U74Av2 dChip PM Database (August/03 Freeze)

Accession number: GN22

    About the mice used to map microarray data:

The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males. All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.

The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 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 data processing:

Probe set data from the .TXT file: These .TXT files were generated using the dChip including perfect match data.

• Step 1: We added an offset of 1 to the .TXT expression values for each cell to ensure that all values could be logged without generating negative values.
• Step 2: We took the log base 2 of each cell.
• Step 3: We computed the Z-score for each cell.
• 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 computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.

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 background noise levels.

    About the chromosome and megabase position values:

The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 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.

    About the array probe set names:

In addition to the _at (anti-sense target) and _st (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.

Probe set name designations

_f_at (sequence family): Includes probes that target identical and/or slightly polymorphic regions of different transcripts.

_s_at (similarity constraint): Probes all target common sequences found in multiple transcripts.

_g_at (common groups): Some of the probes target identical sequences and some target unique sequences regions .

_r_at (rules dropped): "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."

_i_at (incomplete): "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."

Most of the descriptions for the probe set ID extensions above 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.