GSM3956923: HiC-K562-Cell-R1; Homo sapiens; Hi-C
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) . For intact cells: 5 million K562 cells or nuclei were washed twice with 15 mL of HBSS and pelleted at 300 g for 10 min, then resuspended in 2.5 mL of HBSS. The sample was transferred to 20.625 mL crosslinking mix [625 μL of 37% formaldehyde + 20 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 cells 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. Lysis For Hi-C with intact cells: the 5 million cross-linked cells were lysed by adding 1 mL cold lysis buffer [10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 0.2% Igepal CA-630 (NP40)] and 10 µL of 100X Protease inhibitors. The sample was incubated on ice for 15 min to let the cells swell. The cells were lysed on ice using a dounce homogenizer with pestle A by moving the pest Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.17
GEO Accession
GSM3956923