|
| Status |
Public on May 22, 2024 |
| Title |
OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, DMSO (Control), rep1 |
| Sample type |
SRA |
| |
|
| Source name |
OCI-AML3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI-AML3
cell type: acute myeloid leukemia
treatment: DMSO
|
| Treatment protocol |
Prior to experiment, OCI-AML3 cells were engineered with the FLAG-HA-FKBP12(F36V) tag (dTAG) knocked-in at the start codon of the endogenous DCAF15 genomic locus
Additionally, prior to experiment, OCI-AML3 Nt_FLAG-HA-FKBP12(F36V)_DCAF15 cells were single-cell cloned, and validated for homozygosity and dTAGv1 drug-induced degradation of endogenous DCAF15 protein
Cells were treated with DMSO, 250nM dTAGv1 drug for 24h, or 250nM dTAGv1 drug for 72h
At the end of the treatment time, cells were harvested and frozen for RNA extraction
|
| Growth protocol |
OCI-AML3 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 |
total RNA |
| Extraction protocol |
Total RNA was extracted from OCI-AML3 cells using the RNeasy Mini Kit (QIAGEN, 74104) per the manufacturer's instructions
Total RNA was shipped to GENEWIZ (Azenta Life Sciences) for Standard RNA-Seq service, where polyA+ transcripts were isolated and RNA-seq library was prepared per their in-house protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were mapped and analyzed with a bioinformatic pipeline based on STAR, SAMTOOLS, and the R package DESeq2
Assembly: GRCh38
Supplementary files format and content: normalized_OCI-AML3_counts.csv: csv file includes normalized counts for each OCI-AML3 Sample
|
| |
|
| Submission date |
Apr 27, 2024 |
| 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 |
GPL24676 |
| Series (2) |
| GSE241581 |
DCAF15 control of cohesin dynamics sustains acute myeloid leukemia |
| GSE266010 |
CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation [RNA-seq_dTAG] |
|
| Relations |
| BioSample |
SAMN41099242 |
| SRA |
SRX24383464 |
