Single-cell RNA-seq of human cancer cell lines and their resistant variants treated with cytostatic kinase inhibitors
Intent of the experiment was to identify common factors associated with proliferation in multiple cancer cell lines from different tissue of origin. Cell lines and their resistant variants were treated with 0, 0.8, 4, 20, 100, 500 nM drug concentration at 2, 6, 12, and 24 hour time points. Experiments were performed on one 24 well plate per cell line, and after the drug treatment, each row and column were labeled with a different hashtag oligo for each row and column, which resulted in a unique barcode combination for each well. All 24 conditions per cell line were multiplexed into one Chromium chip well, and the RNA-seq was performed with 10x Genomics 3' v3 workflow. Drugs: NCI-H1975: Osimertinib, RKO: Trametinib, HCT116: Trametib, KBM-7 Imatinib. HAP1 cell line was analyzed as the resistant counterpart of KMB-7 and for the other cell lines, resistant variant was generated by PTEN knockout.