|
| Status |
Public on Jan 17, 2020 |
| Title |
Mettl3_Control_H3K4me3_r2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
strain: C57BL/6
genotype: Mettl3_Control
chip antibody: rabbit anti-H3K4me3 (ab8580, Abcam)
|
| Treatment protocol |
mESCs were resuspended in growth media with a concentration of 10e6 ml-1 and cross-linked by adding 1% formaldehyde directly to the media, slow shaked 10 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature with slowly shaking. The media was removed and the cells were washed twice with ice-cold PBS.
|
| Growth protocol |
Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was performed using Auto iDeal ChIP-seq kit for Histone (diagenode) with spike-in Chromatin (Active Motif) and spike-in Antibody (Active Motif) following the manufacturer’s protocols.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, and then uniquely mapped to mouse genome (mm10, version M19, 2018-08-30) and Drosophila melanogaster chromatin (Spike-in Chromatin) using bowtie (version 1.2.2) allowing one mismatch.
Peaks were called usin MACS2 with default paramters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations together with peak summit and pvalue reported by MACS2 for each sample.
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Jan 17, 2020 |
| Contact name |
Xiaoyang Dou |
| E-mail(s) |
[email protected]
|
| Organization name |
Center for Excellence in Molecular Cell Science, CAS
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE133579 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_histoneChIP] |
| GSE133600 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription |
|
| Relations |
| BioSample |
SAMN12172197 |
| SRA |
SRX6385203 |
