ArticleNucleic acids research2022
Accurate expression quantification from nanopore direct RNA sequencing with NanoCount.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed, 118 citations in OpenAlex.
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- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- A comprehensive long RNA landscape of multi-regional porcine lung-derived small extracellular vesicles.BMC genomics · 2026Article
- MASQ: A multiplex qPCR platform for quantitative alternative splicing analysis in clinical specimens.Molecular therapy. Nucleic acids · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- HERV-K HML-2 transcriptional profiling and splicing pattern unveiled by direct single-molecule long-read RNA sequencing.Mobile DNA · 2026Article
- Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution.Nature communications · 2026Article
- Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.Nature communications · 2026Article
- The 5-Methylcytosine RNA Modification in Hepatitis B Virus-Negative Hepatocellular Carcinoma: Insights From Long-Read Nanopore Sequencing.Molecular carcinogenesis · 2026Article
- Transcriptomic and RNA Modification Landscape of Severe Fever with Thrombocytopenia Syndrome Virus Revealed by Nanopore Direct RNA Sequencing.Microorganisms · 2026Article
- Exon skipping as a potential diagnostic biomarker in colorectal cancer: an integrated epigenomic-transcriptomic analysis.Human genomics · 2026Article
- The impact of Hnrnpl deficiency on transcriptional patterns of developing muscle cells.FEBS open bio · 2026Article
- Conserved spatial patterning of gene expression in independent lineages of CThe New phytologist · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Changes in the Anopheles arabiensis transcriptome and gut microbiota profiles associated with the endosymbiotic Microsporidia MB.BMC genomics · 2025Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Sequencing full-length native RNAs using long-read direct RNA sequencing (DRS) has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation, cDNA synthesis or PCR. However, there are a lack of tools specifically designed for DRS and its ability to identify differential expression in complex organisms is poorly characterised. We developed NanoCount for fast, accurate transcript isoform quantification in DRS and demonstrate it outperforms similar methods. Using synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that DRS accurately quantifies RNA expression and identifies differential expression of genes and isoforms. Differential expression of 231 genes, 333 isoforms, plus 27 isoform switches were detected between undifferentiated and differentiated SH-SY5Y cells and samples clustered by differentiation state at the gene and isoform level. Genes upregulated in neuron-like cells were associated with neurogenesis. NanoCount quantification of thousands of novel isoforms discovered with DRS likewise enabled identification of their differential expression. Our results demonstrate enhanced DRS isoform quantification with NanoCount and establish the ability of DRS to identify biologically relevant differential expression of genes and isoforms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.