|
| Status |
Public on Dec 31, 2021 |
| Title |
SF268_GCN2cr3_N675_3D_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SF268
treatment: neratinib 675 nM
timepoint: 72 hr
|
| Treatment protocol |
Inhibitors or DMSO were added to the cultured cells and treated for indicated times.
|
| Growth protocol |
Cells were cultured in DMEM + 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CRISPR screen sequencing libraries were made with nested PCRs of the sgRNA region.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the TKOv3 library sequences with bowtie.
Sequenced reads aligned to GRCh38 with salmon. Differential expression analysis was performed with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited .txt file
|
| |
|
| Submission date |
Nov 16, 2021 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Colin Tang |
| E-mail(s) |
[email protected]
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Ave.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE188958 |
GCN2 kinase Activation by ATP-competitive Kinase Inhibitors |
|
| Relations |
| BioSample |
SAMN23195527 |
| SRA |
SRX13150050 |
