ArticleNature communications2019
A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers.
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Who cites it
172 citing papers in PubMed.
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- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Derivation of elephant induced pluripotent stem cells.Nature methods · 2026Article
- HyDRA: A pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly.iScience · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Modular RNA:DNA Nanostructures Enable Nanopore Profiling of rRNA Processing and rRNA Variants.ACS nano · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- Efficient reconstruction of full-length RNA isoforms using ISAtools and large-scale PacBio circular consensus sequencing data.Briefings in bioinformatics · 2026Article
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
- Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming during 50S Biogenesis.Biochemistry · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Veterinary Herpesviruses: Experimental Tools for Transcriptomics and Neuroscience.Veterinary sciences · 2026Review
- A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification.Genome biology · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Comparative transcriptomic and transcript-based network analyses revealed genotype-specific alternative splicing induced by Sclerotinia sclerotiorum in Brassica napus.BMC plant biology · 2026Article
- Nanoscale zinc for sustainable groundnut growth: an eco-conscious molecular approach.Scientific reports · 2026Article
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
112 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
A platform for highly parallel direct sequencing of native RNA strands was recently described by Oxford Nanopore Technologies, but despite initial efforts it remains crucial to further investigate the technology for quantification of complex transcriptomes. Here we undertake native RNA sequencing of polyA + RNA from two human cell lines, analysing ~5.2 million aligned native RNA reads. To enable informative comparisons, we also perform relevant ONT direct cDNA- and Illumina-sequencing. We find that while native RNA sequencing does enable some of the anticipated advantages, key unexpected aspects currently hamper its performance, most notably the quite frequent inability to obtain full-length transcripts from single reads, as well as difficulties to unambiguously infer their true transcript of origin. While characterising issues that need to be addressed when investigating more complex transcriptomes, our study highlights that with some defined improvements, native RNA sequencing could be an important addition to the mammalian transcriptomics toolbox.
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Registered trials
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