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SRX5807383: GSM3756109: Male_CAST_DNaseI_Repl2_G163_M13; Mus musculus; DNase-Hypersensitivity
1 ILLUMINA (Illumina NovaSeq 6000) run: 42.1M spots, 4.2G bases, 1.2Gb downloads

Submitted by: NCBI (GEO)
Study: 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.
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Sequencing files provided here are mouse liver DNase-seq in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes RNA-seq and H3K27ac ChIP-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers. Overall design: DNase-seq in male and female mouse liver for two mouse strains
Sample: Male_CAST_DNaseI_Repl2_G163_M13
SAMN11605256 • SRS4736851 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: DNase-Hypersensitivity
Source: GENOMIC
Selection: DNase
Layout: PAIRED
Construction 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.
Experiment attributes:
GEO Accession: GSM3756109
Links:
Runs: 1 run, 42.1M spots, 4.2G bases, 1.2Gb
Run# of Spots# of BasesSizePublished
SRR903010242,147,3324.2G1.2Gb2021-10-28

ID:
7804663

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