|
| Status |
Public on May 01, 2024 |
| Title |
SKMM1 (CUT&RUN2) ARID1A DMSO 1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: SKMM1
cell type: human multiple myeloma
antibody: anti-ARID1A
time: 3 hr
treatment: DMSO
|
| Treatment protocol |
The myeloma cell line SKMM1 qA grown at 0.5 x 10^6 cells/ml and either treated with DMSO or 1000 nM AU15330 for 3 hours. 2 x 10^6 cells were collected for each sample.
|
| Growth protocol |
SKMM1 cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted and processed following the Epicypher Cut&Run Kit protocol.
DNA libraries were prepared for sequencing using standard Epicypher protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
CTRL
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using BOTWIE2
Peaks were called by an inhouse program
Assembly: hg19
Supplementary files format and content: peak-read counts in wig format
|
| |
|
| Submission date |
Jan 19, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
David Huang |
| Organization name |
National Cancer Institute
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892-0001 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE253711 |
IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (CUT&RUN human 8). |
| GSE253716 |
IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma |
|
| Relations |
| BioSample |
SAMN39509785 |
| SRA |
SRX23330458 |
