Extended Data Fig. 10: NANOG Hi-C 3.0 Analysis.

a, Concordance of Hi-C 3.0 replicates data by the analysis of stratum adjusted correlation coefficient (SCC) between two replicates in WT and W8A conditions across different chromosomes. Left and right graphs show the SCC in HEK 293T cells expressing GFP-tagged WT or W8A NANOG, respectively. High scores of correlation indicate strong concordance of replicates. b, Scatter plot showing the correlation between Principal Component Analysis (PCA) E1 values of Hi-C 3.0 in WT NANOG cells (x-axis) versus E1 values in W8A NANOG cells (y-axis). E1 values were calculated for each 20 kb bin in the Hi-C 3.0 data (see Methods). c, An example region of ~100 Mb size from chromosome 1 showing largely identical PCA E1 values, and thus little change of A/B compartments in 293T cells expressing NANOG WT or W8A mutant. d, Saddle plots showing inter-compartment interactions, generated by identifying intra-chromosomal interaction frequencies between any 20-kb genomic bins that are ranked by their PCA E1 scores in the WT condition. The observed interaction frequency between any two bins was then normalized by their expected interaction frequency solely on the basis of genomic distance, which is the basis for the Observed/Expected (O/E) values to make the heatmap. The color was based on a log2 scale of the O/E values. In these plots, B–B compartmental interactions are in the upper left corner, and A–A interactions are in the lower right corner. See methods and Abramo et al⁷⁴. e, Aggregate TAD analysis depicting the average contact frequency across all TADs. Hi-C 3.0 data shown were derived using 2 biologically independent replicates.