ArticleNature communications2024
Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Advances in the detection of Drug-Resistant bacteria: current trends and innovations.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Review
- The potential of mRNA markers in body fluids and personal source analysis based on the QNome nanopore sequencing.International journal of legal medicine · 2026Article
- Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing.Genome biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- A direct RNA-seq-based EBV latency transcriptome offers insights into the biogenesis of EBV gene products.The Journal of general virology · 2025Article
- Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.Nature communications · 2025Article
- Realfreq: real-time base modification analysis for nanopore sequencing.Bioinformatics (Oxford, England) · 2025Article
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- De novo basecalling of RNA modifications at single molecule and nucleotide resolution.Genome biology · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Abundant cellular transcripts occupy most of the sequencing reads in the transcriptome, making it challenging to assay for low-abundant transcripts. Here, we utilize the adaptive sampling function of Oxford Nanopore sequencing to selectively deplete and enrich RNAs of interest without biochemical manipulation before sequencing. Adaptive sampling performed on a pool of in vitro transcribed RNAs resulted in a net increase of 22-30% in the proportion of transcripts of interest in the population. Enriching and depleting different proportions of the Candida albicans transcriptome also resulted in a 11-13.5% increase in the number of reads on target transcripts, with longer and more abundant transcripts being more efficiently depleted. Depleting all currently annotated Candida albicans transcripts did not result in an absolute enrichment of remaining transcripts, although we identified 26 previously unknown transcripts and isoforms, 17 of which are antisense to existing transcripts. Further improvements in the adaptive sampling of RNAs will allow the technology to be widely applied to study RNAs of interest in diverse transcriptomes.
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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.