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Series GSE46748 Query DataSets for GSE46748
Status Public on Jan 16, 2014
Title Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling cancer progression
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary High-fat diet and obesity are high risk factors for colorectal cancer. The underlying mechanism is still unclear. Environmental factors alter the epigenome to affect gene expression thus the phenotype. In response to external stimuli, the cis-regulatory regions, especially enhancer loci, are key elements for regulating selective gene expression. We thus explored the effects of high-fat diet and the accompanying obesity on gene expression and the enhancer landscape in colon epithelium. High-fat diet exposed binding sites of transcription factors downstream of signaling pathways important in the initiation and progression of colon cancer. Meantime, colon specific enhancers were lost rendering the cells potential for dedifferentiation. The alteration at enhancer regions drives a specific transcription program promoting colon cancer progression. The comprehensive interrogation of enhancer changes by high-fat diet in colon epithelium provides a number of insights into the underlying biology of high-fat diet and obesity in increasing colon cancer risk, and provides potential therapeutic targets to treat obese colon cancer patients.
 
Overall design ChIP sequencing of active enhancer mark h3k27ac in colon epithelium from wild type mice and NAG-1 transgenic mice treated with either low-fat diet or high-fat diet.

The gene expression component of the study is included in GSE46843.
 
Contributor(s) Li R, Wade PA, Grimm S
Citation(s) 24703701
Submission date May 08, 2013
Last update date May 15, 2019
Contact name ruifang li
E-mail lir4@niehs.nih.gov
Organization name NIEHS
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (18)
GSM1138117 female.rep1.WT_HF
GSM1138118 female.rep1.WT_LF
GSM1138119 female.rep1.NAG1_HF
Relations
BioProject PRJNA202232
SRA SRP022181

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
GSE46748_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BEDGRAPH)
Raw data are available in SRA
Processed data provided as supplementary file

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