title: GSM6203839: C42B, HiC, rep1; Homo sapiens; Hi-C
library_construction_protocol: The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma. In situ Hi-C was performed in duplicate and 5 x 10^6 cells were used for each experiment. MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). In situ Hi-C ibraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. Library was amplified with PCR and then sequenced using Illumina HiSeq 2000.