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.

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.

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