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. 2024 Apr 11;43(10):1965–1989. doi: 10.1038/s44318-024-00086-5

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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Figure EV1 — (A) Dynamic changes of mESC morphology during the 2iL-to-SL transition from day 0 to day 15 or during the SL-to-2iL transition from day 0 to day 15. Scale bar, 100 μm. (B, C) CpG methylation levels of genomic DNA measured by digestion with the methylation-sensitive restriction enzymes HpaII and McrBC at different time points during the SL-to-2iL (B) and 2iL-to-SL (C) transitions. Quantification of DNA signals of the upper band of the agarose gel using Fiji image analysis software. Data is presented as the mean ± SD. Indicated significances are tested using Student’s t-test analyses (**p < 0.01, ***p < 0.001). n = 3 replications. M, DNA ladder. (D, E) PCA of RNA-seq data (D) and ATAC-seq data (E) during the transition between 2iL-ESCs and SL-ESCs at different time points.