The SG-NEx project: nanopore long-read RNA-sequencing of human cancer cell lines

The ability of RNA-sequencing to generate a high-dimensional, quantitative readout of cells and tissues has made it arguably the most successful functional genomics assay in molecular biology. A new generation of long-read sequencing technology using nanopores enables amplification-free, direct sequencing of native RNA. The technology has the potential to overcome the major limitations of short-read sequencing, promising to provide a richer and more accurate readout of the cellular transcriptome. To systematically evaluate nanopore technology, we started the Singapore Nanopore-Expression Project (SG-NEx). As part of SG-NEx we generated full-length transcript sequencing data of 5 cancer cell lines using PCR-cDNA sequencing (PCR-cDNA), amplification-free cDNA sequencing (direct cDNA), and direct sequencing of native RNA (direct RNA) on the MinION, GridION, and PromethION platforms.

In this webinar I will introduce the SG-NEx project, compare the data obtained from the different RNA-Seq protocols, and show a comparison with short-read sequencing data. I will include an overview of the computational workflow and highlight considerations for experimental design of a long-read transcriptomics experiment.

Key Learning Objectives:

An introduction to the Singapore Nanopore-Expression Project (SG-NEx) and how to access the first batch of SG-NEx RNA-Seq data
What to expect from the different RNA-Seq protocols from Oxford Nanopore (direct RNA vs cDNA vs PCR)
How long-read RNA-Seq data compares to short-read RNA-Seq data

Overview

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