GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM851668 Query DataSets for GSM851668
Status Public on Feb 21, 2012
Title DMC1
Sample type SRA
Source name adult testis
Organism Mus musculus
Characteristics age: adult
gender: male
genetic background: 9R female x 13R male F1
chip antibody: DMC1 (C-20)
chip antibody catalog number: sc 8973
chip antibody lot: G0909
chip antibody vendor: Santa Cruz
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. Library construction was done using enzymes from New England Biolabs or Illumina and standard Illumina protocol. Size selection of library fragments of 150~250 bp was performed after PCR amplification. “Klenow exo(-)” sample was prepared by substituting Klenow fragment and T4 DNA polymerase from the end repair step of the standard protocol with Klenow exo(-) enzyme and performing end repair at 37 °C for 1h. “Klenow exo(-), 12 °C“ sample was prepared the same way followed by incubation at 20 °C for 2h and at 12 °C overnight. "Kinetic enrichment" samples were denatured and quickly renatured before adapter ligation.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Standard ChIP-Seq.
Data processing DMC1.sorted.ssDNA_type1.bed; genome build: mm9
DMC1.sorted.ssDNA_type2.bed; genome build: mm9
DMC1.sorted.dsDNA.bed; genome build: mm9
DMC1.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) ( or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.
Submission date Dec 20, 2011
Last update date May 15, 2019
Contact name Pavel P Khil
Phone 301-496-4638
Fax (301)-496-9878
Organization name NIDDK
Lab Genetics and Biochemistry Branch
Street address 5 Memorial Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL13112
Series (1)
GSE34592 Sequencing-based ssDNA detection
SRA SRX112538
BioSample SAMN00767721

Supplementary file Size Download File type/resource
GSM851668_DMC1.sorted.1K_100.wig.gz 237.0 Mb (ftp)(http) WIG
GSM851668_DMC1.sorted.dsDNA.bed.gz 93.6 Mb (ftp)(http) BED
GSM851668_DMC1.sorted.ssDNA_type1.bed.gz 5.9 Mb (ftp)(http) BED
GSM851668_DMC1.sorted.ssDNA_type2.bed.gz 1.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap