|
| Status |
Public on Jul 02, 2024 |
| Title |
Cetuximab-sensitive LIM1215-S – biol rep 1 [S46] |
| Sample type |
SRA |
| |
|
| Source name |
LIM1215
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LIM1215
cell type: colon cancer cells
genotype/phenotype: cetuximab-sensitive
treatment: none
|
| Treatment protocol |
Cetuximab-resistant DiFi and LIM1215 cancer cells were cultured under continuous treatment with 25 µg/mL cetuximab (Erbitux 5 mg/mL; Merck #L01XC06).
|
| Growth protocol |
DiFi cells were cultured in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12; #11330032, Thermo Fisher Scientific) while LIM1215 cells were grown in RPMI-1640 medium + GlutaMAX (#61870-010, Thermo Fisher Scientific). Media were supplemented with 10% heat-inactivated fetal bovine serum (FBS; F7524, Sigma-Aldrich), and 1% penicillin-streptomycin (#15140163, Thermo Fisher Scientific), and cells were maintained in exponential growth in 5% CO2/95% air in a humidified incubator at 37°C. All cell lines were tested for mycoplasma contamination with the PCR-based MycoplasmaCheck service from Eurofins Genomics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen cell pellets with the Monarch Total RNA Miniprep kit (New England Biolabs) by following manufacturer’s protocol. Total RNA (300 ng/sample) was ribodepleted by using the NEBNEXT rRNA Depeletion kit (New England Biolabs) according to manufacturer’s instructions.
Ribodepleted RNA was then used for the library preparation with the NEBNext Ultra II Directional RNA library prep kit for Illumina (New England Biolabs) according to manufacturer’s instructions.
Libraries were paired-end sequenced (2*100 base pairs) on a NextSeq2000 device (Illumina), with a minimal depth of 10 million reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fa file.
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: Excel file with the matrix of raw counts.
|
| |
|
| Submission date |
Mar 29, 2024 |
| Last update date |
Jul 02, 2024 |
| Contact name |
Jérôme Ambroise |
| E-mail(s) |
jambroise83@gmail.com
|
| Organization name |
Université catholique de Louvain
|
| Department |
Institut de Recherche Expérimentale et Clinique
|
| Street address |
Avenue Hippocrate 54
|
| City |
Woluwé |
| ZIP/Postal code |
1200 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE262796 |
Gene expression changes associated with acquired resistance to anti-EGFR therapy (cetuximab) in colorectal cancer cells |
|
| Relations |
| BioSample |
SAMN40655509 |
| SRA |
SRX24100933 |
