|
| Status |
Public on Mar 01, 2024 |
| Title |
KMS11, p52KD, ATAC-seq, biorep2 |
| Sample type |
SRA |
| |
|
| Source name |
Haematopoietic and Lymphoid
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Haematopoietic and Lymphoid
cell line: KMS-11
cell type: Plasma Cell Myeloma
genotype: WT
Sex: Female
treatment: p52KD
|
| Treatment protocol |
Cells were transduced with TLCV2-containing virus and selected with 0.5 µg/ml puromycin for 72H. Transduced cells were subjected to 1 µg/ml Doxycycline to induce Cas9 expression before GFP sorting.
|
| Growth protocol |
Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were resuspended cold ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and incubated on ice for 3 min. The cells were then washed in RBS containing 0.1% Tween-20 at 500 g at 4 °C before subjecting the nuclei to the transposase reaction for 30 min at 37 °C. Termination of the reaction and DNA purification was performed using Zymo DNA clean and Concentrator kit.
The purified DNA was amplified with NEBNext High-Fidelity 2x PCR Master Mix then purified and size selected twice with AMPure beads. Nextera Tn5 Transposase is employed for tagmentation.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls
|
| |
|
| Submission date |
Apr 21, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Yinghui Li |
| E-mail(s) |
liyh@ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
05n-21
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE230277 |
Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [ATAC-seq] |
| GSE230526 |
Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma |
|
| Relations |
| BioSample |
SAMN34289093 |
| SRA |
SRX20051262 |
