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Fig. 1 | Genome Biology

Fig. 1

From: CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Fig. 1

The outline of Capture Hi-C. a Outline of the CHi-C protocol. A Hi-C library is hybridized to a capture system that consists of biotinylated RNA probes targeting the ends of DNA restriction fragments. After hybridization, streptavidin pulldown is performed to filter for fragments that have hybridized with the RNA probes, leading to enrichment in baited fragments (“baits”). Following a limited-cycle PCR amplification, the CHi-C library is ready to be analysed by massively parallel paired-end sequencing. b The interactome of the LPHN2 promoter region in GM12878 cells. The top panel shows a 1.8-Mb region containing the LPHN2 gene. The middle panel shows raw read pairs from the Hi-C library. All read pairs sequenced for these regions are shown in grey. In purple, we show only the read pairs that contain the LPHN2 promoter in one of the fragment ends. The bottom panel shows raw read pairs from the Promoter CHi-C library from [3]. The WashU EpiGenome Browser [58, 59] was used to create this figure

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