Comment[ArrayExpressAccession]	E-GEOD-46748
MAGE-TAB Version	1.1			
Public Release Date	2014-01-16
Investigation Title	Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling cancer progression			
Comment[Submitted Name]	Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling cancer progression
Experiment Description	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. 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.			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	li	Li	Wade	Grimm
Person First Name	ruifang	Ruifang	Paul	Sara
Person Mid Initials			A	
Person Email	lir4@niehs.nih.gov			
Person Affiliation	NIEHS			
Person Address	NIEHS, 111 T.W. Alexander Drive, RTP, NC, USA			
Person Roles	submitter			
Protocol Name	P-GSE46748-3	P-GSE46748-1	P-GSE46748-2	
Protocol Description	Basecalls performed using CASAVA version 1.8.2 Raw data was filtered to remove reads with average base quality score <20. Reads were mapped against mm9 reference genome with Bowtie (v0.12.8) with the following parameters: -m1 -v2 Replicate sequencing lanes from the same library were merged with MergeSamFiles.jar from the Picard suite (v1.62). Duplicate mapped reads were removed with MarkDuplicates.jar from the Picard suite (v1.62). Peak calls were performed with SICER (v1.03) with parameters window size 200, gap size 200, fragment size 200, and FDR cutoff 0.001. Input sequence was used for background. Mapped reads were extended at their 3' end to a length of 200 bases and converted to aggregate coverage (bedGraph format). Genome_build: mm9 Supplementary_files_format_and_content: bedGraph file per sample showing aggregate coverage of mapped extended reads; generated by BEDtools genomeCoverageBed. Supplementary_files_format_and_content: Called peaks or H3K27ac enrichment in BED format; peaks identified by SICER with parameters window size 200, gap size 200, fragment size 200, and FDR cutoff 0.001.	Female h-NAG-1 transgenic mice and wild type C57BL/6J mice at 5 weeks of age were placed on either 10% fat diet (D12450B) or 60% fat diet (D12492, Research Diets, New Brunswick, NJ) for 20 weeks. Male C57BL/6J mice on either 10% fat diet (380056 DIO controls) or 60% fat diet (380050 DIO high fat diet) were purchased from Jackson Laboratories and acclimated for one more week after transfer. The male mice were used for experiments after 15 weeks on high-fat diet.	Colonic epithelial cells were isolated as previously described (Roediger et al, 1979, Gut, 20: 484-488). Cells were treated with 1% formaldehyde in PBS for 10 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed with ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. h3k27ac antibody (Active Motif, cat no. 39133) was used for ChIP. Libraries were prepared using TruSeq™ RNA Sample Preparation kit (Illumina) following the manufacturer’s instructions. Illumina TruSeq RNA Sample Preparation Kit v1 was used for library preparation.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	
Experimental Factor Name	CHIP ANTIBODY	GENOTYPE	SEX	TREATMENT
Experimental Factor Type	chip antibody	genotype	sex	treatment
Comment[SecondaryAccession]	GSE46748			
Comment[GEOReleaseDate]	2014-01-16			
Comment[ArrayExpressSubmissionDate]	2013-05-08			
Comment[GEOLastUpdateDate]	2014-03-12			
Comment[AEExperimentType]	ChIP-seq			
Comment[SecondaryAccession]	SRP022181			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1029116-SRR847774			
SDRF File	E-GEOD-46748.sdrf.txt