GSM2587509: Akata-Tet Z, LGNFR+ HiC rep 1; Homo sapiens; Human gammaherpesvirus 4; OTHER
In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI as described (Rao et al., 2014) with slight modifications. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0 and transferred to new tubes. Sequencing libraries were created from bound DNA using the Ovation Ultralow Library System V2 kit (NuGEN) with one modification. After adapter ligation, because DNA is still attached to the beads, water instead of SPRI beads was added to the reaction. DNA bound to the beads was purified with a magnet, washed, and the beads were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0. After library amplification, SPRI beads were added as directed to purify the amplified DNA.