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. 2020 Apr 1;11:1617. doi: 10.1038/s41467-020-15449-9

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© The Author(s) 2020

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. 6 — An overview of the multiple layers of gene regulation that have been integrated in this study. Examples of genes that undergo specific regulation at the transcriptional, translational, or post-translational levels are shown. Genes that could not be assigned to any specific mode of gene regulation (e.g. because the RFP, RNA, or protein could not be uniquely integrated in different conditions) are indicated with NA. Genes were also assigned to signaling pathways downstream of CH or PD, as indicated in the figure. “C/P” refers to the proteins that require either PD or CH to maintain expression similar to 2iL ESCs; only removing both inhibitors from 2iL induces changes resembling the SL/EPI states. “2i” refers to the proteins that require both PD and CH signaling to maintain expression similar to 2iL state; removing either PD or CH from 2iL induces changes similar to SL/EPI state. “P” refers to the proteins that require PD to maintain an expression pattern similar to 2iL; removing PD from 2iL medium induces changes similar to SL/EPI state. “C” refers to the proteins that require CH to maintain an expression pattern similar to 2iL; removing CH from 2iL medium induces changes similar to SL/EPI state.