A guide to the BRAIN Initiative Cell Census Network data ecosystem.

Autor: Hawrylycz M; Allen Institute for Brain Science, Seattle, Washington, United States of America., Martone ME; Department of Neuroscience, University of California San Diego, San Diego, California, United States of America.; San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America., Ascoli GA; Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, United States of America., Bjaalie JG; Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway., Dong HW; UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America., Ghosh SS; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America., Gillis J; Department of Physiology, University of Toronto, Toronto, Ontario, Canada., Hertzano R; Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.; Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Haynor DR; Department of Radiology, University of Washington, Seattle, Washington, United States of America., Hof PR; Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America., Kim Y; Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, United States of America., Lein E; Allen Institute for Brain Science, Seattle, Washington, United States of America., Liu Y; SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China., Miller JA; Allen Institute for Brain Science, Seattle, Washington, United States of America., Mitra PP; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America., Mukamel E; Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America., Ng L; Allen Institute for Brain Science, Seattle, Washington, United States of America., Osumi-Sutherland D; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Peng H; SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China., Ray PL; Allen Institute for Brain Science, Seattle, Washington, United States of America., Sanchez R; Allen Institute for Brain Science, Seattle, Washington, United States of America., Regev A; Genentech, South San Francisco, California, United States of America., Ropelewski A; Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America., Scheuermann RH; J. Craig Venter Institute, La Jolla, California, United States of America., Tan SZK; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Thompson CL; Allen Institute for Brain Science, Seattle, Washington, United States of America., Tickle T; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America., Tilgner H; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, United States of America., Varghese M; Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America., Wester B; Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America., White O; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Zeng H; Allen Institute for Brain Science, Seattle, Washington, United States of America., Aevermann B; Chan Zuckerberg Initiative, Redwood City, California, United States of America., Allemang D; Kitware Inc., Albany, New York, United States of America., Ament S; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Athey TL; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America., Baker C; CatalystNeuro, Benicia, California, United States of America., Baker KS; Allen Institute for Brain Science, Seattle, Washington, United States of America., Baker PM; Allen Institute for Brain Science, Seattle, Washington, United States of America., Bandrowski A; Department of Neuroscience, University of California San Diego, San Diego, California, United States of America., Banerjee S; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America., Bishwakarma P; Allen Institute for Brain Science, Seattle, Washington, United States of America., Carr A; Chan Zuckerberg Initiative, Redwood City, California, United States of America., Chen M; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America., Choudhury R; Kitware Inc., Albany, New York, United States of America., Cool J; Chan Zuckerberg Initiative, Redwood City, California, United States of America., Creasy H; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., D'Orazi F; Chan Zuckerberg Initiative, Redwood City, California, United States of America., Degatano K; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America., Dichter B; CatalystNeuro, Benicia, California, United States of America., Ding SL; Allen Institute for Brain Science, Seattle, Washington, United States of America., Dolbeare T; Allen Institute for Brain Science, Seattle, Washington, United States of America., Ecker JR; Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America., Fang R; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America., Fillion-Robin JC; Kitware Inc., Albany, New York, United States of America., Fliss TP; Allen Institute for Brain Science, Seattle, Washington, United States of America., Gee J; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America., Gillespie T; Department of Neuroscience, University of California San Diego, San Diego, California, United States of America., Gouwens N; Allen Institute for Brain Science, Seattle, Washington, United States of America., Zhang GQ; Texas Institute for Restorative Neurotechnologies, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America., Halchenko YO; Department of Psychological and Brain Sciences, Dartmouth College, Hannover, New Hampshire, United States of America., Harris NL; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America., Herb BR; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Hintiryan H; UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America., Hood G; Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America., Horvath S; Kitware Inc., Albany, New York, United States of America., Huo B; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America., Jarecka D; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America., Jiang S; SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China., Khajouei F; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America., Kiernan EA; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America., Kir H; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Kruse L; Allen Institute for Brain Science, Seattle, Washington, United States of America., Lee C; Allen Institute for Brain Science, Seattle, Washington, United States of America., Lelieveldt B; Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands.; Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands., Li Y; Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America., Liu H; Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America., Liu L; SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China., Markuhar A; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Mathews J; Allen Institute for Brain Science, Seattle, Washington, United States of America., Mathews KL; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America., Mezias C; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America., Miller MI; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America., Mollenkopf T; Allen Institute for Brain Science, Seattle, Washington, United States of America., Mufti S; Allen Institute for Brain Science, Seattle, Washington, United States of America., Mungall CJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America., Orvis J; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Puchades MA; Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway., Qu L; SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China., Receveur JP; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America., Ren B; Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America.; Ludwig Institute for Cancer Research, La Jolla, California, United States of America., Sjoquist N; Microsoft Corporation, Seattle, Washington, United States of America., Staats B; Allen Institute for Brain Science, Seattle, Washington, United States of America., Tward D; UCLA Brain Mapping Center, University of California, Los Angeles, California, United States of America., van Velthoven CTJ; Allen Institute for Brain Science, Seattle, Washington, United States of America., Wang Q; Allen Institute for Brain Science, Seattle, Washington, United States of America., Xie F; Department of Chemistry and Biochemistry, University of California Los Angeles, California, United States of America., Xu H; School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America., Yao Z; Allen Institute for Brain Science, Seattle, Washington, United States of America., Yun Z; SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China., Zhang YR; J. Craig Venter Institute, La Jolla, California, United States of America., Zheng WJ; School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America., Zingg B; UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America.
Jazyk: angličtina
Zdroj: PLoS biology [PLoS Biol] 2023 Jun 30; Vol. 21 (6), pp. e3002133. Date of Electronic Publication: 2023 Jun 30 (Print Publication: 2023).
DOI: 10.1371/journal.pbio.3002133
Abstrakt: Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: AR is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and, until 31 July 2020, was a scientific advisory board member of Thermo Fisher Scientific, Syros Pharmaceuticals, Asimov, and Neogene Therapeutics. From 1 August 2020, AR is an employee of Genentech and has equity in Roche. AR is a named inventor on multiple patents related to single cell and spatial genomics filed by or issued to the Broad Institute.
(Copyright: © 2023 Hawrylycz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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