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. 2020 Apr 14;11:1813. doi: 10.1038/s41467-020-15607-z

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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 — a Heatmaps of chromatin interaction frequencies showing a CC TAD unreprogrammed example (magenta) and a CC TAD reprogrammed (cyan) example during SCNT embryo development. The bottom track shows the H3K9me3 signal in CCs. b RTIs of H3K9me3-maked and H3K9me3-unmarked TADs identified in CCs. RTI values in CC, 6-hpa, 12-hpa and early-2-cell embryos are shown (n = 2184). Boxes show 25th, 50th and 75th percentiles and whiskers show 1.5× the inter-quartile range. The two-sided p values were calculated by the Kruskal–Wallis test with Dunn’s multiple comparison test and adjusted by default with the holm method. Source data and exact p-value are provided as a Source Data file. c Heatmaps showing normalized chromatin interaction frequencies (100-kb bin, chromosome 16) in SCNT, SCNT with Kdm4d mRNA injection, SCNT with TSA treatment and fertilization-derived early 2-cell embryos. Both ICE and Binless normalization approaches are used. d RTIs of H3K9me3-maked TAD in early 2-cell embryos. RTI values in CC, SCNT, SCNT with Kdm4d mRNA injection, SCNT with TSA treatment and fertilization-derived are shown (n = 2184). Boxes show 25th, 50th and 75th percentiles and whiskers show 1.5× the inter-quartile range. The two-sided p values were calculated by the Kruskal–Wallis test with Dunn’s multiple comparison test and adjusted by default with the holm method (N.S., not significant). Source data and exact p-value are provided as a Source Data file. e Virtual 4C test showing the interaction frequencies between Zscan4d promoter and its adjacent region in chromosome 7. Black dots represent observed values, red line represents fitted value by Binless.