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| Status |
Public on Oct 24, 2018 |
| Title |
C3-rep2.FOXA1_ChIP |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H/HeN
Sex: male
replicate animal: 2
chip antibody: FOXA1 (abcam, ab5089)
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| Treatment protocol |
Frozen livers were fixed with 1% formaldehyde at room temperature for 10 min. The fixed tissues were treated with a hypotonic buffer. Nuclei were resuspended with a lysis buffer containing 20 mM Tris- HCl pH 8.0, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF, 5 mM sodium butyrate, 0.1 % SDS and protease inhibitor cocktail).
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| Growth protocol |
Animals were housed in a pathogen-free environment, and no pathogens were identified in sentinel testing of serum and feces. At 20 weeks, all animals were euthanized by carbon dioxide asphyxiation. All animal studies were approved by the Alion Animal Care and Use Committee.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fragmented by sonication with Covaris S220. Immunoprecipitation was performed with FOXA1 antibody (abcam, ab5089)
NEXTflex Rapid DNA-Seq Library Prep Kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
C3.FOXA1_ChIP.downsampled.bigWig
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| Data processing |
For ChIP-seq data, cutadapt v1.2.1 was used to remove adapter from raw reads (parameters -a GATCGGAAGAG -O 5 -q 0), then read pairs were filtered out if average base quality was <20 or if shorter than 30nt after removing adapter.
Reads were mapped against mm9 reference genome with Bowtie v1.2 (parameters: -m 1 -X 1000 --chunkmbs 1024).
Duplicate read pairs were removed via Picard v1.110 MarkDuplicates.jar.
Replicates were combined via Picard v1.110 MergeSamFiles.jar, then downsampled to match lowest read total among the 4 sample conditions (N=33055298).
For visualization of ChIP-seq data, each read pair was converted to a single fragment by filling in the gap between ends, converted to bedGraph format via Bedtools v2.24.0 genomeCoverageBed, then converted to bigWig via UCSC utility bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: Genomic depth after merging replicates and downsampling; format=bigWig.
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| Submission date |
Jun 29, 2018 |
| Last update date |
Oct 24, 2018 |
| Contact name |
Paul A Wade |
| E-mail(s) |
[email protected]
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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 |
GPL24247 |
| Series (1) |
| GSE106379 |
Genetics, sex and life experience influence DNA methylation in the mouse |
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| Relations |
| BioSample |
SAMN09519095 |
| SRA |
SRX4325336 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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