Capture Hi-C Library Preparation and Target Enrichment

Capture Hi-C libraries were prepared according to the protocol described in (Jäger et al., 2015 (link)). The protocol consists of two parts: Hi-C library preparation and target enrichment (Figure 1A). A SureSelect Custom Target Enrichment Library covering a 3 Mb region in the 8p23.1 (hg19 coordinates: chr8:8,190,000–11,838,000) was designed using eArray software (Agilent). Hi-C library preparation, comprising chromatin fixation, HindIII digestion, biotin labelling, ligation, and crosslink reversal was performed as described in (Rao et al., 2014 (link)) with minor modifications described in (Jäger et al., 2015 (link)). Target enrichment was performed according to the SureSelect protocol (Agilent) with minor modifications described in (Jäger et al., 2015 (link)). We have prepared 10 capture Hi-C libraries from 5 independent batches of NA07000 cells and 4 capture Hi-C libraries from 2 independent batches of NA07056 cells. The libraries were sequenced on Illumina HiSeq 2,500 system, producing 461 million and 206 million paired-end 2 × 125 bp reads for NA07000 and NA07056, respectively.