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. 2020 Mar 31;2(2):lqaa020. doi: 10.1093/nargab/lqaa020

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© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 6. — Demonstrations of PHi-C for Hi-C data of mESCs. (A) PHi-C analysis for chromosomes 6 (left) and 17 (right) of mESCs. (Upper) Contact matrices of the Hi-C experiment (binned at 500 kb), and contact probabilities as a function of genomic distance. (Middle) 4C-like profiles of Nanog (left) and Oct4 (right) loci. High-interaction regions are highlighted (pink). (Lower) Optimized contact matrices by PHi-C, and correlation plots between and . (B) Theoretical MSD curves of Nanog and Oct4 loci. (C) Probability densities of the gyration radius of 10⁵ conformations for the 50.5-Mb genomic regions around Nanog and Oct4 loci in mESCs. (D) Polymer models derived from PHi-C analysis for Nanog and Oct4 loci on chromosomes 6 and 17, respectively. Pink highlighted regions on the polymer models correspond to the regions in the 4C-like profile of (A).

Inline graphic — Demonstrations of PHi-C for Hi-C data of mESCs. (A) PHi-C analysis for chromosomes 6 (left) and 17 (right) of mESCs. (Upper) Contact matrices of the Hi-C experiment (binned at 500 kb), and contact probabilities as a function of genomic distance. (Middle) 4C-like profiles of Nanog (left) and Oct4 (right) loci. High-interaction regions are highlighted (pink). (Lower) Optimized contact matrices by PHi-C, and correlation plots between and . (B) Theoretical MSD curves of Nanog and Oct4 loci. (C) Probability densities of the gyration radius of 10⁵ conformations for the 50.5-Mb genomic regions around Nanog and Oct4 loci in mESCs. (D) Polymer models derived from PHi-C analysis for Nanog and Oct4 loci on chromosomes 6 and 17, respectively. Pink highlighted regions on the polymer models correspond to the regions in the 4C-like profile of (A).