UTHSC Brain mRNA U74Av2 (Nov05) RMA

Accession number: GN96

    Summary:

This November 2005 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. Data were generated at the University of Tennessee Health Science Center (UTHSC). Over 200 brain samples from 32 strains were hybridized in small pools (n=3) to 75 arrays. Data were processed using the RMA protocol and are presented with secondary normalization to an average expression value of 8 units. The variance of each array has been stabilized to 2 units for easy comparison to other transforms (see below).

    About the cases used to generate this set of data:

This data set includes estimate of gene expression for 32 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 29 BXD recombinant inbred (RI) strains derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations. 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. A 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.

BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced 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). Only two of these incipient strains are included in the current data set (BXD67 and BXD68).

In this mRNA expression database we generally used progeny of stock obtained from The Jackson Laboratory between 1999 and 2001. Animals were generated in-house at the University of Alabama by John Mountz and Hui-Chen Hsu and at the University of Tennessee Health Science Center by Lu Lu and Robert Williams.

The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from three mice.

ID tube ID strain age sex scale factor background average present absent marginal AFFX-b-Actin AFFX-Gapdh chip by 1 S172F1 C57BL/6J 197 F 4.258 77.85 0.406 0.566 0.029 1.19 0.78 DP 2 S337F1 C57BL/6J 400 F 13.85 48.52 0.307 0.668 0.025 1.21 0.87 DP 3 S092F1 C57BL/6J 79 M 4.242 73.54 0.406 0.567 0.027 1.54 0.87 DP 4 S092F2 C57BL/6J 79 M 3.397 69.95 0.341 0.636 0.024 1.94 1 TS 5 S169F1 DBA/2J 71 F 5.409 82.14 0.374 0.598 0.028 1.64 0.84 DP 6 S286F1 DBA/2J 146 F 7.153 58.85 0.38 0.593 0.027 1.34 0.84 DP 7 S101F1 DBA/2J 224 M 12.767 73.57 0.464 0.519 0.017 1.77 0.85 DP 8 S098F1 DBA/2J 224 M 6.463 73.6 0.443 0.538 0.019 1.76 0.82 DP 9 S238F1 B6D2F1 62 F 4.413 66.75 0.4 0.576 0.025 1.26 0.86 DP 10 S191F1 B6D2F1 68 F 5.946 79.59 0.366 0.609 0.025 1.54 0.9 DP 11 S273F1 B6D2F1 182 F 6.343 56.54 0.389 0.584 0.027 1.68 0.93 DP 12 S233F1 BXD1 58 F 5.693 61.85 0.427 0.548 0.025 1.65 0.81 DP 13 S280F1 BXD1 396 F 8.435 57.1 0.369 0.601 0.03 1.53 0.94 DP 14 S342F1 BXD1 139 F 8.106 52.79 0.377 0.596 0.027 1.33 0.86 DP 15 UT701F1 BXD2 142 F 3.502 49.39 0.316 0.661 0.024 1.71 0.82 TS 16 S011F1 BXD2 64 M 9.868 111.34 0.356 0.623 0.02 1.65 0.9 DP 17 S340F1 BXD2 361 F 8.769 51.87 0.395 0.578 0.027 1.74 0.83 DP 18 UT744 BXD5 56 F 2.927 55.02 0.369 0.609 0.021 1.6 0.95 TS 19 UT728F1 BXD5 71 M 1.94 60.54 0.355 0.623 0.023 1.46 0.86 TS 20 UT746F1 BXD5 71 M 5.451 51.81 0.279 0.701 0.02 1.54 0.78 Ts 21 S378F1 BXD6 61 F 11.907 64.64 0.334 0.64 0.026 2.27 1.02 DP 22 S167F1 BXD8 72 F 5.004 67.36 0.397 0.576 0.027 1.26 0.78 DP 23 S343F1 BXD8 143 F 8.388 108.64 0.223 0.751 0.026 1.44 0.82 DP 24 S193F1 BXD9 432 F 4.356 65.64 0.433 0.543 0.024 2.42 1.06 DP 25 S270F1 BXD9 173 F 6.365 58.9 0.388 0.584 