Transcriptomics

Dataset Information

33

CAST x C57 QTLs Effect on Gene Expression for Chromosomes 2, 11, and 17


ABSTRACT: Three congenic mouse strains were profiled with microarrays and were analyzed using a QTL/Microarray approach to identify candidate genes that regulate biometric phenotypes: HG2D (HG.CAST-(D2Mit329-D2Mit457)), HG11 (HG.CAST-(D11Mit260-D11Mit255, MGI reference: 3771218), and HG17 (HG.CAST-(D17Mit196-D17Mit190); MGI reference: 3771215). All these congenic strains isolate CAST/EiJ (CAST) alleles in a C57BL/6Jhg/hg (C57) background and bare the hg deletion in the high growth locus on chromosome 10. F2 animals from intercrossing congenic males and C57 control females were profiled for gene expresion on brain, liver and gonadal white fat. To detect differential expression produced by allelic effects of biometric QTLs on chromosomes 2, 11, and 17. Three strains were profiled: HG2D, HG11, and HG17, isolating CAST alleles in a high growth (HG) background on chromosomes 2, 11, and 17 respectively. Four biological replicates were assayed per strain for brain, liver and gonadal white adipose tissue. Experiments for each chromosomes were done independently. Only genotype comparisons within tissue in each strain were performed.

ORGANISM(S): Mus musculus  

SUBMITTER: Craig H Warden  Juan F Medrano   Ricardo A Verdugo   Ricardo Alejandro Verdugo    

PROVIDER: E-GEOD-22042 | ArrayExpress| 2012-03-27

SECONDARY ACCESSION(S): GSE22042PRJNA128995

REPOSITORIES: GEO, ArrayExpress

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Publications

Serious limitations of the QTL/microarray approach for QTL gene discovery.

Verdugo Ricardo A RA   Farber Charles R CR   Warden Craig H CH   Medrano Juan F JF  

BMC biology 20100712


It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL). However, the effectiveness of this approach has not been assessed.Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Thre  ...[more]

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