Transcriptomics,Multiomics

Dataset Information

5

MRLxSM eQTL in Liver by RMA on Ensembl transcripts


ABSTRACT: A QTL analysis between inbred mouse strains MRL/MpJ and SM/J was performed to identify genetic loci influencing high-density lipoprotein (HDL) cholesterol and triglycerides (TG) at eight weeks of age in F2 mice fed a chow diet. In order to narrow down lists of candidate genes, expression levels from liver tissue were used to test for differential expression among parental and F1 strains and to scan for eQTL in F2 animals. We provide evidence for Mppe1 (Chr 18) as an HDL QTL candidate gene and Cyp2d26 (Chr 15) as a TG QTL candidate gene. MRL/MpJ (MRL) mice were crossed with male SM/J (SM) mice; their progeny were intercrossed to produce 371 F2 animals. Of these, 282 F2 males and females were profiled with Affy Mouse Gene 1.0 ST arrays for an eQTL study. Three animals from each parental and the F1 strains from each sex, i.e. 18 in total, were also profiled for testing differential expression. A total of 300 samples are included in the dataset. The mice were weaned at 3 weeks on a chow diet. At 13 weeks of age, mice were single housed for 3 days and fasted for 4 hours prior to being sacrificed. Tissue collection was performed between noon and 1pm to avoid variations due to circadian rhythm.

OTHER RELATED OMICS DATASETS IN: PRJNA134845

ORGANISM(S): Mus musculus  

SUBMITTER: Gary A Churchill   Rachael S Hageman  Ricardo A Verdugo  Magalie S Leduc  Kenneth Walsh  Beverly Paigen  Shirng-Wern Tsaih  Ricardo Alejandro Verdugo 

PROVIDER: E-GEOD-25322 | ArrayExpress | 2011-11-28

SECONDARY ACCESSION(S): GSE25322PRJNA134845

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-25322.README.txt Txt
E-GEOD-25322.idf.txt Idf
E-GEOD-25322.processed.1.zip Processed
E-GEOD-25322.raw.1.zip Raw
E-GEOD-25322.raw.2.zip Raw
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Publications

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice.

Leduc Magalie S MS   Hageman Rachael S RS   Verdugo Ricardo A RA   Tsaih Shirng-Wern SW   Walsh Kenneth K   Churchill Gary A GA   Paigen Beverly B  

Journal of lipid research 20110526 9


To identify genetic loci influencing lipid levels, we performed quantitative trait loci (QTL) analysis between inbred mouse strains MRL/MpJ and SM/J, measuring triglyceride levels at 8 weeks of age in F2 mice fed a chow diet. We identified one significant QTL on chromosome (Chr) 15 and three suggestive QTL on Chrs 2, 7, and 17. We also carried out microarray analysis on the livers of parental strains of 282 F2 mice and used these data to find cis-regulated expression QTL. We then narrowed the li  ...[more]

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