|
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
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|
|
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 |