Supplementary Figure 2: Quality metrics and reproducibility of sequencing datasets.

(a) Smoothed scatterplot of the Hi-C contacts between biological replicates for each stage. bin size = 100 kb. Spearman correlation coefficients are indicated on top of each sample pair. (b) Hierarchical clustering of Hi-C contact matrices based on 1-PCC (Spearman correlation coefficients) of the contacts between all samples, bin size = 100 kb. (c) Hierarchical clustering of the compartment A/B scores (PC1 values) between samples. (d) Hierarchical clustering of the insulation scores between samples. (e) Boxplot showing the number of reads for each sample. (f) Boxplot showing the percentage of alignments to human genome for each sample. (g) Boxplot showing the percentage of potential duplicated reads for each sample. (h) Boxplot showing the number of peaks called for each ChIP-seq sample. (e-h) For each boxplot the sample size N=12, the elements of the boxplot are: center line, median; box limit, upper and lower quartiles; whiskers, 1.5x interquartile range. (i) Barplots showing the relative expression levels (by RNA-seq) of representative genes during cardiomyocyte differentiation.