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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. 6 — a Distribution of H3K27ac, H3K4me1 and ATAC-seq signal in the enhancer regions shown in (b). The boxes show the interquartile range, with the median marked as a heavy horizontal band. Whiskers represent the highest (lowest) datapoint within 1.5 times the interquartile range of the 75th (25th) percentile. Statistical outliers are plotted separately as individual points beyond the whiskers on the boxplot. n = 2 biologically independent samples. b Enhancer classification during endoderm differentiation: ActEnh_dist (H3K27ac+, H3K4me1+, H3K4me3−, <3 kb); ActEnh_prox (H3K27ac+, H3K4me1+, H3K4me3+, <3 kb); Poised_Enh (H3K27ac−, H3K4me1+); SupEnh_dist (H3K27ac+, H3K4me1+, H3K4me3−, > 3 kb); SupEnh_prox (H3K27ac+, H3K4me1+, H3K4me3+, > 3 kb). c Hierarchical clustering of Jaccard Index values obtained for overlaps between different enhancer regions. The squares (i) highlight the conversion of poised into active enhancers, while the arrows (ii) indicate the similarity of super-enhancers at 0 and 72 h with other time points. d Endoderm-specific super-enhancers are a subset of those established at 36 h. e Schematic model of the super-enhancer establishment during endoderm differentiation at each consecutive cell division.