|
| Status |
Public on Aug 16, 2024 |
| Title |
REC-1, Ibrutinib Resistant, Hi-C |
| Sample type |
SRA |
| |
|
| Source name |
REC-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: REC-1
cell type: Mantle Cell Lymphoma
treatment: Ibrutinib
|
| Treatment protocol |
Parental and resistant cells were tretated with DMSO (parental) or ibrutinib (reistant) for 24 hours followed by BCR crosslinking with IgM for 5min. Cells used for Hi-C were subsequently fixed with 2% formaldehyde
|
| Growth protocol |
RPMI 1640 supplemented with 10% fetal bovine serum , 2 mM L-glutamine, 100 U/mL and 100 μg/mL penicillin/streptomycin, 100 mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Arima HiC kit used per manufacture’s instructions
Accel-NGS 2S Plus DNA library kit
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads for each HiC sample were processed with HiC-Pro (version v2.8.1) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE and GENOME_FRAGMENT provided by Arima.
Assembly: hg19
Supplementary files format and content: .hic formatted file for juicebox viewing of contact matrices
|
| |
|
| Submission date |
May 23, 2024 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
|
| Phone |
215-573-8220
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathology
|
| Lab |
Faryabi Lab
|
| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE268226 |
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (HiC) |
| GSE268228 |
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance |
|
| Relations |
| BioSample |
SAMN41511577 |
| SRA |
SRX24667516 |
