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. 2023 Jan 25;14:405. doi: 10.1038/s41467-023-36116-9

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — We took advantage of the Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) reporter to develop a culture system allowing the differentiation of human embryonic stem cells (hESCs) synchronised in their early G1 phase of the cell cycle to assess the epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. Our data comprise multiple time points spanning each successive cell cycle and include simultaneous analysis of RNA-seq, ATAC-seq and ChIP-seq. A summary of the results is shown together with a map of Waddington’s epigenetic landscape for endoderm cell fate specification upon differentiation of human pluripotent stem cells. Overall, these data reveal key successive interplays between epigenetic modifications during differentiation and provide a valuable resource to investigate mechanisms in germ layer specification. Created with BioRender.com.