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Genome-wide 10K SNP profiles in heterogeneous stock rats that differ in glucose tolerance

ABSTRACT: Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE57117 | GEO | 2014/09/18

SECONDARY ACCESSION(S): PRJNA245470

REPOSITORIES: GEO

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Genome-wide 10K SNP profiles in heterogeneous stock rats that differ in glucose tolerance

Project description:Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance HS rats were euthanized at 17 weeks of age and tail sample was taken. Genomic DNA was extracted from tail of 23 HS rats with glucose intolerance and 23 HS rats with normal glucose. The Affymetrix 10K SNP array was used to genotype these animals.

2014-09-18 | E-GEOD-57117 | biostudies-arrayexpress

Gene expression profiles in heterogeneous stock rats that differ in glucose tolerance

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Project description:Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance HS rats were euthanized at 17 weeks of age and liver was immediately frozen in liquid nitrogen. RNA was extracted from liver of 23 HS rats with glucose intolerance and 23 HS rats with normal glucose. The Affymetrix 230_2 array was used to probe transcript abundance levels.

2014-09-18 | E-GEOD-54935 | biostudies-arrayexpress

RNA-seq from amygdala tissue of 205 heterogeneous stock rats

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Project description:Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.

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Project description:These Heterogeneous Stock (HS) rats are derived from eight inbred progenitors through more than 60 generations of outbreeding. As a result they are fine-grained mosaics of the founder genomes, and well suited for high-resolution genetic mapping of complex traits. This experiment provides dense genotyping data for 1407 HS rats, 15 duplicates, and the 8 progenitors. From these data, each HS rat chromosome can be reconstructed as a mosaic of progenitor haplotypes. Together with phenotype and sequence data available elsewhere (DOI:10.1038/ng.2644), these data allowed fine-mapping of 160 complex traits, and identified causal genes at the QTLs. The sequences of the progenitors are available from ENA (study accession PRJEB3358, http://www.ebi.ac.uk/ena/data/view/PRJEB3358). A series of supporting data files are available from http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2332 , with an accompanying list (suppl_files_description.xlsx) describing each supporting file.

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