Bibliografisk note

Funding Information:
We greatly thank Laure Bailly-Cuif for suggestions and insightful comments. We acknowledge Jacob-Sebastian Seeler for helpful discussions and re-reading of the manuscript. We acknowledge Heather Marlow, François Spitz, and Baptiste Saudemont for assistance with initial scRNA-seq experiments. We are grateful to David M. Suter (Swiss Federal Institute of Technology, Switzerland) for the Sox1:EGFP-T:mCherry double reporter ESCs and Pablo Navarro (Institut Pasteur, Paris) for the LF2 ES cell line. We thank Andrey Aristov for help with image analysis, Sandrine Schmutz and the Cytometry and Biomarkers Platform (Institut Pasteur, Paris) for cell sorting, Juliana Pipoli Da Fonseca and the Biomics Platform (Institut Pasteur, Paris) for scRNA sequencing, as well as Samy Gobaa and the Biomaterials and Microfluidics Platform (Institut Pasteur, Paris) for microfluidic chip manufacturing. Sequencing for ChIP-seq/RNA-seq/Methyl-seq was performed by the GenomEast platform, a member of the “France Génomique”consortium (ANR-10-INBS-0009). This work was supported by grants from European Research Council (AdG SUMiDENTITY), Agence Nationale de la Recherche (ANR-19-CE12-0011-01), Odyssey, and LNCC (Equipe labellisée) (to A.D.); Région Île-de-France DIM-ELICIT (to C.N.B.); the Helmholtz Association and German Research Foundation (DFG) Project-ID 213249687 (SFB 1064) (to M.-E.T.-P.); and the Novo Nordisk Foundation (NNF14CC0001) and the European Union Horizon 2020 (EPIC-XS-823839) (to M.L.N.). J.-C.C. and A.D. conceived and designed the study. J.-C.C. T.T. and S.S. performed most of the experiments and analyzed the data. S.S. and C.N.B. designed the droplet microfluidic platform. Y.L.-M. performed the bioinformatics analysis. M.G. performed the in vivo experiments, and M.G. and M.-E.T.-P. interpreted the data. I.A.H. performed the SUMO mass spectrometry experiments, and I.A.H. and M.L.N. analyzed the data. I.T. contributed to initial experiments. J.-C.C. T.T. S.S. and A.D. wrote the manuscript with input from all co-authors. J.-C.C. T.T. S.S. C.N.B. and A.D. are designated as inventors of the patent application WO 2023/002057 A2 covering the aspects of the in vitro generation of organized 3D cell structures and the microfluidic device described in the manuscript.

Funding Information:
We greatly thank Laure Bailly-Cuif for suggestions and insightful comments. We acknowledge Jacob-Sebastian Seeler for helpful discussions and re-reading of the manuscript. We acknowledge Heather Marlow, François Spitz, and Baptiste Saudemont for assistance with initial scRNA-seq experiments. We are grateful to David M. Suter (Swiss Federal Institute of Technology, Switzerland) for the Sox1:EGFP-T:mCherry double reporter ESCs and Pablo Navarro (Institut Pasteur, Paris) for the LF2 ES cell line. We thank Andrey Aristov for help with image analysis, Sandrine Schmutz and the Cytometry and Biomarkers Platform (Institut Pasteur, Paris) for cell sorting, Juliana Pipoli Da Fonseca and the Biomics Platform (Institut Pasteur, Paris) for scRNA sequencing, as well as Samy Gobaa and the Biomaterials and Microfluidics Platform (Institut Pasteur, Paris) for microfluidic chip manufacturing. Sequencing for ChIP-seq/RNA-seq/Methyl-seq was performed by the GenomEast platform, a member of the “France Génomique”consortium (ANR-10-INBS-0009). This work was supported by grants from European Research Council (AdG SUMiDENTITY), Agence Nationale de la Recherche ( ANR-19-CE12-0011-01 ), Odyssey , and LNCC (Equipe labellisée) (to A.D.); Région Île-de-France DIM-ELICIT (to C.N.B.); the Helmholtz Association and German Research Foundation (DFG) Project-ID 213249687 (SFB 1064) (to M.-E.T.-P.); and the Novo Nordisk Foundation ( NNF14CC0001 ) and the European Union Horizon 2020 ( EPIC-XS-823839 ) (to M.L.N.).

Publisher Copyright:
© 2023 The Author(s)