|
| Status |
Public on Oct 26, 2021 |
| Title |
AA2_input_SSDS [re-analysis] |
| Sample type |
SRA |
| |
|
| Source name |
Human testes
|
| Organism |
Homo sapiens |
| Characteristics |
population: NA
Sex: Male
sequencing technique: ChIP-Single Stranded DNA Sequencing (SSDS)
antibody: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Sequencing libraries were prepared following the method described in (Khil et al., 2012).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
GSM1447329
AA2_input_SSDS
|
| Data processing |
Basecalling was performed using Illumina HCS 1.5.15.1
The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome (https://github.com/kevbrick/SSDSpipeline.git). Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS] -g mm --bw 1000 --keep-dup all --slocal 5000. (https://github.com/kevbrick/callHotspotsSSDS.git) and using the matching input dlibrary as a control. DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously (Brick & Pratto et al., Meth. Enzym. 2019).
BIGWIG files were generated from ssDNA type1 data using the deeptools3.0.1 bamCoverage function and the following arguments: --binSize 150 --normalizeUsing RPKM --ignoreDuplicates
Genome_build: hg38
Supplementary_files_format_and_content: BIGWIG: Genomic coverage
Supplementary_files_format_and_content: BAM: Processed ssDNA aligned to reference genome
Supplementary_files_format_and_content: BAI: Index files for BAMs
Supplementary_files_format_and_content: BEDGRAPH: DMC1-SSDS peaks with associated strength
Supplementary_files_format_and_content: HOTSPOTS TABLE: SSDS peaks in each individual
Supplementary_files_format_and_content: HAPLOTYPES TABLE: PRDM9 genotyping information for all individuals
|
| |
|
| Submission date |
Feb 09, 2021 |
| Last update date |
Oct 26, 2021 |
| 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 |
GPL16791 |
| Series (1) |
| GSE166483 |
Cataloging human PRDM9 variability utilizing long-read sequencing technologies reveals PRDM9 population-specificity and two distinct groupings of related alleles |
|
| Relations |
| Reanalysis of |
GSM1447329 |
| BioSample |
SAMN17844651 |
| SRA |
SRX10061497 |
