|
| Status |
Public on Mar 01, 2024 |
| Title |
Safe NoTNF and Safe TNF |
| Sample type |
SRA |
| |
|
| Source name |
K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Safe
cell line: K562
time: Day 4 after infection with relevant sgRNA
treatment: None
|
| Treatment protocol |
Cells were infected with relevant sgRNAs for 4 days prior to harvest. TNF treatment was performed for 6hrs at 25ng/ml.
|
| Growth protocol |
K562 cells were cultured in RPMI-1640 supplemented with 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using a plate based in-house library prep method based on DRUG-seq (Ye et al., 2018).
The method results in 3’ RNA-seq libraries containing a UMI and a well ID on read 1, and the unique transcript information on read 2. Libraries were sequenced on the NextSeq500 using the 75bp single end chemistry, run with paired-end settings. 25bps was allocated for the Read1 and 50bps for Read
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
STARsolo was used to generate a STAR index for the human (hg19) genome
STARsolo is used to map the reads to the STAR reference genome. R1 sample contains the sample barcode and the UMI. R2 contains the cDNA sequence.
Seurat is used to extract raw count tables from the STAR solo output folder.
DESeq2 is used to do differential analyses.
Assembly: hg19
Supplementary files format and content: Raw count matrices and sample info sheets
|
| |
|
| Submission date |
Mar 18, 2022 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Charles C Bell |
| E-mail(s) |
charles.bell@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Cancer Research
|
| Street address |
VCCC, Gate 1, 14 Flemington Road
|
| City |
Melbourne |
| State/province |
VICTORIA |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE198942 |
Comparative cofactor screens reveal the influence of transactivation domains and core promoters on the mechanisms of transcription [RNA-seq] |
| GSE198944 |
Comparative cofactor screens reveal the influence of transactivation domains and core promoters on the mechanisms of transcription. |
|
| Relations |
| BioSample |
SAMN26794584 |
| SRA |
SRX14499817 |
