GSM3956915: HiC-K562-DpnII-predigest-4h-R1; Homo sapiens; Hi-C
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.10
GEO Accession
GSM3956915