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| Status |
Public on Jan 16, 2014 |
| Title |
male.rep3.WT_LF |
| Sample type |
SRA |
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| Source name |
male_WT_LF
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
gender: male
cell type: colon epithelial cells
treatment: low-fat diet
chip antibody: H3K27ac
chip antibody vendor: active motif
chip antibody cat. #: 39133
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| Treatment protocol |
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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Data processing |
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.
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| Submission date |
Nov 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
ruifang li |
| E-mail(s) |
lir4@niehs.nih.gov
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| Organization name |
NIEHS
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| Street address |
111 T.W. Alexander Drive
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| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE46748 |
Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling cancer progression |
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| Relations |
| BioSample |
SAMN02401999 |
| SRA |
SRX376979 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1263322_male.rep3.WT_LF.H3K27ac.SICER_peaks.bed.gz |
271.3 Kb |
(ftp)(http) |
BED |
| GSM1263322_male.rep3.WT_LF.H3K27ac.bedGraph.gz |
147.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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