A nanopore long-read transcriptome in pancreatic cancer cells

This project aims to leverage Oxford Nanopore Technologies (ONT) long-read RNA sequencing to achieve a comprehensive analysis of the human pancreatic cancer transcriptome. Traditional short-read sequencing methods often struggle with accurately reconstructing full-length transcripts and discerning complex splicing events due to their limited read lengths. In contrast, ONT's long-read sequencing can generate reads that span entire RNA molecules, facilitating precise identification of transcript isoforms, alternative splicing patterns, and poly(A) tail length. By applying this technology, we seek to enhance the annotation of the pancreatic cancer transcriptome, uncover novel transcripts, and gain deeper insights into gene expression dynamics. The findings from this study have the potential to advance our understanding of gene regulation and contribute to the development of novel therapeutic strategies. Overall design: This project employs Oxford Nanopore Technologies (ONT) long-read RNA sequencing to achieve a comprehensive analysis of the human pancreatic cancer transcriptome. Ten pancreatic cancer cell lines are collected, two replicates for each, were used for ONT long-read RNA sequencing. Transcript expression patterns, alternative splicing, poly(A) tail length, and integration with proteomics were performed across pancreatic cancer cells.