title: GSM8897000: 9E cells, extrachromosomal HPV31, biol rep2; Homo sapiens; Hi-C
library_construction_protocol: In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH8.0. 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 pH8.0. After library amplification, SPRI beads were used to purify the amplified DNA.