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Series GSE34592 Query DataSets for GSE34592
Status Public on Feb 21, 2012
Title Sequencing-based ssDNA detection
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Meiotic DNA double stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. Although DSBs can be directly mapped using ChIP-Seq and antibody against ssDNA-associated proteins, genome-wide mapping of recombination hotspots in mammals is still a challenge due to the low frequency of recombination, high heterogeneity of the germ cell population and the relatively low efficiency of ChIP. To overcome these limitations we have developed a novel method, single-stranded DNA (ssDNA) sequencing (SSDS), that specifically detects protein-bound single-stranded DNA at DSB ends. SSDS consists of a computational framework for the specific detection of ssDNA-derived reads in a sequencing library and a new library preparation procedure for the enrichment of fragments originating from ssDNA. When applied to mapping meiotic DSBs, the use of SSDS reduces the non-specific dsDNA background more than ten-fold. Our method can be extended to other systems where the identification of ssDNA or DSBs is desired.
Overall design Development and validation of the method, SSDS, for the specific detection of ssDNA-derived and dsDNA-derived fragments in sequencing libraries and enrichment of ssDNA-derived fragments. SSDS was used to detect meiotic DSBs in 9R/13R mice.
Contributor(s) Khil PP, Smagulova FO, Brick KM, Gregoretti IV, Camerini-Otero RD, Petukhova GV
Citation(s) 22367190
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
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (11)
GSM851661 DMC1 Hop2-/-
GSM851662 RAD51 Hop2-/- rep1
GSM851663 RAD51 Hop2-/- rep2
SRA SRP009907
BioProject PRJNA150489

Download family Format
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Supplementary file Size Download File type/resource
GSE34592_RAW.tar 3.5 Gb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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