After nick-labeling with either the two- or three-color schemes, the samples were treated with 6 mAU of QIAGEN Protease at 56°C for 30 min, and the reaction was stopped with 1 µL of IrysPrep stop solution (BioNano Genomics). The DNA backbone was stained with 333 nM YOYO-1 (Invitrogen) and is shown in blue in all figures. The stained samples were loaded and imaged inside the nanochannels following the established protocol (Lam et al. 2012 (link)). BioNano Genomics labeling kit and IrysChip were used to generate the nick labeling data. The next generation mapping system from BioNano has dramatically improved the throughput; our custom-made systems are very similar to this new BioNano Genomics system. Each IrysChip contains two nanochannel devices, which can generate at least 60 Gb of data (molecules >150 kb). Normally, 60× coverage (180 Gb) is needed to generate 30 molecules of each chromosome end containing the telomeres. This assay runs 3 d, collecting over 24,000 images. It currently costs $1000 per sample to run whole-genome mapping. The image analysis was done using BioNano commercial software for segmenting and detecting DNA backbone based on the YOYO-1 staining similar to early optical mapping method (Lin et al. 1999 (link)), and localizing the green labels by fitting the point-spread functions.