Promoter Capture-C analysis of Hepatocyte-like cells

The goal of this study is to identify chromatin interactions in hepatocyte-like cells Methods: hepatocyte-like cells (HLC) were produced by differentiating three biological replicates of iPSCs (which in turn were generated from peripheral blood mononuclear cells using a previously published protocol (Pashos et al 2017.) 10 million cells were used for promoter Capture-C library generation. Custom capture baits were designed using an Agilent SureSelect library design targeting both ends of DpnII restriction fragments encompassing promoters (including alternative promoters) of all human coding genes, noncoding RNA, antisense RNA, snRNA, miRNA, snoRNA, and lincRNA transcripts, totaling 36,691 RNA baited fragments shows the custom bait map boundaries in hg19 coordinates). Each library was then sequenced on an Illumina NovaSeq. HiCUP was used to process the raw FastQ files into loop calls; we then used CHiCAGO to define significant looping interactions; a default score of 5 was defined as significant.