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Sample GSM3731674 Query DataSets for GSM3731674
Status Public on Jun 07, 2019
Title B6_wt_Input
Sample type SRA
 
Source name Testis
Organism Mus musculus
Characteristics strain: PWD/Ph
age: 12 days post partum
genotype: wild-type
tissue: Testis
antibody: N/A
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; Input DNA
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 SAMN11467498
SRA SRX5713443

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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