A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.

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Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.
Authors: Chen Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore. chen_ying@gis.a-star.edu.sg., Davidson NM; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia., Wan YK; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Yao F; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Su Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Gamaarachchi H; School of Computer Science and Engineering, UNSW Sydney, Sydney, New South Wales, Australia.; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia., Sim A; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Patel H; Seqera, Barcelona, Spain., Low HM; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Hendra C; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Institute of Data Science, National University of Singapore, Singapore, Singapore., Wratten L; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Hakkaart C; Seqera, Barcelona, Spain., Sawyer C; Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK., Iakovleva V; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY, USA., Lee PL; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Xin L; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore., Ng HEV; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore., Loo JM; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Ong X; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore., Ng HQA; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Wang J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Koh WQC; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Poon SYP; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Stanojevic D; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Department of Electronic Systems and Information Processing, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia., Tran HD; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Lim KHE; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Toh SY; National Cancer Centre Singapore, Singapore, Singapore., Ewels PA; Seqera, Barcelona, Spain., Ng HH; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Iyer NG; National Cancer Centre Singapore, Singapore, Singapore.; Duke-NUS Medical School, Singapore, Singapore., Thiery A; Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore., Chng WJ; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.; Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore., Chen L; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore., DasGupta R; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Sikic M; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Department of Electronic Systems and Information Processing, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia., Chan YS; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Tan BOP; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore., Wan Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Tam WL; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore., Yu Q; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Khor CC; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Duke-NUS Medical School, Singapore, Singapore.; Singapore Eye Research Institute, Singapore, Singapore., Wüstefeld T; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; National Cancer Centre Singapore, Singapore, Singapore.; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore., Lezhava A; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Pratanwanich PN; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.; Chula Intelligent and Complex Systems Research Unit, Chulalongkorn University, Bangkok, Thailand., Love MI; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Goh WSS; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China., Ng SB; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore., Oshlack A; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia., Göke J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore. gokej@gis.a-star.edu.sg.; Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore. gokej@gis.a-star.edu.sg.
Corporate Authors: SG-NEx consortium
Source: Nature methods [Nat Methods] 2025 Apr; Vol. 22 (4), pp. 801-812. Date of Electronic Publication: 2025 Mar 13.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
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  Data: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.
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              M: 04
              Text: 2025 Apr
              Type: published
              Y: 2025
          Identifiers:
            – Type: issn-electronic
              Value: 1548-7105
          Numbering:
            – Type: volume
              Value: 22
            – Type: issue
              Value: 4
          Titles:
            – TitleFull: Nature methods
              Type: main
ResultId 1