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- SJUT M430 Cerebellum Database (January/04 Freeze) About the mice used to map microarray data: - -The set of mouse strains used for mapping (a mapping panel) consists of groups of genetically unique BXD recombinant inbred strains. The ancestral strains from which all BXD lines are derived are C57BL/6J (B6 or B) and DBA/2J (D2 or D). Both B and D strains have been almost fully sequence (8x coverage for B6, and 1.5x coverage for D by Celera Genomics). Chromosomes of the two parental strains are recombined randomly in the many different BXD strains. BXD lines 2 through 32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through 42 were also produced by Dr. Taylor, but they were generated in the 1990s. All of these strains are available from The Jackson Laboratory. Lines such as BXDA12, BXDA20, etc. are BXD Advanced recombinant inbred strains that are part of a large set now being produced by Drs. Lu Lu, Guomin Zhou, Lee Silver, Jeremy Peirce, and Robert Williams. There will eventually be ~45 of these BXDA strains. For additional background on recombinant inbred strains, - please see http://www.nervenet.org/papers/bxn.html. -- - About the tissue used to generate these data: -The January04 data is same as the October03 data these were processed in two large batches. We did correction for the two batches based on the October03 data set.The first batch (the May03 data set) consisted of samples from 20 samples and 20 strains run on Affymetrix MOE 430A and MOE430B GeneChip pairs (40 arrays total). The second batch of 29 samples, included may biological replicates, 2 technical replicates, and data for 9 new strains. Each individual array experiment involved a pool of brain tissue (intact whole cerebellum) taken from three adult animals usually of the same age. RNA was extracted at UTHSC and all samples were processed at the Hartwell Center (SJCRH, Memphis). We will eventually achieve a sample with good, but not perfect, balance of samples by sex and age. The age range may look broad, but translated into human terms corresponds to a range from about 20 years to 50 years. - -- -- - About data processing: - -Probe (cell) level data from the .CEL file: These .CEL values produced by MAS 5.0 are ~ 75% quantiles from a set of 22 pixel values per cell (6th-ranked pixel). -- - About the chromosome and megabase position values: - -The chromosomal locations of probe sets and gene markers on the 430A and 430B microarrays were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Feb 2002 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.- - Resolving Gene Identity and Position Problems: - -Probe sets that are intended to target transcripts from a single gene occasionally map to different chromosomes; for example, M430 probe sets that supposedly target the thyroid hormone alpha receptor (Thra, 1416958_at on M430A) maps to Chr 14 at 13.556 Mb. Since Thra maps to Chr 11 rather than Chr 14, it is likely that one or all of these Thra probe sets are mismapped or mislabeled as Thra. To determine which problem is more likely, we suggest that you re-BLAT the perfect match probe sequence. -This is quite simple. Just paste all of the perfect match probes (odd numbered probes) into a single -BLAT query. WebQTL will do this automatically for you from the bottom of any Probe Sequence -Table To do this:- - -- - (NOTE: BLAT is insensitive to sequence overlap and extra spaces. The sequence above is a concatenation of all PM probes without any concern for probe overlap. The Perfect Match sequences are available on WebQTL by selecting the Probe link on the Trait Data and Editing window).- - This will return this BLAT Search Results- - The result confirms that the probe set maps to Chr 14 (a score of 211 is good). However if you click on the browser link in the BLAT Search Results window you will see that the gene that these probes target is actually BC008556 (a nuclear receptor subfamily 1, group D, member 2 gene), not Thra.- - Data source acknowledgment: --Data were generated with funds contributed equally by The UTHSC-SJCRH Cerebellum Transcriptome Profiling Consortium. Our members include:- - Reference: None yet specifically for this project and data set - -- - - - |
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