Illumina NovaSeq 6000 paired end sequencing; RNA-seq of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points
RNA-seq of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points
Cells were trypsinized, harvested and washed with PBS 1%. Then, the pellet was immediately used for RNA extraction or frozen and stocked at -80°C until use.  HCT116 cells were grown in DMEM supplemented with 10% Fetal Bovine Serum. HT29 cells were grown in RPMI supplemented with 10% Fetal Bovine Serum and 1mM Sodium Pyruvate. Cells were plated, and after 24h were treated with FOLFOX or FOLFIRI at the following concentration: 5-FU 100µM + OXA 100µM (FOLFOX) or 5-FU 100µM + SN-38 100nM (FOLFIRI) for 8h or 16h. Then, cells were harvested for experimental purposes. For long term (2 weeks) treatments, cells were plated and exposed to 5-FU 10µM + OXA 1µM (FOLFOX) or 5-FU 10µM + SN-38 10nM (FOLFIRI). RNA extraction was performed using the RNeasy kit (74106) from Qiagen. Ribo minus total RNA stranded kit was used.