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Sample GSM869782 Query DataSets for GSM869782
Status Public on May 22, 2012
Title Anti-DMC1 B6 Sample 2
Sample type SRA
Source name Anti-DMC1 B6_testis_SSDS
Organism Mus musculus
Characteristics strain: C57Bl/6J
genotype/variation: wild type
tissue: testis
chip antibody: Anti-DMC1 (C-20)
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-8973
sequencing technique: Single Stranded DNA Sequencing (SSDS)
Growth protocol Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.
Extracted molecule genomic DNA
Extraction protocol Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Sample 2
processed data file: B6_DSB_hotspots.bedGraph (available on Series records)
Data processing For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background. Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline. Reads with less than two mismatches were not aligned. MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
C57_SSDS_Sample2_Testis_ssDNA_type1.bed: mm9
Submission date Feb 02, 2012
Last update date May 15, 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 GPL11002
Series (1)
GSE35498 Genetic recombination is directed away from functional genetic sites in mice.
Reanalyzed by GSM2664283
SRA SRX118373
BioSample SAMN00780104

Supplementary file Size Download File type/resource
GSM869782_C57_SSDS_Sample2_Testis_ssDNA_type1.bed.gz 55.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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