Mouse Diversity Genotyping Array - CEL files
The Center for Genome Dynamics has made the Mouse Diversity Genotyping Array CEL files from its projects available to download.
1. ICR/HaJ: An Inbred ICR Strain
Outbred ICR mice, exemplified by the Crl:CD-1® (ICR) stock, are known for their fecundity. ICR/HaJ (009122), imported from Dr. Rosemary Elliott at the Roswell Park Cancer Institute, is fully inbred but maintains the excellent reproductive characteristics of outbred ICR mice. Inbreeding has fixed genes for susceptibility to certain carcinogens as colon tumors and adenocarcinomas were reported in 100% of mice by 24 wk following subcutaneous injection of 1,2-dimethylhydrazine [Jacoby et. al. (1994)22:381]. This strain shares the diabetogenic H2g7 MHC haplotype with another ICR-derived inbred strain, NOD/Shi LtJ (001976). However, ICR/HaJ are insulitis-and diabetes-free. Hence, like the NOR/LtJ strain, ICR/HaJ mice represent an additional control strain for studies designed to investigate the genetics of diabetes susceptibility and resistance.
We hybridized an ICR/HaJ DNA sample on the Mouse Diversity Genotyping Array. Raw data file: SNP_mDIV_A2-SNP10_143_080910.CEL
2. Reference Set
We hybridized 351 mouse DNA samples on the Mouse Diversity Genotyping Array. This sample set included classical inbred strains, wild-derived strains with varying degrees of inbreeding, consomic strains, recombinant inbred strains, samples from early generations of the Collaborative Cross, F1 hybrids created by crossing classical and/or wild-derived strains and wild mice.
Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, Pardo-Manuel de Villena F, Churchill GA
BMC Genomics. 2012 Jan 19;13(1):34. PMCID: PMC3305361 [ Full Text ] [ software ] [ datasets 1 ] [ datasets 2 ]
Supplemental Table S1 – Description of 351 Samples
Inbred samples used in the VINO analysis are listed first, followed by genotyping controls. CEL ID corresponds to the name of the Affymetrix CEL file containing raw
intensity data, which are available for download. Genetic distance is calculated as the fraction of non-reference allele calls out of all genotype calls.
Table Key - References
1. Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Hon-Tsen Yu A, Nachman MW, Pialek J, Tucker P,
Boursot P, McMillan L, Churchill GA, Pardo-Manuel de Villena F: Subspecific origin and haplotype diversity in the laboratory
mouse. Nat Genet 2011, 43:648–655.
2. Collaborative Cross Consortium: The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population. Genetics 2011, In press.
3. Peirce JL, Lu L, Gu J, Silver LM, Williams RW: A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 2004, 5:7.
4. Gregorová S, Divina P, Storchova R, Trachtulec Z, Fotopulosova V, Svenson KL, Donahue LR, Paigen B, Forejt J: Mouse consomic strains:
exploiting genetic divergence between Mus m. musculus and Mus m. domesticus subspecies. Genome Res 2008, 18:509-515.
5. This manuscript
7. Bonhomme F and Boursot P Montpellier, France
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All CEL files
To download All CEL files use this link: CEL_351files.zip (11 GB)
Individual CEL files
To download an individual CEL file click the CEL ID link in the table below. To download more than one CEL
file at a time select the files via the check boxes on the left hand side and hit the download button.