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U74Av2 dChip PM Database (December/03 Freeze) 
Accession number: GN23
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 100 arrays were used: 74 were female pools and 26 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). you can select the strain symbol in the table above to review some details about the specific cases. You can also click on the individual symbols (males or females) to view the array image.
About data processing:
Probe set data: The expression values
were generated using the dChip
including perfect match data.
- Step 1: We added an offset of 1 to the 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 6.1: We computed the arithmetic mean of the values for the
set of microarrays for each of technical duplicate for the individual
strains.
- Step 6.2: 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.
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.
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