|
| Status |
Public on May 22, 2024 |
| Title |
HEL cells, LRCherry2.1-sgDCAF15#2, total-SMC3, ChIP |
| Sample type |
SRA |
| |
|
| Source name |
HEL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEL
cell type: acute myeloid leukemia
genotype: DCAF15-KO
chip antibody: total-SMC3 (Bethyl Laboratories, A300-060A)
|
| 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 |
Cells were fixed with 1% paraformaldehyde in PBS for 10minutes; after quenching and cell lysis, chromatin was sonicated using a Covaris Ultrasonicator
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA library prep with sample purification beads (NEB, E7103S) following the manufacturer’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
fastq files were aligned with BOWTIE2
Reads were sorted and duplicates removed with SAMTOOLS
Peaks were called with Macs2
Further analysis was performed in RStudio using the R packages Rsamtools, DESeq2, GenomicAlignments, soGGi, ggplot2, and profileplyr
Assembly: hg19
Supplementary files format and content: bigWig
|
| |
|
| 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) |
| GSE241579 |
CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation [ChIP-seq] |
| GSE241581 |
DCAF15 control of cohesin dynamics sustains acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN37129349 |
| SRA |
SRX21473913 |
