Fig. 3: FA-EGS crosslinking HiChIP protocol improves stripe detection and enables the building of accurate loop extrusion models. | Communications Biology

Fig. 3: FA-EGS crosslinking HiChIP protocol improves stripe detection and enables the building of accurate loop extrusion models.

From: Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

Fig. 3

A Number of stripes called by Stripenn and gStripe for the cohesin HiChIP datasets analysed in this study. gStripe results were calculated using nf-HiChIP, HiCCUPS or ChIA-PIPE loops as an input. B Juicebox interaction maps at 5 kb resolution and the stripes of the exemplary region (chr6: 15,550,000-16,850,000) for the cohesin HiChIP samples. Lower (below diagonal) and upper (above diagonal) corners present SMC1 FA-EGS HiChIP (HG00731) and SMC1 HiChIP (GM12878), respectively. Stripes were called by the algorithms indicated above the maps. Each stripe set is shown on top of data used to generate it: the interaction heatmap and, in the case of gStripe, the nf-HiChIP, HiCCUPS or ChIA-PIPE loop set (blue dots). C IGV browser view of the example region for SMC1 HG00731 FA-EGS HiChIP sample used for loop extrusion modelling. The first three tracks show the output of the nf-HiChIP pipeline: read coverage, peaks called by MACS3 and loops called by nf-HiChIP. The fourth track shows the stripes identified by gStripes (with the nf-HiChIP loop set). D Final structure obtained after running LoopSage simulation for the region and sample indicated in panel (C). E Experimental (above diagonal) versus simulated(below diagonal) heatmaps (at the 5 kb resolution) for the region and data shown in panel C.

Back to article page