|
| Status |
Public on Jun 15, 2023 |
| Title |
SCAR_410_stranded_input_K27ac_T0_r2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14JU
strain: 129/Ola
genotype: wildtype
|
| Treatment protocol |
Cells were incubated in EdU media (f.c. 10 µm) for 10, 15 or 30 min (see data S1 for details) and then either collected (T0) or cultured for indicated maturation intervals (T1; T3; T8) in media without EdU before collection.
|
| 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 SCAR-seq: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced. Crosslinked SCAR-seq: Cells were crosslinked with formaldehyde for 10 min. Nuclei were isolated and chromatin was solubilized using a Covaris sonicator. See methods for more details.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
EdU-labelled genomic DNA
|
| Data processing |
Library strategy: SCAR-seq
adapters and low quality reads were filtered with cutadapt version 2.5
reads were mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Genome_build: mm10
Supplementary_files_format_and_content: SCAR-seq Partition scores in bigwig format
|
| |
|
| 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) |
| GSE154380 |
Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity [SCAR-seq] |
| GSE154391 |
Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity |
|
| Relations |
| BioSample |
SAMN25638517 |
| SRA |
SRX14034011 |
