|
| Status |
Public on Nov 20, 2024 |
| Title |
GCN1 KO, sgRNAs 1 and 2, replicate 1, no harringtonine |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
genotype: gcn1 ko sgrnas 1 and 2
treatment: none
batch: Replicate 1
|
| Treatment protocol |
Harringtonine was added to a concentration of 1mM for samples labeled as ‘6h’. All other samples were harvested without treatment.
|
| Growth protocol |
HEK293T were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Doxycycline was added to a final concentration of 2μg/ml to induce Cas9 for 4 days (group 1) or for 7 days (group 2)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymo) following manufacturer’s instructions. polyA RNA was selected using oligo dT25 magnetic beads (NEB) following manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
FASTQ reads aligned to GRCh38 with Ensembl v108 transcript annotations using STAR v2.7.11a with parameters `--runMode alignReads --alignSJoverhangMin 300 --alignSJDBoverhangMin 6 --outSAMmultNmax 1 --quantMode GeneCounts`.
Full analysis pipeline in https://github.com/rasilab/nugent_2024/blob/main/analysis/rnaseq/scripts/run_analysis.smk
Assembly: GRCh38
Supplementary files format and content: ReadsPerGene.out.tab in tab-delimted text format as output by STAR
|
| |
|
| Submission date |
Nov 19, 2024 |
| Last update date |
Nov 20, 2024 |
| Contact name |
Arvind R Subramaniam |
| E-mail(s) |
[email protected]
|
| Organization name |
Fred Hutchinson Cancer Center
|
| Department |
Basic Sciences Division
|
| Street address |
1100 Fairview Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE282328 |
Decoding RNA metabolism by RNA-linked CRISPR screening in human cells |
|
| Relations |
| BioSample |
SAMN41637179 |
| SRA |
SRX24774226 |
