Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Journal

bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187

Informations de publication

Date de publication:
27 Jul 2023
Historique:
pubmed: 7 8 2023
medline: 7 8 2023
entrez: 7 8 2023
Statut: epublish

Résumé

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as

Identifiants

DOI: 10.1101/2023.07.25.550582 PMID: 37546854 PMC: PMC10402094
pubmed: 37546854
doi: 10.1101/2023.07.25.550582
pmc: PMC10402094
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG008759
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM136886
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM138122
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM142647
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : UM1 HG009443
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG011469
Pays : United States
Organisme : NHGRI NIH HHS
ID : F31 HG010999
Pays : United States

Déclaration de conflit d'intérêts

Competing Interests Design of the project was discussed with Oxford Nanopore Technologies (ONT), Pacific Biosciences, and Lexogen. ONT provided partial support for flow cells and reagents. S.C-S and A.N.B. have received reimbursement for travel, accommodation, and conference fees to speak at events organized by ONT. A.N.B. is a consultant for Remix Therapeutics, Inc.

Auteurs

Francisco J Pardo-Palacios (FJ)

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
These authors contributed equally to this work.

Dingjie Wang (D)

Department of Biomedical Informatics, The Ohio State University, Columbus, USA.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.
These authors contributed equally to this work.

Fairlie Reese (F)

Developmental and Cell Biology, University of California, Irvine, Irvine, USA.
Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.
These authors contributed equally to this work.

Mark Diekhans (M)

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.
These authors contributed equally to this work.

Sílvia Carbonell-Sala (S)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
These authors contributed equally to this work.

Brian Williams (B)

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
These authors contributed equally to this work.

Jane E Loveland (JE)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
These authors contributed equally to this work.

Maite De María (M)

Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.
Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA.
These authors contributed equally to this work.

Matthew S Adams (MS)

Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.
These authors contributed equally to this work.

Gabriela Balderrama-Gutierrez (G)

Developmental and Cell Biology, University of California, Irvine, Irvine, USA.
Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.
These authors contributed equally to this work.

Amit K Behera (AK)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
These authors contributed equally to this work.

Jose M Gonzalez (JM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
These authors contributed equally to this work.

Toby Hunt (T)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
These authors contributed equally to this work.

Julien Lagarde (J)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain.
These authors contributed equally to this work.

Cindy E Liang (CE)

Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.
These authors contributed equally to this work.

Haoran Li (H)

Department of Biomedical Informatics, The Ohio State University, Columbus, USA.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.
These authors contributed equally to this work.

Marcus Jerryd Meade (M)

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.
These authors contributed equally to this work.

David A Moraga Amador (DA)

Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA.
These authors contributed equally to this work.

Andrey D Prjibelski (AD)

Department of Computer Science, University of Helsinki, Helsinki, Finland.
Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
These authors contributed equally to this work.

Inanc Birol (I)

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.

Hamed Bostan (H)

Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA.

Ashley M Brooks (AM)

Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA.

Muhammed Hasan Çelik (M)

Developmental and Cell Biology, University of California, Irvine, Irvine, USA.
Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.

Ying Chen (Y)

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.

Mei R M Du (MRM)

Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.

Colette Felton (C)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Jonathan Göke (J)

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore.

Saber Hafezqorani (S)

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.

Ralf Herwig (R)

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.

Hideya Kawaji (H)

Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

Joseph Lee (J)

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.

Jian Liang Li (J)

Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA.

Matthias Lienhard (M)

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.

Alla Mikheenko (A)

Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.

Dennis Mulligan (D)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Ka Ming Nip (K)

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.

Mihaela Pertea (M)

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.
Center for Computational Biology, Johns Hopkins University, Baltimore, USA.

Matthew E Ritchie (ME)

Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
Department of Medical Biology, The University of Melbourne, Parkville, Australia.

Andre D Sim (AD)

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.

Alison D Tang (AD)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Yuk Kei Wan (Y)

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.

Changqing Wang (C)

Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.

Brandon Y Wong (BY)

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.
Center for Computational Biology, Johns Hopkins University, Baltimore, USA.

Chen Yang (C)

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.

If Barnes (I)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Andrew Berry (A)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Salvador Capella (S)

Barcelona Supercomputing Cente, Barcelona, Spain.

Namrita Dhillon (N)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Jose M Fernandez-Gonzalez (JM)

Barcelona Supercomputing Cente, Barcelona, Spain.

Luis Ferrández-Peral (L)

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.

Natàlia Garcia-Reyero (N)

Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA.

Stefan Goetz (S)

Biobam Bioinformatics SL, Valencia, Spain.

Carles Hernández-Ferrer (C)

Barcelona Supercomputing Cente, Barcelona, Spain.

Liudmyla Kondratova (L)

Genetics Institute, University of Florida, Gainesville, USA.

Tianyuan Liu (T)

Cardiff University, Cardiff, UK.

Alessandra Martinez-Martin (A)

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.

Carlos Menor (C)

Biobam Bioinformatics SL, Valencia, Spain.

Jorge Mestre-Tomás (J)

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.

Jonathan M Mudge (JM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Nedka G Panayotova (NG)

Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA.

Alejandro Paniagua (A)

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.

Dmitry Repchevsky (D)

Barcelona Supercomputing Cente, Barcelona, Spain.

Eric Rouchka (E)

Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA.

Brandon Saint-John (B)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Enrique Sapena (E)

European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK.

Leon Sheynkman (L)

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.

Melissa Laird Smith (M)

Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA.

Marie-Marthe Suner (MM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Hazuki Takahashi (H)

Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.

Ingrid Ashley Youngworth (IA)

Department of Genetics, Stanford University, Palo Alto, USA.

Piero Carninci (P)

Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.
Human Technopole, Milano, Italy.

Nancy D Denslow (ND)

Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.
Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA.

Roderic Guigó (R)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.

Margaret E Hunter (ME)

U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA.

Hagen U Tilgner (HU)

Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA.

Barbara J Wold (BJ)

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.

Christopher Vollmers (C)

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Adam Frankish (A)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Kin Fai Au (K)

Department of Biomedical Informatics, The Ohio State University, Columbus, USA.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.

Gloria M Sheynkman (GM)

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.
Center for Public Health Genomics.
UVA Cancer Center, University of Virginia, Charlottesville, USA.

Ali Mortazavi (A)

Developmental and Cell Biology, University of California, Irvine, Irvine, USA.
Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.

Ana Conesa (A)

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA.

Angela N Brooks (AN)

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Classifications MeSH