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| Status |
Public on Jun 07, 2019 |
| Title |
B6xPWD F7 Prdm9ko DMC1 SSDS (A) |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J x C57Bl/6J F7
age: Adult
genotype: Prdm9-/- (tm1Ymat/tm1Ymat)
antibody: Anti-DMC1 Santa Cruz (C-20, sc 8973)
sequencing technique: ChIP-Single Stranded DNA Sequencing (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 (Khil et al., 2012; Brick et al., 2018) with minor modifications.
Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
B6 x PWD F7 Prdm9 knockout; DMC1 SSDS; Sample A
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| Data processing |
For DMC1-SSDS samples, samples were aligned to the mm10 reference genome, peak calling was performed, and hotspot strength was calculated as described in (Brick et al. 2018).
genome build: mm10
processed data files format and content: For each SSDS experiment, the associated BAM file contains all paired end ssDNA reads 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 bedgraph format for each DMC1 SSDS sample. Background corrected hotspot strength is listed in the fourth column. A bedgraph file is provided for H3K4me3 ChIP-Seq peaks. This contains the mm10 coordinates of each H3K4me3 peak. Column 4 is peak strength.
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| Submission date |
Jan 30, 2018 |
| Last update date |
Jun 09, 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) |
| GSE109874 |
Histone methyltransferase PRDM9 is not essential for meiosis in male mice |
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| Relations |
| BioSample |
SAMN08438565 |
| SRA |
SRX3630641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2971935_mix_PrKO_A.ssDNA_type1.bam |
825.2 Mb |
(ftp)(http) |
BAM |
| GSM2971935_mix_PrKO_A.ssDNA_type1.bam.bai.gz |
1.5 Mb |
(ftp)(http) |
BAI |
| GSM2971935_mix_PrKO_A_peaks.bedgraph.gz |
158.3 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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