ArticleNAR genomics and bioinformatics2023
Pervasive effects of RNA degradation on Nanopore direct RNA sequencing.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
- Review
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive long RNA landscape of multi-regional porcine lung-derived small extracellular vesicles.BMC genomics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Stalled translation on transcripts cleaved by RNase L activates signaling important for innate immunity.RNA (New York, N.Y.) · 2026Article
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
- Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E. coli throughout its life cycles reveals a complex transcriptional activity to control and maintain its growth.Virology journal · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Review
- In-depth comparison of methods to isolate RNA from common human cell lines.BMC genomics · 2026Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain.Genome biology · 2025Article
- Isoform-level profiling of mScience advances · 2025Article
- Stalled translation on transcripts cleaved by RNase L activates signaling important for innate immunity.bioRxiv : the preprint server for biology · 2025Article
- An analysis of RNA quality metrics in human brain tissue.Journal of neuropathology and experimental neurology · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oxford Nanopore direct RNA sequencing (DRS) is capable of sequencing complete RNA molecules and accurately measuring gene and isoform expression. However, as DRS is designed to profile intact RNA, expression quantification may be more heavily dependent upon RNA integrity than alternative RNA sequencing methodologies. It is currently unclear how RNA degradation impacts DRS or whether it can be corrected for. To assess the impact of RNA integrity on DRS, we performed a degradation time series using SH-SY5Y neuroblastoma cells. Our results demonstrate that degradation is a significant and pervasive factor that can bias DRS measurements, including a reduction in library complexity resulting in an overrepresentation of short genes and isoforms. Degradation also biases differential expression analyses; however, we find that explicit correction can almost fully recover meaningful biological signal. In addition, DRS provided less biased profiling of partially degraded samples than Nanopore PCR-cDNA sequencing. Overall, we find that samples with RNA integrity number (RIN) > 9.5 can be treated as undegraded and samples with RIN > 7 can be utilized for DRS with appropriate correction. These results establish the suitability of DRS for a wide range of samples, including partially degraded
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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.