NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE8885 Query DataSets for GSE8885
Status Public on Oct 28, 2007
Title Recurrent DNA copy number variation in the laboratory mouse
Organism Mus musculus
Experiment type Genome variation profiling by genome tiling array
Summary We have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high resolution microarrays to identify 38 CNVs between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. These recurrent CNVs are distributed throughout the genome, affect 43 genes, and fluctuate in copy number over mere hundreds of generations, observations that raise questions about their contribution to natural variation.
Keywords: comparative genomic hybridization, DNA copy number variation, structural variation, inbred mice, spontaneous mutation rate
 
Overall design IIn order to verify, precisely map, and accurately score spontaneous copy number mutations identified by our previous analysis using representational oligonucleotide microarray analysis (ROMA, see related submission), we performed comparative genome hybridization (CGH) for each strain using high resolution oligonucleotide microarrays (tiling arrays). These arrays contain 385,213 probes placed at high density (~1 per 46 bp) across each locus identified by ROMA. We performed at least two independent experiments for each of 25 strains, each compared to a single pedigreed individual of the C57BL6/J strain.
 
Contributor(s) Egan CM, Sridhar S, Wigler M, Hall IM
Citation(s) 17965714
Submission date Aug 27, 2007
Last update date Mar 17, 2012
Contact name Ira M Hall
E-mail(s) hall@cshl.edu
Phone 516-287-3764
Organization name Cold Spring Harbor Laboratory
Lab Hall
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platforms (1)
GPL5777 tiling-mouse-385K-v1.0
Samples (68)
GSM225066 B6ByJ.vs.B6J_hyb1
GSM225067 B6ByJ.vs.B6J_hyb2
GSM225068 B6Icr.vs.B6J_hyb1
Relations
BioProject PRJNA102263

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
GSE8885_RAW.tar 746.6 Mb (http)(custom) TAR (of FTR, PAIR)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap