NJ 2 0.475 55.24 44.8% 3.8% 51.4% 1.33 0.74
FVB/NJ 3 0.527 56.07 42.6% 3.5% 53.9% 1.31 0.86
FVB/NJ 4 0.447 62.56 41.7% 3.5% 54.8% 1.24 0.82
KK/HIJ 1 0.309 93.54 49.6% 4.3% 46.1% 1.57 0.74
KK/HIJ 2 0.298 63.24 48.0% 4.4% 47.6% 1.37 0.72
KK/HIJ 4 0.223 93.03 44.7% 4.0% 51.3% 1.39 0.74
KK/HIJ 5 0.153 136.67 51.9% 4.6% 43.5% 1.24 0.71
MOLF/EiJ 1 0.339 67.11 49.1% 4.3% 46.6% 1.55 0.83
MOLF/EiJ 2 0.319 80.73 49.1% 4.2% 46.7% 1.52 0.78
MOLF/EiJ 3 0.380 69.03 49.1% 4.2% 46.7% 1.29 0.82
MOLF/EiJ 4 0.238 95.19 48.7% 4.1% 47.2% 1.35 0.79
NOD/LtJ 1 0.356 78.42 49.1% 4.2% 46.7% 1.35 0.76
NOD/LtJ 2 0.422 59.71 47.4% 4.0% 48.5% 1.25 0.73
NOD/LtJ 3 0.377 77.84 49.8% 4.0% 46.2% 1.24 0.75
NOD/LtJ 4 0.535 60.86 50.6% 4.4% 45.0% 1.28 0.74
NOD/LtJ 5 0.336 74.58 46.6% 3.9% 49.5% 1.32 0.72
NZW/LacJ 2 0.442 50.31 44.6% 4.1% 51.3% 1.33 0.82
NZW/LacJ 3 0.331 56.86 44.2% 4.0% 51.7% 1.60 0.78
NZW/LacJ 4 0.338 55.23 44.1% 4.0% 51.9% 1.31 0.78
NZW/LacJ 5 0.351 56.90 49.3% 4.3% 46.5% 1.30 0.75
PWD/PhJ 1 0.444 57.65 47.2% 3.9% 48.9% 1.62 0.78
PWD/PhJ 2 0.328 67.58 47.3% 4.2% 48.5% 1.36 0.76
PWD/PhJ 3 0.322 73.90 47.5% 4.0% 48.5% 1.46 0.81
PWD/PhJ 4 0.271 75.79 46.1% 4.0% 50.0% 1.39 0.79
PWD/PhJ 5 0.191 144.73 57.7% 5.0% 37.3% 1.36 0.67
SJL/J 1 0.528 54.58 41.1% 3.4% 55.4% 1.16 0.80
SJL/J 3 0.663 56.21 41.8% 3.3% 55.0% 1.22 0.75
SJL/J 4 0.646 52.96 40.5% 3.2% 56.3% 1.13 0.81
SJL/J 5 0.639 61.91 44.8% 3.4% 51.9% 1.37 0.79

    About the array platform:

Affymetrix MOE430v2 GeneChip: The expression data were generated using 248 MOE430v2 arrays. The chromosomal locations of MOE430v2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6). This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).

    About data processing:

Probe set data: The expression data were processed by Laura Saba (UCDHSC). 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 within the rma function in R. This data set includes further normalization to produce final estimates of expression that can be compared directly to the other transforms.

This includes an initial quantile normalization on the RMA normalized probe set data followed by a transformation to force an array average of 8 units and stabilized standard deviation of 2 units within each array. Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other methods of processing Affymetrix array data sets.

Expression estimates (strain averages) range from a low of about 3.8 for probe set 1457109_x_at to a high of 15 for Gapdh (probe set 1418625_s_at). The mean expression of 8.0 actually represents a relatively low value of expression (roughly 250 on the original scale) because it is the average of all transcripts on the array, including those that are not expressed. Nonetheless, it is possible to obtain good signal down to very low values. For example, probe set 1437432_a_at (Trim12) has an average expression of 4.56 (extremely low), but it still is associated with a strong QTL (LRS of 45) precisely at the location of the parent gene (Chr 7 at 104 Mb). This demonstrates unequivocally that the small strain differences in expression of Trim12 measured by probe set 1437432_a_at is not noise but is generated by true allelic differences in Trim12 mRNA binding to the arrays.

    Data source acknowledgment:

Data was generated with funds from NIAAA for Gene Array Technology Center (AA013162) and from the NIAAA Integrated Neuroinformatics Resource for Alcoholism (AA013524).

    Information about this text file:

This text file originally generated by RWW, YHQ, August for UTHSC Brain mRNA U74Av2 (Aug05) RMA. Updated for UC Denver Whole Brain M430v2 BXD (Nov06) RMA Data by LMS, November 2006. Updated by RWW, Feb 2008.