|
| Status |
Public on Jun 07, 2019 |
| Title |
B6_wt_H3K4me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Testis
|
| Organism |
Mus musculus |
| Characteristics |
strain: PWD/Ph
age: 12 days post partum
genotype: wild-type
tissue: Testis
antibody: Millipore/EMD 07-473
sequencing technique: ChIP-Seq
|
| Growth protocol |
Crude isolation of germ cells was conducted from male mice at 12 days post-partum (dpp). For detailed protocol see publication
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
B6 wild-type; H3K4me3 ChIP-Seq
|
| Data processing |
H3K4me3 ChIP-Seq data were aligned to the reference mm10 genome using bwa 0.7.12 (Li 2013). H3K4me3 ChIP-Seq data were aligned to the reference mm10 genome using bwa 0.7.12 (Li 2013). Aligned BAM files were converted to BED files with bedtools (Quinlan and Hall 2010) and duplicate reads were discarded. NCIS (Liang and Keleş 2012) was used to determine the background correction ratio (rBG). MACS 2.1.0.20150731 (Zhang et al. 2008) was used with the following arguments to call peaks: --ratio {rBG} -g mm --bw 1000 --keep-dup all --slocal 5000 -t {ChIP bed file} -c {input bed file}.
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.
|
| |
|
| Submission date |
Apr 19, 2019 |
| Last update date |
Jun 07, 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) |
| GSE109874 |
Histone methyltransferase PRDM9 is not essential for meiosis in male mice |
|
| Relations |
| BioSample |
SAMN11467499 |
| SRA |
SRX5713442 |
