Alternative transcript isoform detection with single cell and spatial resolution

Overview

Alternative transcript isoforms have a range of implications in development, health, and disease. However, studying alternative splicing and transcript isoforms has previously been challenging with legacy short-read sequencing technologies, which collapse all isoforms into a single gene expression measurement. Nanopore sequencing can generate reads of any length, enabling characterisation at the isoform level from full-length cDNA strands to identify alternative transcript isoforms with single-cell and spatial resolution.

This application note demonstrates that Oxford Nanopore Technologies, in combination with 10x Genomics cDNA preparation, is a reliable platform to accurately detect alternative transcript isoforms.

In this application note, you will:

• Learn the importance of sequencing full-length cDNA from single cells for high-resolution isoform detection
• Discover the methods and analysis tools used to generate high-quality data
• View our benchmarking data generated using nanopore sequencing

Workflow: single-cell transcriptomics

To learn more about the protocol in this application note, you can download the end-to-end workflow for single-cell transcriptome analysis from 10x Genomics cDNA libraries, using the PromethION device and the EPI2ME analysis platform.