|
| Status |
Public on May 17, 2024 |
| Title |
Osimertinib-treated SG2 HCC4006 cells |
| Sample type |
SRA |
| |
|
| Source name |
lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung adenocarcinoma
cell line: HCC4006
cell type: epithelial cell
subcloned: yes
treatment: osimertinib 1 µM
|
| Treatment protocol |
FUCCI-transduced HCC4006 subcloned cells were expanded in untreated (DMSO), osimertinib (1 µM) or osimertinib (1 µM) + tipifarnib (1 µM)-containing medium for 4, 20 and 12 days respectively. Drug-containing medium was changed 24h before sorting. Cells were dissociated by trypsinisation, recovered in FACS buffer (0,04% BSA in PBS) and kept on ice. G1 (red) and S/G2 (green) cells were sorted at 4°C using FACS Melody (BD Biosciences).
|
| Growth protocol |
The human NSCLC cell lines HCC4006 (CRL-2871, EGFR∆L747-E749, A750P) was obtained from the American Type Culture Collection (ATCC), and cultured in 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. Cells were transduced with the Incucyte® Cell Cycle Green/Red lentivirus based on the FUCCI system, and selected by puromycin treatment for one week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the experiment, 6 000 cells of each sample were loaded in Chromium device for emulsion-based production of single cell mRNA libraries with the 10X Genomics platform chemistry 3’V2 according to manufacturer’s instructions. Reverse transcription was performed on the C1000 Touch Thermal Cycler, and cDNA were amplified for 12 cycles. cDNA quality control and dosage were performed on Fragment Analyzer, and then by PCR.
single-cell RNA-seq 3’ chemistry; Chromium Controller Single-Cell Instrument and Chromium Single Cell 3' Library & Gel Bead Kit (V2) were used to prepare individually barcoded single-cell RNA-Seq libraries. Double sided size selection of PCR products was performed with SPRIselect Reagent Kit (Beckman Coulter, France). The sequencing-ready library was cleaned up with SPRIselect beads and the sequencing was performed on a NextSeq 550 instrument (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
10X Genomics
SG2_OSI_4006
|
| Data processing |
bcl2 files conversion to FASTQ format using cellranger-mkfastq™ algorithm (10x Genomics)
align to the GRCh38 reference transcriptome using cellranger-count
Preprocessing, normalization of UMI, and QC for discarding cell doublets and dying cells were performed using the R package Seurat 4
The integrated (cell x gene) matrices of all single cells are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell for all samples
|
| |
|
| Submission date |
Nov 22, 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) |
| GSE248450 |
Farnesyltransferase inhibition overcomes the adaptive resistance to targeted therapies in oncogene-addicted non-small cell lung cancer |
|
| Relations |
| BioSample |
SAMN38370311 |
| SRA |
SRX22613098 |
