|
| Status |
Public on Jun 12, 2024 |
| Title |
WT_UT_3 |
| Sample type |
SRA |
| |
|
| Source name |
AID-DivA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AID-DivA
cell type: osteosarcoma
genotype: WT
treatment: untreated
treatment2: no BRG1 inhibitor
replicate: 3
|
| Treatment protocol |
We used both WT AID-DivA cells and AID-DivA cells with an ARID1A knock-out. Cells were either untreated (UT) or treated with 300 nM 4-hydroxytamoxifen (4OHT) and incubated for 4h. Then treated with Auxin to stop the enzymatic generation of the double-strand breaks. Cells were collected immediately after auxin treatment (T0) or 2h after addition of auxin (T2), or 4h (T4), or 12h (T12). Some cells were untreated with 4OHT but collected 12h after auxin treatment (UT12). Cells were either treated with a BRG1 inhibitor (BRM014) or not.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 viable cells were pelleted and washed in PBS. Subsequently, nuclei were isolated and resuspended in 2x transposition buffer (20mM Tris-HCl pH 7.6, 3mM MgCl2, 20% Dimethyl Formamide) and the tagmentation reaction was performed by adding 2.5µl of Tagment DNA Enzyme 1 (Illumina). The mixture was incubated for 30 minutes at 37°C with mixing at 1000 rpm. Reaction was stopped by 5M Guanidinium thiocyanate (Sigma-Aldrich) and DNA was further purified using AMPure XP beads.
Libraries were amplified in PCR reactions by adding 25 µl of NEBNext High Fidelity 2x Master Mix (NEB), 0.8 µl of 10 µM Custom Nextera PCR Primer 1, and 0.8 µl of 10 µM Custom Nextera PCR Barcode to 25 µl of the transposed DNA. The libraries were purified with AMPure XP beads. The concentration of the library was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequencing reads were processed using the CWL-based ATAC-Seq workflow available at https://github.com/CompEpigen/ATACseq_workflows
Assembly: GRCh37
Supplementary files format and content: bigwig tracks
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Christoph Plass |
| E-mail(s) |
c.plass@dkfz.de
|
| Organization name |
DKFZ (German Cancer Research Center)
|
| Department |
Division of Cancer Epigenomics
|
| Street address |
Im Neueneimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE249439 |
ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response [ATAC-seq] |
| GSE249492 |
ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response |
|
| Relations |
| BioSample |
SAMN38682758 |
| SRA |
SRX22788284 |
