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Sample GSM3756044 Query DataSets for GSM3756044
Status Public on Oct 27, 2021
Title Male_CAST_H3K27ac_Repl1_G162_M11
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: C57BL/6J (Jackson Labs, cat#:000664)
chip antibody: Abcam anti H3K27ac (cat# Ab4729)
Sex: Male
age: 8 weeks
Growth protocol Male and female C57BL/6J and CAST/EiJ mice, 8-9 weeks of age, were purchased from Jackson Labs.
Extracted molecule genomic DNA
Extraction protocol Liver was dounce homogenized, passed through a 70 micron filter, and then crosslinked with 1% formaldehyde for 10 minutes. Samples were sonicated with a Bioruptor Pico (Diagenode, cat#:B01060010) until the majority of DNA fragments were between 100-400bp (25 cycles total, 30 sec ON 30 sec OFF). Chromatin was quantified and 15 ug of chromatinized DNA was incubated with anti-H3K27ac antibody (Abcam, cat#:ab4729).
Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description ChIP-seq Library
Data processing READ MAPPING: ChIP-seq reads were aligned using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using Macs2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9
Supplementary_files_format_and_content: Replicate merged peak lists for H3K27ac ChIP-seq, merged by strain and sex. Samples were combined at the fastq level and processed through a standard ChIP-seq pipeline as described. Columns are in BED6+4 format from MACS2 narrowPeak defaults. Specifically, columns 1-3 represent genomic coordinates of the indicated peak; column 4 is the peak name (unique identifier); column 5 is an integer score for display calculated as -10*log10(qvalue); column 6 indicates the strand; column 7 indicates the fold-change over background; column 8 indicates -(log10pvalue); column 9 indicates -log10(qvalue); and column 10 indicates the summit position relative to the 5' end of the peak.
 
Submission date May 08, 2019
Last update date Oct 27, 2021
Contact name David J. Waxman
E-mail(s) djw@bu.edu
Organization name Boston University
Department Department of Biology and Bioinformatics Program
Street address 5 Cummington Mall
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL24247
Series (2)
GSE130909 Mouse liver H3K27ac histone marks in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ.
GSE130914 Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model
Relations
BioSample SAMN11605312
SRA SRX5807324

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

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