|
| Status |
Public on Sep 11, 2013 |
| Title |
Spo11 Gal/Gal Hop2 -/- Anti-DMC1 Sample A |
| 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 Hop2-/-
|
| 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 |
SAMN02223073 |
| SRA |
SRX317219 |
