Journal article Open Access

The Organoid Cell Atlas: A Rosetta Stone for Biomedical Discovery and Regenerative Therapy

Bock, Christoph; Boutros, Michael; Camp, J. Gray; Clarke, Laura; Clevers, Hans; Knoblich, Juergen A.; Liberali, Prisca; Regev, Aviv; Rios, Anne C.; Stegle, Oliver; Stunnenberg, Hendrik G.; Teichmann, Sarah A.; Treutlein, Barbara; Vries, Robert G.J.


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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>Human organoids &ndash; three-dimensional structures of cells that recapitulate important aspects of organ development in vitro &ndash; hold tremendous potential for biomedical applications. To help deliver on the promises of combining human organoids with single-cell technology, we have launched an Organoid Cell Atlas pilot project, as a &lsquo;Biological Network&rsquo; within the Human Cell Atlas (HCA), focusing on single-cell profiling of organoids and in vitro cell models (<a href=\"https://www.humancellatlas.org/coordinators/\">https://www.humancellatlas.org/coordinators/</a>). The Organoid Cell Atlas will foster the production, quality control, dissemination, and utilization of single-cell and spatial genomics data for human organoids, and it will connect such datasets with the comprehensive profiles of primary tissue that are being generated within the HCA. A first step toward establishing the Organoid Cell Atlas has recently been funded by the European Union Horizon 2020 call for &ldquo;Pilot actions to build the foundations of a human cell atlas&rdquo; through the &ldquo;HCA|Organoid&rdquo; project (<a href=\"http://hca-organoid.eu/\">http://hca-organoid.eu/</a>). This preprint outlines the rationale for combining human organoids with single-cell technology and the concrete plans for established the Organoid Cell Atlas as a Rosetta Stone for biomedical discovery and regenerative therapy.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria", 
      "@id": "https://orcid.org/0000-0001-6091-3088", 
      "@type": "Person", 
      "name": "Bock, Christoph"
    }, 
    {
      "affiliation": "Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany", 
      "@type": "Person", 
      "name": "Boutros, Michael"
    }, 
    {
      "affiliation": "Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland", 
      "@type": "Person", 
      "name": "Camp, J. Gray"
    }, 
    {
      "affiliation": "European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK", 
      "@type": "Person", 
      "name": "Clarke, Laura"
    }, 
    {
      "affiliation": "Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Oncode Institute and University Medical Center Utrecht, Utrecht, The Netherlands", 
      "@type": "Person", 
      "name": "Clevers, Hans"
    }, 
    {
      "affiliation": "Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria", 
      "@type": "Person", 
      "name": "Knoblich, Juergen A."
    }, 
    {
      "affiliation": "Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland", 
      "@type": "Person", 
      "name": "Liberali, Prisca"
    }, 
    {
      "affiliation": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge", 
      "@type": "Person", 
      "name": "Regev, Aviv"
    }, 
    {
      "affiliation": "Princess M\u00e1xima Center for Pediatric Oncology, Utrecht, The Netherlands; Department of Cancer Research, Oncode Institute, Hubrecht Institute, KNAW Utrecht, Utrecht, The Netherlands; Cancer Genomics Center, Utrecht, The Netherlands", 
      "@type": "Person", 
      "name": "Rios, Anne C."
    }, 
    {
      "affiliation": "Divison of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany", 
      "@type": "Person", 
      "name": "Stegle, Oliver"
    }, 
    {
      "affiliation": "Princess M\u00e1xima Center for Pediatric Oncology, Utrecht, The Netherlands", 
      "@type": "Person", 
      "name": "Stunnenberg, Hendrik G."
    }, 
    {
      "affiliation": "Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK; Cavendish Laboratory, University of Cambridge, Cambridge, UK", 
      "@type": "Person", 
      "name": "Teichmann, Sarah A."
    }, 
    {
      "affiliation": "Eidgen\u00f6ssische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland", 
      "@type": "Person", 
      "name": "Treutlein, Barbara"
    }, 
    {
      "affiliation": "Foundation Hubrecht Organoid Technology, Utrecht, The Netherlands", 
      "@type": "Person", 
      "name": "Vries, Robert G.J."
    }
  ], 
  "headline": "The Organoid Cell Atlas: A Rosetta Stone for Biomedical Discovery and Regenerative Therapy", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "datePublished": "2020-08-30", 
  "url": "https://zenodo.org/record/4001718", 
  "keywords": [
    "Organoids", 
    "Single-cell profiling", 
    "High-throughput imaging", 
    "Multi-omics technology", 
    "Data resources", 
    "Bioinformatic tools", 
    "Integrative analysis", 
    "Biomedical applications"
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.4001718", 
  "@id": "https://doi.org/10.5281/zenodo.4001718", 
  "@type": "ScholarlyArticle", 
  "name": "The Organoid Cell Atlas: A Rosetta Stone for Biomedical Discovery and Regenerative Therapy"
}
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