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Sample GSM1179921 Query DataSets for GSM1179921
Status Public on Sep 11, 2013
Title Spo11 Gal/Gal Anti-DMC1 Sample B
Sample type SRA
 
Source name Testis
Organism Mus musculus
Characteristics antibody: Anti-DMC1 Santa Cruz (C-20, sc 8973)
strain: C57Bl/6J
genotype: Spo11 Gal/Gal
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-H3K4me3 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 OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description library strategy: SSDS
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. Fragments where both reads had a Qscore >= 30 were used.
Peak calling was performed on pooled SSDS samples for each genetic background as per Brick et al., Nature 2012. 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 Analyser CASAVA 1.8 Pipeline. MACS v.1.4 was used to define peaks.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files: 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.
Supplementary_files_format_and_content: ssDNA.bed files: Processed ssDNA (type 1) for each sample - see Khil et al., Genome Research 2012. ssDNA coordinates are from the start to the end of the sequenced fragment. Column 4 contains quality scores for read 1 and read 2 separated by an underscore. Column 5 contains the ITR length and Microhomology length separated by an underscore.
 
Submission date Jul 02, 2013
Last update date May 15, 2019
Contact name Kevin Brick
E-mail(s) brickkm@mail.nih.gov, kevbrick@gmail.com, brickkm@niddk.nih.gov
Organization name NIDDK
Department GBB
Street address 5/205 Memorial Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL13112
Series (1)
GSE48493 Supression of genetic recombination in the pseudoautosomal region and at subtelomeres in mice with a hypomorphic spo11 allele
Relations
BioSample SAMN02223070
SRA SRX317218

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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