Fig. 1: FA-EGS crosslinking improves the quality of the cohesin HiChIP experiment.

A Schematic of the HiChIP experiment and its data representation. B IGV browser coverage tracks of the HiChiP and ChIP-seq experiments analysed in this study. The following example genomic regions are shown: (1) 300 kb window - chr19:45,417,401-45,717,713; (2) 150 kb window - chr19:43,508,033-43,658,922; (3) 50 kb window - chr17:49,677,416-49,727,883. C Heatmap showing Pearson correlation coefficient between the samples processed in this study. D IGV browser coverage tracks and called peaks for the indicated cohesin HiChIP (SMC1) and ChIP-seq (SA1) experiments. The following example genomic regions are shown: (1) 300 kb window - chr5:150,332,698-150,635,698; (2) 150 kb window - chr7:55,939,000-56,089,000; (3) 50 kb window - chr17:40,160,000-40,210,000. E Venn diagrams showing common peaks between SMC1 HiChIP HG00731 and SA1 ChIP-seq GM12878. F Venn diagrams showing common peaks between SMC1 HiChIP GM12878 and SA1 ChIP-seq GM12878. G Heatmap showing the distribution of SMC1 FA-EGS HiChIP HG00731 reads and SMC1 HiChIP GM12878 reads within a 20 kb window centred on the cohesin (SA1) ChIP-seq GM128787 peaks. H Distribution of -log(10) qvalue of peaks called by MACS3 in the indicated cohesin HiChIP and ChIP-seq samples. The horizontal red line inside each boxplot indicates the median. The bottom edge of the box marks the first quartile, and the top edge marks the third quartile and the whiskers extend to the minimum and maximum values, excluding outliers, which are not shown. I Fingerprint analysis plot (45) showing the comparison of ChIP enrichment in the indicated cohesin HiChIP and ChIP-seq samples.