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Uncovering the hepatic gene expression variations and sex-differences as response to high-fat diet consumption in the highly genetically diversity of the Collaborative Cross mouse model

ABSTRACT: Hepatic gene expression variations and sex-differences due to high-fat diet consumption using the Collaborative Cross mouse model

ORGANISM(S): Mus musculus

PROVIDER: GSE126490 | GEO | 2019/12/10

REPOSITORIES: GEO

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Uncovering the hepatic gene expression variations and sex-differences as response to high-fat diet consumption in the highly genetically diversity of the Collaborative Cross mouse model

Project description:Uncovering the hepatic gene expression variations and sex-differences as response to high-fat diet consumption in the highly genetically diversity of the Collaborative Cross mouse model

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Phenotypic and Gene Expression Features Associated with Variation in Chronic Ethanol Consumption in Heterogeneous Stock Collaborative Cross Mice

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Project description:The data was used for eQTL analysis of cecum gene expression in the Collaborative Cross Breeding Population.

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Project description:RNA-Seq was performed on all 8 mouse founder strains of the Collaborative Cross to obtain a comprehensive splicing landscape of each strain.

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Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel. We have mapped white spot, a discrete trait; body weight, a highly polygenic complex trait; and more than 11,000 liver gene expression traits. These analyses provide a glimpse of the potential mapping power and resolution of the CC. The goal of this project was to identify eQTLs for genome-wide gene expression from liver tissue in pre-CC mice. Gene expression profiling from liver tissue from pre-CC males. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 4-11 generations. One animal was sampled from 157 pre-CC strain. Hybridizations were performed at the Gene Expression Core Facility at The Jackson Laboratory. Samples were divided in six batches of about 11 to 24 samples. Two batches were performed per day. Probe-level data was summarized by a custom CDF file based on Ensembl genes (NCBI 37, Ensembl 49; htttp://brainarray.mbni.med.umich.edu). The parental strains are not part of this submission.

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