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| Status |
Public on Dec 19, 2017 |
| Title |
HFD_male_HNF4a_ChIPSeq_replicate1 |
| Sample type |
SRA |
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| Source name |
colon epithelium
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| Organism |
Mus musculus |
| Characteristics |
tissue: colon epithelium
strain: C57BL/6
Sex: male
chip antibody: HNF4a (Abcam, ab41898)
diet: high fat diet
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chip-seq libraries were prepared by Bioo NEXTflex Rapid DNA-seq Kit (cat# 514402).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
ChIP-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered reads were mapped to mm9 via Bowtie (v0.12.8) with parameters -m 1 -X 2000 --chunkmbs 1024.
Duplicate read pairs were removed via MarkDuplicates.jar from the Picard tools suite v1.110.
For histone modification ChIPseq data, uniquely-mapped non-duplicate reads were downsampled to 10 million prior to peak-calling with SICER. SICER parameters were window size 200, gap size 200, FDR 0.001 for H3K27ac and window size 200, gap size 400, and FDR 0.001 for H3K4me1.
For NHF4a ChIPseq data, uniquely-mapped non-duplicate reads were downsampled to 20 million, then peak calls were made by HOMER at default parameters.
For all ChIP-seq data, mapped read depth files were generated by BEDtools genomeCoverageBed then by UCSC utility bedGraphToBigWig, after read pairs were converted to a single fragment by filling in region between read ends with Ns. Mapped depths are normalized to 10M for histone modification ChIP-seq data and 20M for HNF4a ChIP-seq data.
RNA-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered read pairs were mapped to mm9 via STAR v2.5 with the following paramters: --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000.
For each sample, counts per gene were extracted by subread featureCounts v1.5.0-p1 with parameters -s2 -Sfr -p.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq normalized mapped read depth in bigWig format.
Supplementary_files_format_and_content: ChIP-seq peak calls in BED format.
Supplementary_files_format_and_content: RNA-seq raw counts per gene per sample in tab-delimited text file.
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| Submission date |
Dec 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul A Wade |
| E-mail(s) |
wadep2@niehs.nih.gov
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| Phone |
919-541-3392
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| Organization name |
NIEHS
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| Department |
Laboratory of Molecular Carcinogenesis
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| Street address |
111 TW Alexander Drive
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE99670 |
Metabolic products of an obesity-associated microbiome impact host metabolism and disease risk by altering the epigenome |
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| Relations |
| BioSample |
SAMN08166449 |
| SRA |
SRX3466128 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2886563_HFD_male_HNF4a_ChIPSeq_replicate1.norm20M.bigWig |
263.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM2886563_HFD_male_HNF4a_ChIPSeq_replicate1_homerpeak.bed.gz |
191.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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