|
| Status |
Public on May 22, 2024 |
| Title |
MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgROSA26(Control), rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MV4-11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MV4-11
cell type: acute myeloid leukemia
genotype: TP53-KO
|
| Treatment protocol |
Prior to experiment, MV4-11 and HEL cells were engineered to stably express SpCas9 protein
Additionally, prior to experiment, SpCas9-expressing MV4-11 cells were lentivirally-infected with the LRG2.1 vector containing an sgRNA targeted against ROSA26(Control) or TP53, and cells were sorted for GFP positivity
On Day 0 of experiment, cells were lentivirally-infected with the LRCherry2.1 vector containing an sgRNA targeted against ROSA26(Control) or DCAF15
On Day 3 of experiment, cells were sorted for mCherry and GFP double positivity
On Day 4 of experiment, cells were harvested and frozen for RNA extraction
|
| Growth protocol |
MV4-11 and 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 |
total RNA |
| Extraction protocol |
Total RNA was extracted from MV4-11 and HEL 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 |
| |
|
| Description |
normalized_MV411_counts.csv
|
| 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_MV411_counts.csv: csv file includes normalized counts for each MV4-11 Sample
Supplementary files format and content: normalized_HEL_counts.csv: csv file includes normalized counts for each HEL Sample
|
| |
|
| 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 |
GPL24676 |
| Series (2) |
| GSE241578 |
CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation [RNA-seq_CRISPR] |
| GSE241581 |
DCAF15 control of cohesin dynamics sustains acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN37129341 |
| SRA |
SRX21473688 |
