Illumina NovaSeq 6000 sequencing; Single cell RNA-seq analysis of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points
Single cell RNA-seq analysis of cancer cell lines upon administration of FOLFOX or FOLFIRI at different time points
Cells were trypsinized, harvested and washed with PBS/0.04% BSA and immediately used. 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 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). Nucleic acids were directly processed on intact cells following standard Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics) using Chromium platform (10x Genomics). Target cell recovery was 5'000. Libraries were prepared using Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics). Library quality was assessed using TapeStation (Agilent Technologies). Libraries were sequenced on NovaSeq 6000 platform (Illumina) aiming at 50'000 clusters/cell.