Published August 30, 2020 | Version v1
Journal article Open

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

  • 1. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
  • 2. Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
  • 3. Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
  • 4. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
  • 5. Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Oncode Institute and University Medical Center Utrecht, Utrecht, The Netherlands
  • 6. Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
  • 7. Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
  • 8. 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
  • 9. 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
  • 10. Divison of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
  • 11. Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
  • 12. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK; Cavendish Laboratory, University of Cambridge, Cambridge, UK
  • 13. Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
  • 14. Foundation Hubrecht Organoid Technology, Utrecht, The Netherlands


Human organoids – three-dimensional structures of cells that recapitulate important aspects of organ development in vitro – 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 ‘Biological Network’ within the Human Cell Atlas (HCA), focusing on single-cell profiling of organoids and in vitro cell models ( 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 “Pilot actions to build the foundations of a human cell atlas” through the “HCA|Organoid” project ( 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.


The Organoid Cell Atlas - A Rosetta Stone for Biomedical Discovery and Regenerative Therapy (preprint).pdf