0.028 1.95 0.97 DP 26 S009F1 BXD9 79 M 5.54 108.74 0.419 0.564 0.017 1.49 0.87 DP 27 S194F1 BXD11 441 F 5.918 60.19 0.41 0.564 0.026 2.54 1.08 DP 28 S234F1 BXD11 51 F 13.033 51.65 0.34 0.631 0.028 1.47 0.84 DP 29 UT745F1 BXD11 97 F 3.28 71.75 0.314 0.666 0.021 1.98 1.02 TS 30 S281F1 BXD12 413 F 6.338 57.37 0.411 0.563 0.025 1.89 0.94 DP 31 S607F1 BXD12 178 M 4.064 104.51 0.357 0.619 0.024 1.73 0.81 DP 32 UT748F1 BXD13 86 F 1.67 73.3 0.394 0.585 0.021 1.72 0.96 TS 33 S195F1 BXD14 412 F 5.228 63.85 0.398 0.574 0.028 1.82 1.06 DP 34 UT705F1 BXD14 190 F 4.838 41.24 0.329 0.651 0.02 1.89 1.76 TS 35 UT706F1 BXD14 134 F 9.609 42.32 0.213 0.77 0.017 1.42 1.02 TS 36 S382F1 BXD16 354 F 15.561 59.63 0.307 0.667 0.027 2.06 0.98 DP 37 S334bF1 BXD18 57 F 13.787 52.44 0.301 0.674 0.025 1.84 0.94 DP 38 S362F2 BXD18 376 F 7.121 76.92 0.368 0.606 0.026 1.77 0.88 DP 39 S606F1 BXD18 200 M 4.381 57.38 0.427 0.542 0.031 1.56 0.9 DP 40 S236F1 BXD19 56 F 4.935 59.44 0.374 0.599 0.026 1.29 0.84 DP 41 S271F1 BXD19 163 F 4.705 64.74 0.425 0.546 0.029 1.68 0.84 DP 42 UT743F1 BXD21 64 F 2.996 49.56 0.391 0.587 0.022 1.12 0.83 TS 43 UT740F1 BXD21 67 F 5.069 49.3 0.288 0.691 0.021 1.82 0.87 TS 44 S120F2 BXD21 236 M 4.765 51.11 0.432 0.543 0.025 1.82 0.87 DP 45 S170F1 BXD22 176 F 5.278 72.7 0.39 0.582 0.028 1.45 0.8 DP 46 S383F1 BXD22 363 F 6.689 53.68 0.403 0.57 0.028 1.94 0.93 DP 47 UT815F1 BXD23 88 F 4.964 50.33 0.31 0.669 0.02 1.53 0.75 TS 48 S283F1 BXD24 394 F 5.714 52.6 0.421 0.552 0.027 1.66 0.85 DP 49 S384F1 BXD25 355 F 4.931 55.46 0.45 0.527 0.024 2 0.91 DP 50 S373F1 BXD25 74 F 3.81 55.67 0.472 0.504 0.024 1.49 0.76 DP 51 S376F2 BXD25 198 F 9.208 46.29 0.429 0.546 0.025 2.18 0.83 DP 52 S532F1 BXD25 90 F 9.489 47.05 0.406 0.567 0.027 1.64 0.84 DP 53 S197F1 BXD28 427 F 7.854 57.94 0.365 0.609 0.026 2.42 1.14 DP 54 S171F1 BXD28 192 F 15.407 59.24 0.321 0.653 0.026 1.37 0.82 DP 55 S381F1 BXD28 46 F 4.924 57.61 0.439 0.535 0.026 1.97 0.93 DP 56 S284F1 BXD29 416 F 5.16 54.1 0.447 0.53 0.023 2.61 1.19 DP 57 S344F1 BXD31 139 F 7.434 60.53 0.383 0.592 0.026 1.24 0.8 DP 58 S198F1 BXD31 98 F 3.634 76.61 0.414 0.558 0.028 1.73 0.97 DP 59 S336bF1 BXD31 70 F 15.326 49.99 0.295 0.681 0.024 1.41 0.85 DP 60 S534F2 BXD31 262 F 8.057 52.88 0.412 0.561 0.026 1.74 0.9 DP 61 S272F1 BXD32 178 F 7.488 76.4 0.34 0.635 0.025 1.69 0.87 DP 62 S341F2 BXD32 365 F 7.82 56.4 0.375 0.598 0.027 1.66 0.83 DP 63 Z621F1 BXD32 218 M 2.227 54.86 0.467 0.507 0.026 2 1.6 DP 64 Z633F1 BXD33 124 F 1.515 75.52 0.469 0.506 0.025 2.21 1.13 DP 65 UT704F1 BXD33 184 F 4.242 47.71 0.339 0.642 0.019 2.19 0.97 TS 66 Z632F1 BXD33 124 M 2.446 64.45 0.438 0.538 0.024 3.22 1.59 DP 67 UT747F1 BXD38 69 F 2.111 61.16 0.404 0.575 0.021 1.67 0.78 TS 68 UT780 BXD38 55 F 5.97 47.19 0.297 0.683 0.02 1.45 0.81 TS 69 UT749F1 BXD38 69 M 1.15 84.52 0.435 0.544 0.021 1.48 0.82 TS 70 S598F1 BXD39 119 F 3.619 117.44 0.308 0.662 0.03 1.56 0.73 DP 71 S603-IFI BXD40 66 M 5.426 83.22 0.381 0.594 0.025 1.42 0.74 DP 72 Z640F1 BXD42 109 M 1.935 60.72 0.444 0.529 0.027 1.92 0.96 DP 73 UT767F1 BXD67 57 F 1.688 58.3 0.403 0.575 0.022 1.95 0.82 TS 74 S536F1 BXD67 79 F 3.886 98.34 0.358 0.616 0.026 1.65 0.92 TS 75 UT768F1 BXD68 276 M 2.627 79.2 0.32 0.659 0.02 1.69 1.07 TS

