|
| Status |
Public on Mar 01, 2024 |
| Title |
KMS11, control, H3K27ac HiChIP, biorep1 |
| 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: control
chip antibody: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb (#8173; Cell Signaling Technology)
|
| 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. Cells were frozen in LN2.
|
| Growth protocol |
Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10 million frozen cells per biological replicate were processed following the standard Dovetail HiChIP MNase Kit (Dovetail Genomics)
HiChIP libraries were prepared using the Dovetail HiChIP MNase Kit (Dovetail Genomics).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Contact matrix across 2500 bp windows generated by cooler
Significant interactions called by FitHiChIP in L+M mode with 2500 bp bin size, lower/upper distance thresholds of 10KB/2MB and coverage bias regression.
Assembly: hg38
Supplementary files format and content: cool, contact matrix generated by cooler
Supplementary files format and content: bedpe, significant interactions called by FitHiChIP
Library strategy: HiChIP Mnase
|
| |
|
| 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) |
| GSE230292 |
Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [HICHIP] |
| GSE230526 |
Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma |
|
| Relations |
| BioSample |
SAMN34300138 |
| SRA |
SRX20054330 |
