|
| Status |
Public on Apr 30, 2023 |
| Title |
ATAC_4HT_LS_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESCs
culture conditions: L2i
genotype: FOXD3-iKO
treatment time: 24h
|
| Treatment protocol |
Phase sorting was performed by DNA content labeling with DAPI.
|
| Growth protocol |
Mouse ESCs were seeded on a well of a 6well plate (170k cells) in L2i containing growth medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were constructed using custom adaptors according to
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Nextflow/ATAC
featureCounts read count in OCT4-SOX2-NANOG overlapped peaks
DESeq2 differential enrichment analysis
Genome_build: mm10
Supplementary_files_format_and_content: count matrix
|
| |
|
| Submission date |
Sep 03, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Robert Blelloch |
| Organization name |
UCSF
|
| Department |
Urology
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE183417 |
Characterization of cell cycle phase specific chromatin accessibility using ATAC seq after FOXD3 depletion |
| GSE183420 |
Transcriptional repressor FOXD3 safeguards genome integrity in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN21218329 |
| SRA |
SRX12011144 |
