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Sample GSM2971934 Query DataSets for GSM2971934
Status Public on Jun 07, 2019
Title B6 Prdm9ko DMC1 SSDS (B)
Sample type SRA
Source name Testis
Organism Mus musculus
Characteristics strain: C57Bl/6J
age: Adult
genotype: Prdm9-/- (tm1Ymat/tm1Ymat)
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 (Khil et al., 2012; Brick et al., 2018) with minor modifications.
Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description B6 Prdm9 knockout; DMC1 SSDS; Sample A
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).
genome build: mm10
processed data files format and content: For each SSDS experiment, the associated BAM file contains all paired end ssDNA reads identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection: it : ITR length uh : microhomology length os : microhomology offset mm : # mismatches DSB hotspots are provided in bedgraph format for each DMC1 SSDS sample. Background corrected hotspot strength is listed in the fourth column. A bedgraph file is provided for H3K4me3 ChIP-Seq peaks. This contains the mm10 coordinates of each H3K4me3 peak. Column 4 is peak strength.
Submission date Jan 30, 2018
Last update date Jun 09, 2019
Contact name Kevin Brick
Organization name NIDDK
Department GBB
Street address 5/205 Memorial Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL17021
Series (1)
GSE109874 Histone methyltransferase PRDM9 is not essential for meiosis in male mice
BioSample SAMN08438566
SRA SRX3630640

Supplementary file Size Download File type/resource
GSM2971934_B6_PrKO_B.ssDNA_type1.bam 614.6 Mb (ftp)(http) BAM
GSM2971934_B6_PrKO_B.ssDNA_type1.bam.bai.gz 1.3 Mb (ftp)(http) BAI
GSM2971934_B6_PrKO_B_peaks.bedgraph.gz 172.9 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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