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Series GSE85731 Query DataSets for GSE85731
Status Public on Dec 19, 2017
Title Epigenetic memory of obesity in mouse colonic epithelium
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Colorectal cancer is the third most common cancer. Obesity is a major risk factor with long-lasting effects on the predisposition to colorectal cancer; however, the mechanistic underpinnings remain poorly understood. To explore epigenetic mechanisms involved, we performed whole-genome bisulfite sequencing and RNA-Seq in colonic epithelium from control mice, obese mice, and formerly obese mice. We found that obesity-induced DNA methylation changes reprogrammed the transcriptome leading to a metabolic switch favoring long chain fatty acid oxidation, which is essential to colonic stem cell functions and colon tumorigenesis. Remarkably, persistent changes were observed after weight loss mainly at metabolic and cancer-related genes, underlying the long-term predisposition to colorectal cancer. In summary, we provide the epigenetic and metabolic basis of the link between obesity and colorectal cancer.
Overall design Whole-genome bisulfite sequencing, bisulfite PCR deep sequencing, and RNA-Seq were performed in colonic epithelium from mice on three different dietary regimens as follows: 1) low-fat diet for 20 weeks; 2) high-fat diet for 20 weeks; 3) high-fat diet for an initial 15 weeks then switched to low-fat diet for another 5 weeks.
Contributor(s) Li R, Grimm S, Wade P
Citation(s) 29346762
Submission date Aug 17, 2016
Last update date May 15, 2019
Contact name Paul A Wade
Phone 919-541-3392
Organization name NIEHS
Department Laboratory of Molecular Carcinogenesis
Street address 111 TW Alexander Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (45)
GSM2283268 LF1, RNAseq
GSM2283269 LF2, RNAseq
GSM2283270 LF3, RNAseq
BioProject PRJNA339220
SRA SRP082360

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Supplementary file Size Download File type/resource
GSE85731_BSPseq.pctMeth_at_CpG_sites.txt.gz 9.3 Kb (ftp)(http) TXT
GSE85731_RAW.tar 30.1 Gb (http)(custom) TAR (of BIGWIG)
GSE85731_RNAseq.DESeq2_DEGs.HFLF_vs_LF.txt.gz 874.8 Kb (ftp)(http) TXT
GSE85731_RNAseq.DESeq2_DEGs.HF_vs_LF.txt.gz 863.5 Kb (ftp)(http) TXT
GSE85731_RNAseq.counts_per_gene.txt.gz 861.2 Kb (ftp)(http) TXT
GSE85731_WGBS.HF_vs_LF.DMRs.bed.gz 68.5 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file

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