A guide to single-cell transcriptomics with Oxford Nanopore

Overview

Single-cell RNA sequencing of the human transcriptome is a valuable research tool, shedding light on the complex mechanisms behind developmental processes, immune system functions, and diseases such as cancer. Full-length transcripts can be sequenced in single long nanopore reads, delivering unambiguous detection of isoforms and fusion transcripts that cannot be captured with short-read approaches. Additionally, nanopore reads enable SNV detection across complete transcripts for deep characterisation of clonal evolution and tumour heterogeneity.

This guide introduces the single-cell RNA nanopore sequencing workflow, for ultra-rich data without compromise.

In this getting started guide, you will:

• Find out about the benefits of nanopore sequencing for single-cell transcriptomics, and how it reveals isoform-level information missed by legacy short-read technologies

• Read about the end-to-end single-cell nanopore sequencing workflow

• Discover how to go from 10x Genomics cell-barcoded cDNA samples to sequencing-ready libraries in around three hours

• Find out about the range of high-output PromethION sequencing devices

• Discover how single-cell nanopore sequencing data can be easily analysed using the EPI2ME workflow wf-single-cell

• Read case studies describing how researchers are utilising single-cell nanopore sequencing to enhance research into leukaemia and the mouse retina transcriptome