|
| Status |
Public on Apr 27, 2021 |
| Title |
Day 3 shEVI1-2531 |
| Sample type |
SRA |
| |
|
| Source name |
myeloid leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MUTZ-3
treatment: EVI1 shRNA #2531
time point: day 3
|
| Treatment protocol |
PARP inhibition: 10 µM olaparib, 1 µM talazoparib or the DMSO vehicle control was added to the cell culture medium and the cells were harvested after the indicated time points.
EVI1 Knockdown: MUTZ-3 were lentivirally transduced with the pLKO.1 vector coding for either a commercial non-targeting control (SHC002) or shRNAs directed against EVI1 (TRCN0000002532, TRCN0000002531). Cells were selected with puromycin and harvested at the indicated time points.
|
| Growth protocol |
MUTZ-3 cells were grown in MEMalpha with 20% FBS, 20% conditioned medium from 5637 cells, 10 ng/ml GM-CSF and 1x Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the Qiagen RNeasy Plus Mini Kit.
Library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
100bp PE
|
| Data processing |
Fastq files are aligned to the hg38 human genome using the STAR 2-pass alignment (version 2.7.3a).
Duplicate reads are marked with Picard MarkDuplicate (v. 2.21.2).
Features are counted using the featureCount function from the Rsubread package (v. 2.0.1).
TPM values are computed using a custom R script.
The pipeline is implemented as a Snakemake workflow.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_featureCounts.tsv: Tab-separated counts and tpm.
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
Apr 27, 2021 |
| Contact name |
Stefan Gröschel |
| Organization name |
DKFZ German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 581
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE153307 |
Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia |
| GSE167005 |
Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN17975860 |
| SRA |
SRX10122836 |
