|
| Status |
Public on Jul 02, 2021 |
| Title |
inputSSDS_Human_Prdm9A-A (Sample 2) |
| Sample type |
SRA |
| |
|
| Source name |
Control for DSB hotspot capture in PRDM9 A-A homozygous male using input-SSDS in testis (Sample 2)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Testis
strain: n/a
experiment type: Control for DSB hotspot mapping using Single Stranded DNA Sequencing of Input DNA (Input-SSDS)
dna content: n/a
s-phase sub-stage: n/a
cell-type: n/a
positive selection marker: n/a
negative selection marker: n/a
antibody: n/a
|
| Treatment protocol |
Samples were untreated.
|
| Growth protocol |
All DNA was harvested from organs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. 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).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
GSM1447329: SRR1528832
Input-SSDS
human_AA2.peaks.RC.bedgraph
|
| Data processing |
Library strategy: Input-SSDS
Sequencing reads were aligned to the human hg38 reference genome using bwa 0.7.12 and the single-stranded DNA pipeline (Brick et al. 2018; Khil et al. 2012).
|
| |
|
| Submission date |
Apr 08, 2020 |
| Last update date |
Jul 02, 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) |
| GSE148327 |
Meiotic recombination mirrors patterns of germline replication in mice and humans |
|
| Relations |
| Reanalysis of |
GSM1447329 |
| BioSample |
SAMN14560215 |
| SRA |
SRX8083046 |
