 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| 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 |
SAMN14533663 |
| SRA |
SRX8053170 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4453145_DKO_ab1220.bw |
15.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
