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Common cell type nomenclature for the mammalian brain

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Cite this article as: eLife 2020;9:e59928 doi: 10.7554/eLife.59928

Abstract

The advancement of single cell RNA-sequencing technologies has led to an explosion of cell type definitions across multiple organs and organisms. While standards for data and metadata intake are arising, organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies. To facilitate cross-dataset comparison, the Allen Institute created the Common Cell type Nomenclature (CCN) for matching and tracking cell types across studies that is qualitatively similar to gene transcript management across different genome builds. The CCN can be readily applied to new or established taxonomies and was applied herein to diverse cell type datasets derived from multiple quantifiable modalities. The CCN facilitates assigning accurate yet flexible cell type names in the mammalian cortex as a step towards community-wide efforts to organize multi-source, data-driven information related to cell type taxonomies from any organism.

Data availability

This work describes the creation of a convention that will, with adoption by the community, become a standard. The data cited is open data though the Allen Institute open web portal, https://brain-map.orgAn open Forum is available to engage the community in further development, at https://portal.brain-map.org/explore/classes/nomenclatureData referenced in this study is also made available according the terms of NIH's Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN), through the Brain Cell Data Center portal, https://biccn.org/ and https://biccn.org/data

The following previously published data sets were used

Article and author information

Author details

  1. Jeremy A Miller

    Allen Institute for Brain Science, Seattle, United States
    For correspondence
    jeremym@alleninstitute.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4549-588X
  2. Nathan W Gouwens

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Bosiljka Tasic

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6861-4506
  4. Forrest Collman

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0280-7022
  5. Cindy TJ van Velthoven

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5120-4546
  6. Trygve E Bakken

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3373-7386
  7. Michael J Hawrylycz

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5741-8024
  8. Hongkui Zeng

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0326-5878
  9. Ed S Lein

    Allen Institute for Brain Science, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9012-6552
  10. Amy Bernard

    Allen Institute for Brain Science, Seattle, United States
    For correspondence
    amyb@alleninstitute.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2540-1153

Funding

Allen Institute

  • Jeremy A Miller
  • Nathan W Gouwens
  • Bosiljka Tasic
  • Forrest Collman
  • Cindy TJ van Velthoven
  • Trygve E Bakken
  • Michael J Hawrylycz
  • Hongkui Zeng
  • Ed S Lein
  • Amy Bernard

National Institute of Mental Health (U19MH114830)

  • Hongkui Zeng

National Institute of Mental Health (U01MH114812)

  • Ed S Lein

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Genevieve Konopka, University of Texas Southwestern Medical Center, United States

Publication history

  1. Received: June 12, 2020
  2. Accepted: December 28, 2020
  3. Accepted Manuscript published: December 29, 2020 (version 1)
  4. Version of Record published: January 7, 2021 (version 2)

Copyright

© 2020, Miller et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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