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Sample GSM3731676

Query DataSets for GSM3731676

Status

Public on Jun 07, 2019

Title

PWD_wt_DMC1 SSDS

Sample type

SRA

Source name

Testis

Organism

Mus musculus

Characteristics

strain: PWD/Ph
age: Adult
genotype: wild-type
tissue: Testis
antibody: Anti-DMC1 Santa Cruz (C-20, sc 8973)
sequencing technique: ChIP-Single Stranded DNA Sequencing (SSDS)

Extracted molecule

genomic DNA

Extraction protocol

For DMC1 SSDS, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen).
DMC1 ChIP was performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications. Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Single Stranded DNA Sequencing (SSDS)

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Description

PWD wild-type DMC1 SSDS

Data processing

For DMC1-SSDS samples, samples were aligned to the mm10 reference genome, peak calling was performed, and hotspot strength was calculated as described in (Brick et al. 2018).

Submission date

Apr 19, 2019

Last update date

Jun 07, 2019

Contact name

Kevin Brick

E-mail(s)

brickkm@mail.nih.gov, kevbrick@gmail.com, brickkm@niddk.nih.gov

Organization name

NIDDK

Department

GBB