RNA-seq of OVCAR3 and CCL218 cancer cells with evolved hydroxychloroquine resistance

OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present. Cells were then pelleted and cell pellets were processed for concomitant bulk RNA-seq, whole-exome-sequencing, and single-cell RNA-seq. This project represents the bulk transcriptomic sequencing and analysis. Cells were pooled, representing one-third of each 96-well plate, pelleted, and processed by Genewiz for RNA-seq and whole-exome sequencing (WES). Qiagen AllPrep DNA/RNA kits were used to isolate RNA and DNA from the same sample. Agilent SureSelect Human All Exon V8 kits were used and polyA selection performed for transcriptomes.