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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  <identifier identifierType="DOI">10.5281/zenodo.4001718</identifier>
  <creators>
    <creator>
      <creatorName>Bock, Christoph</creatorName>
      <givenName>Christoph</givenName>
      <familyName>Bock</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6091-3088</nameIdentifier>
      <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</affiliation>
    </creator>
    <creator>
      <creatorName>Boutros, Michael</creatorName>
      <givenName>Michael</givenName>
      <familyName>Boutros</familyName>
      <affiliation>Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Camp, J. Gray</creatorName>
      <givenName>J. Gray</givenName>
      <familyName>Camp</familyName>
      <affiliation>Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland</affiliation>
    </creator>
    <creator>
      <creatorName>Clarke, Laura</creatorName>
      <givenName>Laura</givenName>
      <familyName>Clarke</familyName>
      <affiliation>European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Clevers, Hans</creatorName>
      <givenName>Hans</givenName>
      <familyName>Clevers</familyName>
      <affiliation>Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Oncode Institute and University Medical Center Utrecht, Utrecht, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Knoblich, Juergen A.</creatorName>
      <givenName>Juergen A.</givenName>
      <familyName>Knoblich</familyName>
      <affiliation>Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria</affiliation>
    </creator>
    <creator>
      <creatorName>Liberali, Prisca</creatorName>
      <givenName>Prisca</givenName>
      <familyName>Liberali</familyName>
      <affiliation>Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland</affiliation>
    </creator>
    <creator>
      <creatorName>Regev, Aviv</creatorName>
      <givenName>Aviv</givenName>
      <familyName>Regev</familyName>
      <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</affiliation>
    </creator>
    <creator>
      <creatorName>Rios, Anne C.</creatorName>
      <givenName>Anne C.</givenName>
      <familyName>Rios</familyName>
      <affiliation>Princess Máxima 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</affiliation>
    </creator>
    <creator>
      <creatorName>Stegle, Oliver</creatorName>
      <givenName>Oliver</givenName>
      <familyName>Stegle</familyName>
      <affiliation>Divison of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Stunnenberg, Hendrik G.</creatorName>
      <givenName>Hendrik G.</givenName>
      <familyName>Stunnenberg</familyName>
      <affiliation>Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Teichmann, Sarah A.</creatorName>
      <givenName>Sarah A.</givenName>
      <familyName>Teichmann</familyName>
      <affiliation>Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK; Cavendish Laboratory, University of Cambridge, Cambridge, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Treutlein, Barbara</creatorName>
      <givenName>Barbara</givenName>
      <familyName>Treutlein</familyName>
      <affiliation>Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland</affiliation>
    </creator>
    <creator>
      <creatorName>Vries, Robert G.J.</creatorName>
      <givenName>Robert G.J.</givenName>
      <familyName>Vries</familyName>
      <affiliation>Foundation Hubrecht Organoid Technology, Utrecht, The Netherlands</affiliation>
    </creator>
  </creators>
  <titles>
    <title>The Organoid Cell Atlas: A Rosetta Stone for Biomedical Discovery and Regenerative Therapy</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Organoids</subject>
    <subject>Single-cell profiling</subject>
    <subject>High-throughput imaging</subject>
    <subject>Multi-omics technology</subject>
    <subject>Data resources</subject>
    <subject>Bioinformatic tools</subject>
    <subject>Integrative analysis</subject>
    <subject>Biomedical applications</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-08-30</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="JournalArticle"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4001718</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4001717</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Human organoids &amp;ndash; three-dimensional structures of cells that recapitulate important aspects of organ development in vitro &amp;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 &amp;lsquo;Biological Network&amp;rsquo; within the Human Cell Atlas (HCA), focusing on single-cell profiling of organoids and in vitro cell models (&lt;a href="https://www.humancellatlas.org/coordinators/"&gt;https://www.humancellatlas.org/coordinators/&lt;/a&gt;). 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 &amp;ldquo;Pilot actions to build the foundations of a human cell atlas&amp;rdquo; through the &amp;ldquo;HCA|Organoid&amp;rdquo; project (&lt;a href="http://hca-organoid.eu/"&gt;http://hca-organoid.eu/&lt;/a&gt;). 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.&lt;/p&gt;</description>
  </descriptions>
</resource>
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