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Sample GSM4453145 Query DataSets for GSM4453145
Status Public on Jun 08, 2020
Title P3_DKO_H3K9me2
Sample type SRA
Source name Postnatal male germ cells
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype: Vasa-Cre; Jmjd1a-/-; Jmjd1b-/-
age: P3
tissue: testis
cell type: Postnatal male germ cells
chip antibody: H3K9me2; ab1220 (abcam)
Extracted molecule genomic DNA
Extraction protocol Cells were suspended in 25 μl of 0.3 M sucrose-containing buffer 1 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM DTT, 15 mM Tris-HCl pH 7.5, and protease inhibitor cocktail). The cells were then lysed following the addition of 0.3 M sucrose-containing buffer 1 (25 μl) with 0.8% NP40 on ice for 10 min; 1.2 M sucrose-containing buffer 1 (400 μl) was added and the chromatin was collected as pellets by centrifugation. The pellets were digested with micrococcal nuclease (0.05 U, Takara) in 10 μl of digestion buffer (0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2, 50 mM Tris-HCl pH 7.5) by vortexing at 37°C for 15 min; digestion was stopped with EDTA. The supernatant was obtained by centrifugation and incubated with anti-H3K9me2-conjugated magnetic beads (Dynabeads Protein G, Invitrogen) in 50 μl of incubation buffer (50 mM NaCl, 5 mM EDTA, 0.1% NP40, 20 mM Tris-HCl pH 7.5) at 4°C for 6 h. Then, DNA was extracted from the immune complex according to the standard protocol.
DNA from input and ChIP fractions was processed using SMARTer ThruPLEX DNA-seq Kit (TaKaRa) and sequenced using the Illumina HiSeq 1500 system according to the manufacturer’s instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description P3_DKO_ab1220
Data processing Sequence reads were mapped to mouse mm10 genome using Bowtie2 (v 2.1.0) with default parameter. Only uniquely mapped and non-redundant reads were used for further analysis. The mapped reads were visualized using DeepTools (v.3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage command in Deeptools
Submission date Apr 03, 2020
Last update date Jun 09, 2020
Contact name Ryo Maeda
Organization name Osaka University
Street address Yamadaoka 1-3
City Suita
ZIP/Postal code 565-0871
Country Japan
Platform ID GPL18480
Series (2)
GSE148054 Genome wide map of H3K9me2 in postnatal male germ cells
GSE148055 RNA-seq and H3K9me2 ChIP-seq of postnatal male germ cells
BioSample SAMN14533663
SRA SRX8053170

Supplementary file Size Download File type/resource 15.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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