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Updated: Jan 21, 2026
11:26
Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
14.7K
A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes
Charlotte Soneson1,2,3, Yao Yao4,5, Anna Bratus-Neuenschwander6
1Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland. charlotte.soneson@fmi.ch.
Nature Communications
|August 2, 2019
Summary
Oxford Nanopore Technologies' native RNA sequencing shows promise for transcriptome quantification but faces challenges with full-length transcript recovery and origin inference. Improvements are needed for complex mammalian transcriptomics applications.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Oxford Nanopore Technologies (ONT) offers direct RNA sequencing of native strands.
- Investigating its utility for complex transcriptome quantification is crucial.
Purpose of the Study:
- To evaluate native RNA sequencing for quantifying complex transcriptomes.
- To compare its performance against direct cDNA and Illumina sequencing methods.
Main Methods:
- Native RNA sequencing of polyA+ RNA from two human cell lines (~5.2 million reads).
- Comparative analysis with ONT direct cDNA and Illumina sequencing.
Main Results:
- Native RNA sequencing shows potential but has limitations.
- Frequent inability to obtain full-length transcripts in single reads.
- Difficulties in unambiguously inferring the true transcript of origin.
Conclusions:
- Native RNA sequencing requires improvements for complex transcriptomes.
- It could become a valuable tool in mammalian transcriptomics with defined enhancements.
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