Hi-C of Saccharomyces cerevisiae J005(replicate2)
Yeast cells were cross-linked with 3% formaldehyde for 20 min at room temperature and quenched with 0.375 M glycine for 5 min. The cross-linked cells were homogenized by grinding them to a fine powder in liquid nitrogen to lyse the cell wall. Endogenous nucleases were inactivated with 0.1% SDS, and then chromatin DNA was digested by 100 U MboI (NEB) and labeled with biotin-14-dCTP (Invitrogen). The digested DNA was ligated by 50 U T4 DNA ligase (NEB) and the cross-links were reversed. The ligated DNA was extracted using QIAamp DNA Mini Kit (Qiagen) following the manufacturers instructions. Purified DNA was sheared to 300- to 500-bp fragments and further processed by blunt-end repair, A-tailing and adaptor ligation, followed by biotin-streptavidinmediated pull-down and PCR amplification.