Illumina NovaSeq 6000 paired end sequencing; RNA-seq of HCT116 cells upon administration of FOLFOX or FOLFIRI at time points with or without ULK1 inhibitor
RNA-seq of HCT116 cells upon administration of FOLFOX or FOLFIRI at time points with or without ULK1 inhibitor
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. 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 the combination with ULK1 inhibitor, SBI-0206965 was added at 100µM concentration for 8h or 16h. RNA extraction was performed using the RNeasy kit (74106) from Qiagen. Ribo minus total RNA stranded kit was used.