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| Status |
Public on Oct 27, 2021 |
| Title |
Male_B6_DNaseI_Repl2_G163_M2 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J (Jackson Labs, cat#:000664)
units dnasei: 32U (RQ1; Promega cat#:M6101)
Sex: Male
age: 8 weeks
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| Growth protocol |
Male and female C57BL/6J and CAST/EiJ mice, 8-9 weeks of age, were purchased from Jackson Labs.
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| 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.
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
DNase-seq Library
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| 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.
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| Submission date |
May 08, 2019 |
| Last update date |
Oct 27, 2021 |
| Contact name |
David J. Waxman |
| E-mail(s) |
djw@bu.edu
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| Organization name |
Boston University
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| Department |
Department of Biology and Bioinformatics Program
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| Street address |
5 Cummington Mall
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN11605264 |
| SRA |
SRX5807375 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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