|
| Status |
Public on Apr 06, 2022 |
| Title |
HCC827_DMSO_3 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC827
treatment: DMSO
|
| Treatment protocol |
The NSCLC EGFR mutant cell lines (PC9, NCI-H1975, HCC827, and HCC2935) were treated with 500 nM osimertinib for 21 days (osimertinib DTPs). Cells were either harvested immediately or washed 2x with PBS and then replaced with drug-free media for a further 24 hrs. (short washout), or for a longer time-point (long washout) until exponential cell proliferation resumed (PC9: 7 days; NCI-H1975: 3 days; HCC827: 4 days; HCC2935: 10 days) and then harvested. In parallel, parental cell lines were grown in drug-free media for 21 days then treated with 500 nM osimertinib for 24 hrs. (osimertinib acute) or vehicle DMSO control for 24 hrs. (DMSO control). Experiment was done using biological triplicates. There are 60 total RNA-seq samples.
|
| Growth protocol |
NCI-H1975 human NSCLC adenocarcinoma cells were obtained from American Type Culture Center (ATCC) and were grown in RPMI 1640, supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin-Streptomycin. All cells were maintained and propagated as monolayer cultures at 37°C in a humidified 5% CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in RLT buffer (Qiagen) and RNA extracted using the Qiacube HT according to manufacturer’s instructions, and RNA concentration quantified using the Qubit fluorometer.
Illumina mRNA TruSeq library was used for library preparation.
RNA-seq was sequenced on 9 lanes of Illumina HiSeq4000 with paired end 150bp reads by the CRUK Genomics Core Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastq files were aligned using HISAT2 (v2.1.0)
Counts were quanitied using Salmon (v0.8.2) using Ensembl v79 annotations.
tximport was used to generate gene level count data using option countsFromAbundance = "lengthScaledTPM" and a log2 transcripts per kilobase million, log2(TPM +0.01), abundance matrix.
Genome_build: hg38
Supplementary_files_format_and_content: Count matricies.
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Apr 06, 2022 |
| Contact name |
Paul D Smith |
| Organization name |
AstraZeneca
|
| Street address |
AstraZeneca CRUK Cambridge Institute, Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB20RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE193258 |
The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells [RNA-seq] |
| GSE193259 |
The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells |
|
| Relations |
| BioSample |
SAMN24730033 |
| SRA |
SRX13661753 |
