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Series GSE7628 Query DataSets for GSE7628
Status Public on Mar 04, 2008
Title Evaluation of expression quantitative trait loci within two interacting blood pressure quantitative trait loci
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary Genetic dissection of the S rat genome has provided strong evidence for the presence of two interacting blood pressure (BP) quantitative trait loci (QTLs), termed QTL1 and QTL2, on rat chromosome 5. However, the identities of the underlying interacting genetic factors remain unknown. Further experiments targeted to identify the interacting genetic factors by the substitution mapping approach alone are difficult because of the interdependency of natural recombinations to occur at the two QTLs. We hypothesized that the interacting genetic factors underlying these two QTLs may interact at the level of gene transcription and thereby represent expression QTLs (eQTLs). To detect these interacting eQTLs, a custom QTL chip containing the annotated genes within QTL1 and QTL2 was developed and used to conduct a transcriptional profiling study of S and two congenic strains that retain either one or both the QTLs. The results uncovered an interaction between two transcription factors, DMRTA2 and NFIA. Further, the ‘biological signature’ elicited by these two transcription factors was differential between the congenic strain that retained LEW alleles at both QTL1 and 2 compared to the congenic strain that retained LEW alleles at QTL1 alone. A network of transcription factors potentially affecting BP could be traced, lending support to our hypothesis.
Keywords: rat, hypertension, genetics, polygenic trait, microarray, gene expression
 
Overall design Pairs of Cy5 and Cy3 labeled targets were co-hybridized onto either a custom long oligonucleotide microarray for the interrogation of 231 genes encompassed by QTL1 and QTL2, or a TIGR rat cDNA array consisting of 26,401 probe elements representing 20,465 unique non-QTL genes. A “flip-dye” or “balanced block” design was used as the experimental method of choice to account for potential dye-bias labeling effects. Six “balanced block” normalized files are submitted for the long oligonucleotide array interrogating the hearts from S versus S.LEW(5)x6x9 animals, fourteen “flip-dye” hybridizations are submitted for the cDNA array interrogating the hearts from S versus S.LEW(5)x6x9 animals, and twelve “flip-dye” hybridizations are submitted for the cDNA array interrogating the hearts from S versus S.LEW(5)x6x11 animals.

GPR and MEV files cannot be located.
 
Contributor(s) Joe B, Lee NH, Frank BC
Citation(s) 17938377
Submission date Apr 26, 2007
Last update date Jan 17, 2013
Contact name Norman H Lee
E-mail(s) phmnhl@gwumc.edu
Organization name The George Washington University Medical Center
Department Pharmacology & Physiology
Street address 2300 I Street, N.W.
City Washington, DC
State/province DC
ZIP/Postal code 20037
Country USA
 
Platforms (2)
GPL5126 TIGR_RAT_27k_cDNAarray_1
GPL5127 TIGR_RAT_target_oligoarray_1
Samples (30)
GSM184413 66666 (congenic) vs T2934 (parental)
GSM184466 66668 (congenic) vs T2945 (parental)
GSM184467 66670 (congenic) vs T2936 (parental)
Relations
BioProject PRJNA100255

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

Supplementary data files not provided
Processed data included within Sample table
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