|
| Status |
Public on Jun 15, 2023 |
| Title |
ChIP_439_H3K9me3_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14JU
strain: 129/Ola
genotype: MCM2-2A
antibody: H3K9me3
|
| Treatment protocol |
Samples were untreated.
|
| Growth protocol |
ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 degrees with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase under native conditions. Native Drosophila chromatin was spiked in and mononucleosomal fragments were immunoprecipitated, followed by library preparation and sequencing.
Libraries were prepared using standard Illumina protocols (KAPA Hyper Prep kit).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Files were processed using the ENCODE ChIP-seq pipeline version 1.3.6: adapters and low quality reads were filtered with cutadapt version 2.5 and mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7) and bam files converted to tagAlign files
peaks were called with MACS (version 2.1.0) with parameters –nomodel -p 0.05 (narrow peaks, H3K4me3) or --nomodel --broad -p 0.01 –-broad-cutoff 0.1 (broad peaks, H3K27me3 and H3K9me3)
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq peak bed files called with macs2, narrow peaks (H3K4me3) and broad peaks (H3K27me3,H3K9me3)
|
| |
|
| Submission date |
Jul 14, 2020 |
| Last update date |
Jun 15, 2023 |
| Contact name |
Anja Groth |
| E-mail(s) |
anja.groth@cpr.ku.dk
|
| Organization name |
Novo Nordisk Foundation Center for Protein Research
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE154379 |
Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity [ChIP-seq] |
| GSE154391 |
Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity |
|
| Relations |
| BioSample |
SAMN15524150 |
| SRA |
SRX8725289 |
