|
| Status |
Public on Jun 15, 2023 |
| Title |
ChIP_442_K9me3_input_rescue_exp_r1 |
| Sample type |
SRA |
| |
|
| Source name |
E14JU
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14JU
cell type: Embryonic stem cells
genotype: MCM2-2A
strain: 129/Ola
antibody: none
|
| 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 |
NextSeq 2000 |
| |
|
| 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
Narrow (H3K4me3, H3K27ac and SUZ12) peaks were called with MACS (version 2.1.0) with parameters –nomodel -p 0.05 and either the "optimal overlap" (H3K4me3, H3K27ac) set or the "IDR optimal" (SUZ12) from the encode pipleine was used. Broad peaks (H3K27me3 and H3K9me3) were called using danpos2 regions with default parameters, to obtain a reproducible set of peaks for each clone, peaks were called on pooled replicates and only peaks overlapped by at least 50% bps of peaks in at least 2 out of 3 replicates were kept.
Assembly: mm10
Supplementary files format and content: Bed files of ChIP-seq reproducible peak sets called with macs2 for narrow peaks (H3K4me3, H3K27ac, SUZ12) or danpos2 regions for broad peaks (H3K27me3, H3K9me3)
|
| |
|
| Submission date |
Feb 01, 2023 |
| 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 |
GPL30172 |
| 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 |
SAMN33007504 |
| SRA |
SRX19247470 |
