Transcriptomics

Dataset Information

3

Transcription profiling of rat brain to identify candidate genes for alcohol preference in congenic strains


ABSTRACT: A highly significant quantitative trait locus (QTL) that influenced alcohol preference was identified in the iP/iNP rats on chromosome 4. Congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP (NP.P) exhibited the expected increase in alcohol; consumption compared to the iNP background strain. This study was undertaken to identify genes in the chromosome 4 QTL interval that might; contribute to the differences in alcohol consumption between the alcohol-naïve congenic and background strains. RNA from five brain regions; from each of 6 NP.P and 6 iNP rats was labeled and analyzed separately on an Affymetrix Rat Genome 230 2.0 microarray. Expression levels; were normalized using robust multi-chip average (RMA). Differential gene expression was validated using quantitative real-time PCR. An analysis; combining five brain regions, including nucleus accumbens, frontal cortex, amygdala, hippocampus, and striatum, identified twenty three; transcripts and nine ESTs that were differentially expressed between the NP.P and iNP. Of the twenty three observed transcripts, thirteen; were known genes, 9 were predicted genes and all but one were located in the chromosome 4 QTL interval. Very interesting cis-regulated; candidate genes for alcohol consumption were identified using microarray profiling of gene expression differences in congenic animals carrying; a QTL for alcohol preference. Experiment Overall Design: Brain regions (accumbens, amygdala, frontal cortex, hippocampus, and striatum) from 6 biologic replicates of the selected non-preferring line NP and from a NP.P congenic line were dissected and subjected to microarray analysis for comparison.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Rattus Norvegicus

SUBMITTER: Mark William Kimpel  

PROVIDER: E-GEOD-5849 | ArrayExpress | 2008-06-14

SECONDARY ACCESSION(S): GSE5849PRJNA97253

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-5849.README.txt Txt
E-GEOD-5849.eSet.r Other
E-GEOD-5849.idf.txt Idf
E-GEOD-5849.processed.1.zip Processed
E-GEOD-5849.raw.1.zip Raw
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