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Series GSE4494 Query DataSets for GSE4494
Status Public on Jul 28, 2007
Title Functional Gene Expression Differences between Inbred Alcohol-Preferring (iP) and non-preferring (iNP) Rats
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary The objective of this study was to test the hypothesis that innate differences in gene expression in the brain could
contribute to the differences in alcohol drinking or response to alcohol between adult male inbred alcohol-preferring (iP) and -non-preferring
(iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU) and
hippocampus (HIP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain).
Significant differences between the two strains for each region were determined using Statistical Analysis of Microarrays (SAM).
Using a false discovery rate threshold of 0.2, there were 46 genes with higher expression in iP rats and 61 genes with lower expression in
the ACB, 111 genes with higher and 56 genes with lower expression in the AMYG, 61 genes with higher and 25 genes with lower expression in the FC,
39 genes with higher and 42 genes with lower expression in the CPU, and 35 genes with higher and 51 genes with lower expression in the HIP.
In the AMYG, iP rats had higher expression of genes that are involved in neuronal growth and neurogenesis, e.g., brain derived neurotrophic factor,
neuritin, etc. In contrast, in the ACB, iP rats had lower expression of genes involved in neurogenesis or cellular plasticity,
e.g. cyclin E, vascular endothelial growth factor A. Many of the differences were in genes involved in intracellular signaling,
cell membranes, extracellular matrix, and metabolism. These regional gene differences between the iP and iNP rat lines may contribute to
the divergent alcohol drinking phenotypes of these rats.
Keywords: alcohol, inbred, rat, gene expression, brain, nucleus accumbens, amygdala, frontal cortex, hippocampus, caudate-putamen
 
Overall design Brain regions (accumbens, amygdala, frontal cortex, hippocampus, and striatum) from 6 biologic replicates of the selected inbred alcohol preferring and non-preferring lines iP5C and iNP1 were dissected and subjected to microarray analysis for comparison.
 
Contributor(s) Strother WN, Kimpel MW, McClintick JN, Carr LG, McBride WJ, Edenberg HJ
Citation(s) 17517326
Submission date Mar 17, 2006
Last update date Feb 21, 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)
GPL85 [RG_U34A] Affymetrix Rat Genome U34 Array
Samples (59)
GSM100999 cortex rattus_norvegicus_strain iP animal_number 1
GSM101000 cortex rattus_norvegicus_strain iP animal_number 2
GSM101001 cortex rattus_norvegicus_strain iP animal_number 3
Relations
BioProject PRJNA94373

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
GSE4494_RAW.tar 108.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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