|
| Status |
Public on May 17, 2024 |
| Title |
H3255_NT3 |
| Sample type |
SRA |
| |
|
| Source name |
lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung adenocarcinoma
cell line: H3255
cell type: epithelial cell
subcloned: yes
treatment: DMSO
|
| Treatment protocol |
EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. PC9, HCC4006 and H3255 subclones were treated with DMSO (control) or with erlotinib at 1 µM for 24h, until drug-tolerance (7-to-21 days) or until development of fully resistant proliferative cells (RPC, only for PC9 and HCC4006 cells). RPC were isolated and amplified from individual early-emerging colonies, which were cultured and passaged for more than three months in the presence of the drug. HCC827 were treated with DMSO (control) or with osimertinib at 1 µM until drug-tolerance (11 days).
|
| Growth protocol |
The human EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. Cell lines were authenticated and tested for mycoplasma contamination within the experimental time frame.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using AllPrep DNA/RNA Mini kit (Qiagen, #80204) according to the manufacturer’s protocol. RNA quality was assessed using Fragment Analyzer (Agilent technologies) and the RQN values were provided to confirm the integrity of total RNA. RNA concentration was determined by fluorescent method using Quant-iT™ RNA Assay Kit, Broad Range (ThermoFisher Scientific).
RNA samples were processed with Illumina TruSeq® Stranded mRNA Library Preparation Kit following the manufacturer’s protocol. Library size and quality were confirmed on Fragment analyzer (Agilent Technologies). KAPA quantification kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify the library by qPCR. Indexed libraries were pooled and sequenced on an Illumina NextSeq 550 (2x75 bp paired-end reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
bcl2 files conversion to FASTQ format using bcl2fastq algorithm
align to the GRCh38 reference transcriptome using bowtie2
Preprocessing, normalization, QC, and downstream analysis were performed using Deseq2 in R enviroment
The processed (sample x gene) matrix counts are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw counts for every gene and every sample
|
| |
|
| Submission date |
Dec 08, 2023 |
| Last update date |
May 17, 2024 |
| Contact name |
Juan Pablo Cerapio |
| E-mail(s) |
jcerapioarroyo@gmail.com, juan-pablo.cerapio-arroyo@inserm.fr
|
| Organization name |
CRCT
|
| Street address |
Av 2 Hubert Curien
|
| City |
Toulouse |
| ZIP/Postal code |
31000 |
| Country |
France |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE249721 |
Farnesyltransferase inhibition overcomes the adaptive resistance to targeted therapies in oncogene-addicted non-small cell lung cancer II |
|
| Relations |
| BioSample |
SAMN38739386 |
| SRA |
SRX22839738 |
