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| Status |
Public on Feb 03, 2016 |
| Title |
13R antiDMC1 SSDS |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Mus musculus |
| Characteristics |
maternal strain: B10.F-H2pb1/(13R)J
paternal strain: B10.F-H2pb1/(13R)J
antibody: Anti-DMC1 Santa Cruz (C-20, sc 8973)
sequencing technique: SSDS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For DMC1 SSDS, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen).
DMC1 ChIP was performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications. Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Single Stranded DNA Sequencing (SSDS)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm10 genome assembly. The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome. For each sample, reads were aligned to the SNP modified genome(s) of the mouse strain(s) used. In the case of samples generated from F1 hybrid mice, reads were mapped to both parental genomes. The mapping of each read was compared between the alignments to the two parental genomes and a single mapping for each read was retained as follows: if the mapping was identical in both genomes, the read from the first parental genome was retained. If reads mapped to the same position (or ± 2 bp at either end) in both genomes but with fewer mismatches / indels in one, then that with the fewer mismatches / indels was retained. If a read mapped to one genome and not the other, that read was retained. If reads mapped to different positions in the parental genomes, both reads were discarded.
For SSDS DMC1 data, hotspots were called using MACS version 2.0.10. The following MACS arguments were used (--nomodel; --shiftsize: 400; --bw: 1000; -q: 0.1).
Genome_build: mm10
Supplementary_files_format_and_content: For each SSDS experiment, the associated BAM file contains all ssDNA fragments identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection: it : ITR length uh : microhomology length os : microhomology offset mm : # mismatches DSB hotspots are provided in pseudo-bedgraph format (.tab) for each DMC1 SSDS sample. This is not a true bedgrpah format, as hotspot intervals may overlap as a result of the recentring procedure. Background corrected hotspot strength is listed in the fourth column. DSB hotspots in blacklisted regions were not used for analyses but are provided as separate files. For blacklisted hotspots, the strength is not corrected for background reads.
Supplementary_files_format_and_content: NOTE: The linked bams differ from 'raw' alignment bams, since they are critical for study interpretation. we use a bespoke and computationally intensive alignment pipeline that serves as an impediment to those wishing to examine our data.
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| Submission date |
Nov 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Brick |
| E-mail(s) |
brickkm@mail.nih.gov, kevbrick@gmail.com, brickkm@niddk.nih.gov
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| Organization name |
NIDDK
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| Department |
GBB
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| Street address |
5/205 Memorial Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE75419 |
The evolutionary dynamics of meiotic recombination initiation in mice |
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| Relations |
| BioSample |
SAMN04296554 |
| SRA |
SRX1452668 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1954833_13R_hotspots.tab.gz |
180.2 Kb |
(ftp)(http) |
TAB |
| GSM1954833_13R_hotspots_BLACKLISTED.raw.bedgraph.gz |
3.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM1954833_13R_ssDNA_type1.bam |
2.2 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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