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Sample GSM869789 Query DataSets for GSM869789
Status Public on May 22, 2012
Title Input DNA with Kinetic Enrichment
Sample type SRA
 
Source name Input DNA with Kinetic Enrichment_testis_SSDS
Organism Mus musculus
Characteristics strain: B10.F-H2pb1/(13R)J X B11.S-H2t4/(9R)/J
genotype/variation: wild type
tissue: testis
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 9
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:
F1C_SSDS_Sample1_Testis_ssDNA_type1.bed: mm9
 
Submission date Feb 02, 2012
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 GPL11002
Series (1)
GSE35498 Genetic recombination is directed away from functional genetic sites in mice.
Relations
Reanalysis of GSM851671
SRA SRX118388
SRA SRX118389
BioSample SAMN00780111

Supplementary file Size Download File type/resource
GSM869789_F1C_SSDS_Sample1_Testis_ssDNA_type1.bed.gz 136.9 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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