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. 2021 Sep 3;18(9):1046–1055. doi: 10.1038/s41592-021-01248-7

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© The Author(s), under exclusive licence to Springer Nature America, Inc. 2021, corrected publication 2021

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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Extended Data Fig. 6 — a. H1-hESC loops versus loop anchors. Expected for anchors in one loop: y=2x b,c. FA-DpnII loops subtracted from FA+DSG-DpnII (b) or FA+DSG-MNase (c) Union of loops detected at the same anchors. d,e. Valencies of loop anchors for H1-hESC (d), HFFc6 (e) from FA-DpnII, FA+DSG-DpnII, FA+DSG-MNase. FA-DpnII is used as a guiding example. Categories are: anchors from 1 protocol (FA-DpnII), anchors from 2 protocols (FA-DpnII and either FA+DSG-DpnII or FA+DSG-MNase) and anchors from all 3 protocols. f. CTCF, SMC1, H3K4me3 and H3K27ac enrichments at loop anchors for all protocols (intersection) or FA+DSG-MNase alone in H1-hESC.Average enrichments centered on open chromatin regions within anchor coordinates. g. Top: cCREs from common and FA+DSG-MNase specific loop anchors (Extended Data Fig. 5f). Bottom: stratified percentage of Promoter-Enhancer cCREs without CTCF enrichment. h. Enrichment of CTCF, SMC1, H3K4me3 and H3K27ac for left (Anchor1) and right (Anchor 2) anchor in H1-hESC using FA-DpnII, FA+DSG-DpnII or FA+DSG-MNase.

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