Fig. 2: FA-EGS crosslinking HiChIP protocol improves cohesin-mediated loop detection. | Communications Biology

Fig. 2: FA-EGS crosslinking HiChIP protocol improves cohesin-mediated loop detection.

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

Fig. 2

A IGV browser coverage tracks and nf-HiChIP loops of the indicated HiChIP samples and read coverage tracks for SA1 and CTCF GM12878 ChIP-seq experiments. B Juicebox interaction maps at 5 kb resolution of the example region for the indicated cohesin HiChIP samples. Loops (nf-HiChIP) are shown as green (SMC1 HiChIP HG00731) or blue (SMC1 HiChIP GM12878) rectangles. C APA analysis performed using loops identified by nf-HiChIP for the indicated cohesin and CTCF HiChIP samples. The APA score P2LL (peak to left lower corner) is the ratio of the central bin to the average of the lower left corner and indicates the strength of the loop. D Overlap between loops (with 15 kb tolerance) called by nf-HiChIP in the indicated datasets. A single cell in the matrix represents the percentage of loops in the row sample that overlap with one or more loops from the column sample. Note that the matrix is not symmetric, as one-to-many overlaps are possible.

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