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Sample GSM4453142 Query DataSets for GSM4453142
Status Public on Jun 08, 2020
Title P3_Ctrl_Inp
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: Input
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_Ctrl_Inp
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
E-mail(s) rmaeda@fbs.osaka-u.ac.jp
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
Relations
BioSample SAMN14533666
SRA SRX8053167

Supplementary file Size Download File type/resource
GSM4453142_Ctrl_Inp.bw 13.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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