    About the samples used to generate these data:

Each array was hybridized with labeled cRNA generated from a pool of three brains from adult animals usually of the same age and always of the same sex. The brain region included most of the forebrain and midbrain, bilaterally. However, the sample excluded the olfactory bulbs, retinas, or the posterior pituitary (all formally part of the forebrain). A total of 75 such pooled samples were arrayed: 58 from females and 17 from males. Animals ranged in age from 56 to 441 days, usually with a balanced design: one pool at approximately 8 weeks, one pool at approximately 20 weeks, and one pool at approximately 1 year. Strain averages of mRNA expression level are therefore typically based on three pooled biological replicate arrays. This data set does not incorporate statistical adjustment for possible effects of age and sex. Users can select the strain symbol in the table above to review details about the specific cases and array processing center (DP = Divyen Patel at Genome Explorations, Inc; TS = Thomas Sutter at University of Memphis). You can also click on the individual symbols (males or females) to view the array image.

    About the array platform:

Affymetrix U74Av2 GeneChip: The expression data were generated using 75 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium March 2005 (mm6) assembly. 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 possiible 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 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.

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 variance 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.

    How to download these data:

All standard Affymetrix file types (DAT, CEL, RPT, CHP, TXT) can be downloaded for this data set by selecting the strain names in the table above and then selecting the appropriate file, or download the particular transform in an Excel work book with both individual arrays and strain means and SEMs. Please refer to the Usage Conditions and Limitations page and the References page for background on appropriate use and citations of these data.

    About the array probe set names:

Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:

f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.

s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.

g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.

r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.

i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).

st (sense target) : Designates a sense target; almost always generated in error.

Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.

    Data source acknowledgment:

Data were generated with funds to RWW from the Dunavant Chair of Excellence, University of Tennessee Health Science Center, Department of Pediatrics. The majority of arrays were processed at Genome Explorations by Dr. Divyen Patel. We thank Guomin Zhou for generating advanced intercross stock used to produce most of the new BXD RI strains.

    Information about this text file:

This text file originally generated by RWW, YHQ, and EJC, March 2004. Updated by RWW, November 30, 2005.