Fig. 1
Overview of BL-Hi-C method. a Workflow. Briefly, cells are treated with formaldehyde for protein-DNA crosslinking and lysed to access the nuclei. Then, the DNA is digested by the enzyme HaeIII (which recognizes “GGCC”) and connected with the bridge linker during proximity ligation. After the DNA fragments are purified and shared, the biotin-labeled DNA is captured for sequencing. The sequencing data are processed with ChIA-PET2 to perform linker trimming, the alignment of reads to the genome and the formation of uniquely mapped paired-end tags (PETs), which are adapted for downstream analysis. See Methods for the detailed protocol and Supplementary Fig. 1 for the enrichment models. b Efficiency comparison of BL-Hi-C and the published in situ Hi-C and HiChIP methods. The cis-unique PETs refer to the paired reads uniquely mapped on the same chromosome, and trans-unique PETs refer to paired reads mapped on different chromosomes. For each method, the cells and sequencing depth are determined
