|
| Status |
Public on Feb 06, 2024 |
| Title |
HCC827ASCL1, osimertinib, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCC827
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC827
cell type: human NSCLC cell line
transfection: inducible ASCL1 transfected
treatment: osimertinib for 3 days
|
| Treatment protocol |
vehicle or 100nM osimertinib
|
| Growth protocol |
RPMI 1640 supplemented with 10% tet system-certified FBS, 1μg/ml doxycycline, 1mM sodium pyruvate, 10mM HEPES, 100U/ml penicillin and 100μg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell lines using AllPrep DNA/RNA mini kit (Qiagen, 80204).
RNA-seq libraries were constructed using KAPA mRNA HyperPrep Kit (Kapa Biosystems, KR1352).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HCC827ASCL1_O1
|
| Data processing |
RNA-seq raw data were trimmed of adaptor sequences using Trim Galore and mapped to the human reference genome (hg38) using HISAT2.
The sequencing reads were annotated according to GENCODE v27 model and gene expression levels were quantified using StringTie
Differentially expressed genes were identified using DESeq2.
Assembly: hg38
Supplementary files format and content: excel file including normalized gene counts for all the cell lines and experimental conditions
|
| |
|
| Submission date |
Sep 19, 2023 |
| Last update date |
Feb 06, 2024 |
| Contact name |
Bomiao Hu |
| E-mail(s) |
bomiao.hu@yale.edu
|
| Organization name |
Yale University
|
| Street address |
310 Cedar Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE243565 |
ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [Cell Line RNA-seq] |
| GSE243569 |
ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts |
|
| Relations |
| BioSample |
SAMN37473062 |
| SRA |
SRX21828555 |
