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Series GSE6917 Query DataSets for GSE6917
Status Public on Jul 18, 2007
Title Effects of Phenylethyl Isothiocyanate on N-Nitrosomethylbenzylamine-induced Cytotoxicity in Rat Esophagus
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary To date, there is little information on early molecular events in the development of N-nitrosomethylbenzylamine (NMBA) induced esophageal tumorigenesis and of the effects of chemopreventive agents on these events. In this study, we identified genes in rat esophagus that were differentially expressed in response to short–term NMBA-treatment and modulated by co-treatment with phenethylisothiocyanate (PEITC). Rats were fed AIN-76A diet or AIN-76A diet containing PEITC for three weeks. During the third week of dietary treatment, they were administered three s.c. doses of NMBA (0.5 mg/kg b.w.). Rats were sacrificed 24 h after the last treatment, esophagi excised and processed for histological grading, microarray and real-time PCR analysis. Our histopathological data showed that treatment of rats with PEITC had protective effect on NMBA-induced preneoplastic lesions in the rat esophagus. We identified 2261 genes that were differentially expressed in the NMBA-treated vs. control esophagi and 1936 genes in the NMBA+PEITC- vs. NMBA-treated esophagi. The intersection of these two sets resulted in the identification of 1323 genes in NMBA-treated esophagus that were modulated by PEITC to near-normal levels of expression. The measured changes in the expression levels of 10 selected genes were validated using real-time PCR. Principle components analysis (PCA) was applied to all twelve microarrays in the study, which suggested that in terms of global gene expression, PEITC treatment had a genome-wide modulating effect on NMBA-induced gene expression. Samples obtained from animals treated with PEITC alone or co-treated with NMBA were more similar to controls than they were to NMBA treatment alone.
Keywords: Toxicogenomics,reference design
 
Overall design For each treatment we used a pooling strategy to enable the inclusion of samples from numerous animals. Three replicate microarrays were completed for each of the four treatments (control, PEITC, NMBA and NMBA+PEITC) for a total of twelve microarrays. Each microarray was hybridized using a pooled RNA sample, and each pool was created from equal amounts of total RNA from two or three independent RNA samples, representing individual animals. Each of these samples was obtained from a different animal, and no sample was included in more than one pool. In total, samples from nine animals per group were pooled for control, NMBA, PEITC and NMBA+PEITC microarrays. To facilitate comparisons of gene expression across all treatments, we utilized a reference design in which each microarray was co-hybridized with a common reference sample labeled with Cy3, and RNA from the treatment pool was labeled with Cy5. Stratagene’s Universal Rat reference RNA (Stratagene, La Jolla, CA) was used as the common reference in all microarrays.
 
Contributor(s) Reen RK, Dombkowski AA, Kresty LA, Cukovic D, Mele JM, Salagrama S, Nines R, Stoner GD
Citation(s) 17616710
Submission date Jan 30, 2007
Last update date Dec 06, 2012
Contact name Gary D Stoner
E-mail(s) gary.stoner@osumc.edu
Phone 614-293-3268
Fax 614-293-4072
Organization name Department of Internal Medicine
Department The Ohio State University
Street address 2001 Polaris Pkwy
City Columbus
State/province OH
ZIP/Postal code 43240
Country USA
 
Platforms (1)
GPL2877 Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version)
Samples (12)
GSM159376 Group 1 Control Untreated, pool #EP1 vs. reference pool
GSM159377 Group 1 Control Untreated, pool #EP2 vs. reference pool
GSM159378 Group 1 Control Untreated pool # EP3 vs. reference pool
Relations
BioProject PRJNA98131

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
GSE6917_RAW.tar 133.5 Mb (http)(custom) TAR (of TXT)

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