NCI Mammary mRNA M430 RMA Database RMA (July/04 Freeze)
Used the Affymetrix M430A and M430B pair of arrays (total of 45,137 probe sets). Data available as CEL files from GeneNetwork upon request.
About the mice used to map microarray data:
The lines of mice used in this NCI-sponsored project consist of 18 groups of isogenic F1 progeny made by crossing females from each of 18 AKXD recombinant inbred strains (AKXD2, 3, 7, 9, 10, 11, 13, 14, 16, 18, 20, 21, 22, 23, 24, 25, 27, and 28) to male FVB/N mice that carry a transgene that consistently leads to the development of mammary tumors in females (e.g. Le Voyer et al., 2001). The formal nomenclature of the male transgenic line is FVB/N-TgN(MMTV-PyMT)634Mul. The genomes of each AKXD x FVB F1 consist of one set of FVB chromosomes (including the transgene) and one set of chromosomes inherited from one of the 18 AKXD RI strain mothers. Only the AKXD chromosomes are "recombinant" across this panel of F1 progeny, and the set therefore has a genetic architecture similar to backcross progeny. It is possible to map modifiers that influence tumor characteristics and expression patterns. It is also possible to study covariance of transcript expression levels in tumor tissue. For further background on this special mapping design please see Hunter and Williams (2002).
The ancestral strains from which all AKXD strains are derived are AKR/J (AKR) and DBA/2J (D2 or D). DBA/2J has been partially sequenced (approximately 1.5x coverage by D by Celera Genomics). Significant genomic sequence data for AKR is not currently available. Chromosomes of the two parental strains have recombined in the different AKXD strains. All of these strains are available from The Jackson Laboratory as cryopreserved stocks. For additional background on recombinant inbred strains, please see http://www.nervenet.org/papers/bxn.html.
About the tissue used to generate these data:
Mammary tumors used in this array experiment were derived from 18 sets of AKXD x FVB/N F1 females as described above. After the primary tumor was diagnosed, the animals were aged an additional 40 days to permit metastatic progression. Females were sacrificed and mammary tumors were harvested. Samples were processed and arrayed on Affymetrix M430A and M430B arrays. The majority of the samples were assayed on arrays obtained from the same lot number.
About the array
All samples were processed and arrayed in the Laboratory of Population Genetics at the NCI. The table below lists the arrays by Samples, AKXD strain and Age.
About the data processing:
Probe (cell) level data from the .CEL file: These .CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell.
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 Oct 2003 (mm4) 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.
Data source acknowledgment:
All of the NCI mammary mRNA M430A and M430B data sets have been generated by Kent Hunter at the Laboratory of Population Genetics at the National Cancer Institute in Bethesda. For contact and citations and other information on these data sets please review the INFO pages and contact Dr. Hunter regarding use of this data set in publications or projects..