|
| Status |
Public on Apr 24, 2024 |
| Title |
PXGL,DOX,ATAC,Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: human embryonic stem cell
treatment: DOX
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the MinElute PCR purification kit (QIAGEN).
Transposed DNA were pre-amplified for 5 cycles. The required number of additional cycles for each sample was determined by qPCR as described (Buenrostro et al., 2015). After the final amplification, double-sided bead purification was performed with AMPure XP beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ATAC-seq raw data was processed using the atacseq pipeline (v1.2.1) (https://github.com/nf-core/atacseq/) from nf-core using the default parameters
Adapter trimming using Trim Galore
Reads were aligned using BWA aligner
Duplicates were marked by picard
bigWig tracks were generated by BEDTools.
Assembly: hg38
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Claire Rougeulle |
| E-mail(s) |
claire.rougeulle@u-paris.fr
|
| Organization name |
Université Paris Cité, CNRS
|
| Department |
Epigenetics and Cell Fate
|
| Street address |
35 rue Helene Brion
|
| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE246633 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [ATAC-seq] |
| GSE246643 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development |
|
| Relations |
| BioSample |
SAMN38671860 |
| SRA |
SRX22777807 |
