Common cell type nomenclature for the mammalian brain
- Allen Institute for Brain Science, United States
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
Article and author information
Author details
Cindy TJ van Velthoven
Michael J Hawrylycz
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
- Genevieve Konopka, University of Texas Southwestern Medical Center, United States
Version history
- Received: June 12, 2020
- Accepted: December 28, 2020
- Accepted Manuscript published: December 29, 2020 (version 1)
- 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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Common cell type nomenclature for the mammalian brain
eLife 9:e59928.
https://doi.org/10.7554/eLife.59928
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