title: 3C-seq for NEDD9 for 0 min upon TNFa treatment
design: 3C-seq was performed in duplicates as described (Stadhouders et al., 2013). In brief, ~10 million HUVEC nuclei were isolated at 0, 30, and 60 min post-stimulation, following cross-linking in 1% paraformaldehyde (10 min, 20°C; Electron Microscopy Science), chromatin was cut using ApoI or HindIII (New England Biolabs), and ligated in dilution under conditions that allowed most nuclei to remain intact. Ligated DNA was recut with DpnII and ligated, and PCR was performed for each viewpoint