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Series GSE9186 Query DataSets for GSE9186
Status Public on Nov 06, 2007
Title CGH analysis of inbred mouses strains
Organism Mus musculus
Experiment type Genome variation profiling by genome tiling array
Summary The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes.
Keywords: comparative genomic hybridization
 
Overall design DNA from two individual mice per strain, for each of 42 strains was hybridized onto Agilent CGH arrays along with DNA from a reference C57BL/6J sample. One replicate per strain was labeled with Cy5 and one with Cy3, so each biological replicate is also a dye-flip replicate.
 
Contributor(s) Cutler G, Marshall L, Chin N, Baribault H, Kassner PD
Citation(s) 17989247
Submission date Sep 27, 2007
Last update date Dec 06, 2012
Contact name Gene Cutler
Organization name Amgen Inc
Department Lead Discovery
Street address 1120 Veterans Blvd
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platforms (1)
GPL4092 Agilent-014695 Mouse Genome CGH Microarray 244A (G4415A) (Feature Number version)
Samples (84)
GSM231767 C58/J
GSM231768 C58/J rev
GSM231769 NZB/BINJ
Relations
BioProject PRJNA102755

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9186_RAW.tar 5.1 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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