Transcriptomics

Dataset Information

9

Transcription profiling of rats from inbred alcohol-preferring and -non-preferring strains in five brain regions


ABSTRACT: 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-na√ɬØve 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. Experiment 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.

REANALYSED by: E-GEOD-4494

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Rattus norvegicus  

SUBMITTER: Mark William Kimpel  

PROVIDER: E-GEOD-4494 | ArrayExpress | 2008-11-22

SECONDARY ACCESSION(S): GDS2841GSE4494PRJNA94373

REPOSITORIES: GEO, ArrayExpress

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Publications

Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions.

Kimpel Mark W MW   Strother Wendy N WN   McClintick Jeanette N JN   Carr Lucinda G LG   Liang Tiebing T   Edenberg Howard J HJ   McBride William J WJ  

Alcohol (Fayetteville, N.Y.) 20070301 2


The objective of this study was to determine if there are innate differences in gene expression in selected CNS regions between 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 (HIPP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Using Linear Modeling for Microarray Analysis with a fal  ...[more]

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