Long read transcriptome sequencing of ccRCC tumour cell line RCC4
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. To date, long-read RNA sequencing has not been applied to kidney cancer. Here, we used ONT long-read Direct RNA sequencing to profile the transcriptomes of ccRCC cell line RCC4, with and without exposure to pro-inflammatory cytokines. Our results revealed differentially expressed genes induced by the pro-inflammatory cytokines. Moreover, results here revealed potential tumour origin of novel isoforms and genes that were discovered in the archival tumour samples by long-read sequencing. Overall design: RCC4 cells (with and without exposure to pro-inflammatory cytokines IFNg&TNF for 24h) were harvested for total RNA. Poly(A)+ RNA molecules were isolated, with 500ng used as input for sequencing library preparation (RNA002). Each library was loaded on individual PromethION flow cell (R9) and sequenced for 72h. Reads with Q>7 were used for subsequent bioinformatic analysis.