A community-based transcriptomics classification and nomenclature of neocortical cell types
Nature Neuroscience, vol. 23, pp. 1456–1468
Abstract
To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.
Authors 65
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Rafael Yuste corresponding
Affiliation as printed
Columbia University, New York City, NY, USA. rmy5@columbia.edu
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Michael Hawrylycz corresponding
Allen Institute for Brain Science
Affiliation as printed
Allen Institute for Brain Science, Seattle, WA, USA. MikeH@alleninstitute.org
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Affiliation as printed
University of Copenhagen, Copenhagen, Denmark
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Affiliation as printed
Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
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European Molecular Biology Laboratory
Affiliation as printed
European Molecular Biology Laboratory, Heidelberg, Germany
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George Mason University · BrainScope (United States)
Affiliation as printed
BrainScope Company Inc., Bethesda, MD, USA
George Mason University, Fairfax, VA, USA
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Affiliation as printed
George Mason University, Fairfax, VA, USA
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Universidad Politécnica de Madrid
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Universidad Politécnica de Madrid, Madrid, Spain
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Max Planck Institute for Biological Cybernetics
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Max Planck Institute for Biological Cybernetics, Tübingen, Germany
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University of Copenhagen, Copenhagen, Denmark
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University of Oxford, Oxford, UK
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Department of Biomedicine, Aarhus University, Aarhus, Denmark
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Department of Genetics, Harvard Medical School, Boston, MA, USA
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The University of Edinburgh, Edinburgh, UK
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Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Cajal Institute, Madrid, Spain
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Vanderbilt University, Nashville, TN, USA
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Scuola Normale Superior, Pisa, Italy
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Research Centre Jülich, Jülich, Germany
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HUN-REN Research Centre for Natural Sciences
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Research Centre for Natural Sciences, Budapest, Hungary
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Harvard Medical School, Cambridge, MA, USA
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Christian-Albrechts-Universität zu Kiel
Affiliation as printed
Christian-Albrechts-University Kiel, Kiel, Germany
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European Molecular Biology Laboratory · European Molecular Biology Laboratory
Affiliation as printed
European Molecular Biology Laboratory, Hamburg, Germany
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École Polytechnique Fédérale de Lausanne
Affiliation as printed
École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Ruhr University Bochum, Bochum, Germany
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University of Copenhagen, Copenhagen, Denmark
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Max Planck Institute for Brain Research
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Max Planck Institute for Brain Research, Frankfurt, Germany
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Vanderbilt University, Nashville, TN, USA
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Stockholm University · Science for Life Laboratory · Karolinska Institutet
Affiliation as printed
Karolinska Institutet, Stockholm, Sweden
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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Affiliation as printed
University of Copenhagen, Copenhagen, Denmark
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Affiliation as printed
Karolinska Institutet, Stockholm, Sweden
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Allen Institute for Brain Science
Affiliation as printed
Allen Institute for Brain Science, Seattle, WA, USA
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Rutgers, The State University of New Jersey
Affiliation as printed
WM Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University - New Brunswick, Piscataway, NJ, USA
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University of Copenhagen, Copenhagen, Denmark
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Affiliation as printed
Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
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Henner Koch Aachen
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RWTH Aachen University, Aachen, Germany
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Western University · Robarts Research Institute
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Robarts Research Institute, Western University, London, Ontario, Canada
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CARTANA, Stockholm, Sweden
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Universidad Politécnica de Madrid
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Universidad Politécnica de Madrid, Madrid, Spain
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Boudewijn P. F. Lelieveldt Aachen
Leiden University Medical Center
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Leiden University Medical Center, Leiden, the Netherlands
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Department of Biomedicine, Aarhus University, Aarhus, Denmark
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Stanford University, Stanford, CA, USA
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Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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King's College London, London, UK
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Schulich School of Medicine and Dentistry, Departments of Physiology, Pharmacology and Psychiatry, University of Western Ontario, London, Ontario, Canada
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University of Haifa, Haifa, Israel
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Karolinska Institutet, Stockholm, Sweden
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Charles University, Prague, Czech Republic
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Bar Ilan University, Ramat Gan, Israel
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University of Copenhagen, Copenhagen, Denmark
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Columbia University, New York City, NY, USA
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Sorbonne University, Paris, France
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Harvard University, Cambridge, MA, USA
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J. Craig Venter Institute · University of California San Diego
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Department of Pathology, University of California, San Diego, CA, USA
J. Craig Venter Institute, La Jolla, CA, USA
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Consejo Superior de Investigaciones Científicas · Centro de Biología Molecular Severo Ochoa
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Centro de Biologia Molecular Severo Ochoa (CSIC), Madrid, Spain
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University of Oxford, Oxford, UK
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University of Szeged, Szeged, Hungary
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Baylor College of Medicine, Houston, TX, USA
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Columbia University, New York City, NY, USA
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Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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University of Strathclyde · MSH Medical School Hamburg – University of Applied Sciences and Medical University
Affiliation as printed
MSH Medical School, Hamburg, Germany
University of Strathclyde, Glasgow, UK
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Hertie Institute for Clinical Brain Research · University of Tübingen
Affiliation as printed
Departments of Neurosurgery and of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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Hongkui Zeng corresponding
Allen Institute for Brain Science
Affiliation as printed
Allen Institute for Brain Science, Seattle, WA, USA. HongkuiZ@alleninstitute.org
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Ed S. Lein corresponding
Allen Institute for Brain Science
Affiliation as printed
Allen Institute for Brain Science, Seattle, WA, USA. EdL@alleninstitute.org
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