NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE5849 Query DataSets for GSE5849
Status Public on Feb 01, 2008
Title Identification of Candidate Genes for Alcohol Preference by Expression Profiling of Congenic Strains
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary 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.
Keywords: alcohol, congenic, rat, gene expression, brain, nucleus accumbens, amygdala, frontal cortex, hippocampus, striatum
 
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.
 
Contributor(s) Carr LG, Kimpel MW, Liang T, McClintick JK, McCall K, Grote M, Edenberg HJ
Citation(s) 17451403
Submission date Sep 15, 2006
Last update date Jul 31, 2017
Contact name Mark William Kimpel
E-mail(s) mkimpel@iupui.edu
Organization name Indiana University
Department Psychiatry
Lab W.J. McBride
Street address 15032 Hunter Court
City Westfield
State/province IN
ZIP/Postal code 46074
Country USA
 
Platforms (1)
GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
Samples (60)
GSM136446 accumbens rattus_norvegicus_strain congenic animal_number 1
GSM136447 striatum rattus_norvegicus_strain congenic animal_number 1
GSM136448 frontal_cortex rattus_norvegicus_strain congenic animal_number 1
Relations
BioProject PRJNA97253

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE5849_RAW.tar 259.5 Mb (http)(custom) TAR (of CEL)

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap