|
| Status |
Public on Oct 28, 2021 |
| Title |
KO_1_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
strain: FVB/NJ
genotype: Morc3D41/D41
|
| Treatment protocol |
No treatment
|
| Growth protocol |
All mESC lines were cultured in serum conditions (Knockout DMEM (10829-018; Gibco), 10% FBS (DE14-801F; BioWhittaker), NEAA (11140; Gibco), L-Glutamine (25030-123; Gibco), Sodium Pyruvate (11360; Gibco), 2-Mercaptoethanol (31350; Gibco) and Leukemia Inhibitory Factor (ESG1107; Millipore)) plus MEK inhibitor PD0325901 (1 mM) and GSK3 inhibi- tor CHIR99021 (3 mM) (Axon Medchem) on 0.1% gelatin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq libraries were prepared as previously described (Buenrostro 2015). In brief, fifty thousand mouse embryonic stem cells were resuspended in 50 µL transposition mix (Nextera) and incubated for 30min at 37°C. Libraries were amplified by PCR with barcoded Nextera primers and sequenced on BGISEQ-500
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Quality assessment of the raw sequencing reads was done using FastQC v0.11.2. Adapters were removed by TrimGalore v0.4.5 using default parameters for paired-end Illumina reads, after which, quality filtering was performed by the same software. Reads smaller than 20bps and those with an error rate (TrimGalore option "-e") higher than 0.1 were discarded, after which a final quality assessment of the filtered reads was done with FastQC to identify possible biases left after filtering
The remaining reads were mapped to the mouse reference genome (build mm10) using the Bowtie2 v2.3.5 using default parameters with the following exceptions: “–very-sensitive".
The peak calling was done with MACS2 2.1.4 with default parameters with the expceptions: -BAMPE --shift -100 --extsize 200
Genome_build: mm10
Supplementary_files_format_and_content: Peaks coordinates and differential peaks
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Lucia Daxinger |
| E-mail(s) |
[email protected]
|
| Organization name |
Leiden Univeristy Medica Center
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE173915 |
Morc3 silences endogenous retroviruses in mouse embryonic stem cells [ATAC-seq] |
| GSE173917 |
Morc3 silences endogenous retroviruses in mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN19022989 |
| SRA |
SRX10783424 |
