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Sample GSM3231548 Query DataSets for GSM3231548
Status Public on Oct 24, 2018
Title B6-rep2.input
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6N
Sex: male
replicate animal: 2
chip antibody: none
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).
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.
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
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Description B6.input.downsampled.bigWig
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.
Submission date Jun 29, 2018
Last update date Oct 24, 2018
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
Platform ID GPL24247
Series (1)
GSE106379 Genetics, sex and life experience influence DNA methylation in the mouse
BioSample SAMN09519098
SRA SRX4325333

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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