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Sample GSM3756102 Query DataSets for GSM3756102
Status Public on Oct 27, 2021
Title Male_B6_DNaseI_Repl3_G163_M3
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: C57BL/6J (Jackson Labs, cat#:000664)
units dnasei: 32U (RQ1; Promega cat#:M6101)
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 homogenized, nuclei were suspended in a high sucrose buffer, and then ultra centrifuged to obtain purified intact nuclei. 50 million liver nuclei per sample were incubated with 32 U of RQ1 RNase-free DNase I (Promega, cat#:M6101) for 2 min at 37C. From the purified DNA, fragments between 125-400 bp long were isolated using a sucrose gradient and with Agencourt AMPure XP beads (Beckman Coulter, Cat# A63881) size selection.
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 DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina NovaSeq 6000
 
Description DNase-seq Library
Data processing READ MAPPING: DNase-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 DNase-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)
GSE130912 Mouse liver DNase-seq identification of DNase hypersensitive sites (DHS) 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 SAMN11605263
SRA SRX5807376

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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