|
| Status |
Public on Jun 15, 2023 |
| Title |
ChIP_410_K27ac_input_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14JU
strain: 129/Ola
genotype: wildtype
|
| Treatment protocol |
Samples were untreated.
|
| Growth protocol |
ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C 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 or TrypLE.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native ChIP: Cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Native Drosophila chromatin was spiked in and mononucleosomal fragments were immunoprecipitated, followed by library preparation and sequencing. Crosslinked ChIP: Cells were crosslinked with formaldehyde for 10 min and collected by scraping. Nuclei were isolated and chromatin was solubilized using a Covaris sonicator. Crosslinked Drosophila chromatin was spiked in.
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 and H3K27ac) or --nomodel --broad -p 0.01 –-broad-cutoff 0.1 (broad peaks, H3K27me3, H3K9me3 and SUZ12)
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq peak bed files called with macs2, narrow peaks (H3K4me3, H3K27ac) and broad peaks (H3K27me3, H3K9me3)
|
| |
|
| Submission date |
Feb 03, 2022 |
| 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 |
SAMN25636702 |
| SRA |
SRX14031751 |
