UTHSC Brain mRNA U74Av2 (Mar03) MAS5

Accession number: GN3

    Summary:

This March 2003 data freeze provides estimates of mRNA expression in brains of BXD recombinant inbred mice measured using Affymetrix U74Av2 microarrays. This file is outdated and users are encouraged to use a more recent data set. All data were generated at the University of Tennessee Health Science Center (UTHSC). Samples from 31 strains were hybridized in small pools (n=3) to 92 arrays. Data were processed using the Microarray Suite 5 (MAS 5) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were adjusted to an average of 8 units and a variance of 2 units. In general, MAS 5 does not perform as well as RMA, PDNN, or the new heritability weighted transforms (HW1PM).

    About the cases used to generate this set of data:

This data set includes estimate of gene expression for 35 genetically uniform lines of mice: C57BL/6J (B6, or simply B), DBA/2J (D2 or D), their B6D2 F1 intercross, and 32 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 database (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.

    About the tissue used to generate these data:

Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).

    About the array platform:

Affymetrix U74Av2 GeneChip: The expression data were generated using U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium May 2004 (mm5) 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 (cell) level data from the CEL file: Probe signal intensity estimates in the Affymetrix CEL files are the 75% quantile value taken from a set of 36 (6x6) pixels per probe cell in the DAT image file.

• Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
• Step 2: We took the log2 of each cell signal intensity.
• Step 3: We computed the Z score for each of these log2 cell signal intensity values within a single array.
• Step 4: We multiplied all Z scores by 2.
• Step 5: We added a constant of 8 units to the value of the Z score. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8 units, a variance of 4 units, and a standard deviation of 2 units. The advantage of this modified Z score is that a 2-fold difference in expression level corresponds roughly to 1 unit.
• Step 6: We computed the arithmetic mean of the values for the set of microarrays for each strain. We have not corrected for variance introduced by sex, age, source of animals, or any possible interaction. We have not corrected for background beyond that implemented by Affymetrix in generating the CEL file.

Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefor represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to the noise level.

    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 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, EJC, and YHQ, March 2003. Updated by RWW, October 30, 2004.