|
| Status |
Public on May 22, 2024 |
| Title |
HEL cells, LRCherry2.1-sgDCAF15#2, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEL
cell type: acute myeloid leukemia
genotype: DCAF15-KO
|
| Treatment protocol |
Prior to experiment, HEL cells were engineered to stably express SpCas9 protein
Additionally, prior to experiment, SpCas9-expressing HEL cells were lentivirally-infected with the LRCherry2.1 vector containing an sgRNA targeted against ROSA26(Control) or DCAF15, and cells were sorted for mCherry positivity
|
| Growth protocol |
HEL human acute myeloid leukemia cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed on cells using the Arima High Coverage HiC Kit (Arima Genomics, A101030), following all manufacturer instructions
Hi-C libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645S) and NEBNext Dual Index Primers (New England BioLabs, E7600S), with modifications to the protocol as specified by the Arima High Coverage HiC Kit
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
D15.hic
D15.mcool
|
| Data processing |
Hi-C reads were combined between replicates and aligned to the human hg19 genome with Juicer, using an annotation file based on the Arima restriction enzymes and default settings
Contact matrices were generated by Juicer in .hic format using Knight-Ruiz (KR) normalization, and converted to .cool format at various resolutions using the hicConvertFormat function in HiCExplorer
Assembly: hg19
Supplementary files format and content: hic, mcool
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Luca Busino |
| E-mail(s) |
businol@upenn.edu
|
| Phone |
215-746-2569
|
| Organization name |
University of Pennsylvania
|
| Department |
Cancer Biology
|
| Lab |
Luca Busino Laboratory
|
| Street address |
421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE241580 |
CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation [HiC] |
| GSE241581 |
CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation |
|
| Relations |
| BioSample |
SAMN37127970 |
| SRA |
SRX21472317 |
