Global conservation and local perturbation feature androgen-elicited 3D genome in prostate cancer cells

For cell cross-linking, LNCaP cells were cultured in RPMI1640 + 5% CDS medium and VCaP cells were cultured in DMEM + 5% CDS medium, respectively. After 2 days, cells were treated with Vehicle (control) or androgen (10nM of DHT) for 4hrs. Cells were fixed with formaldehyde and cell lysis was digested by DpnII to produce sticky ends. Terminal repair was performed with biotin-labeled bases to facilitate the cyclization. DNA was de-crosslinked and the purified DNA, was sonicated into 300bp-700bp fragments. The DNA fragments containing interaction were captured by streptavidin magnetic beads for library construction. After passing the library inspection, high-throughput sequencing was carried out on the Illumina platform, and the sequencing read length was PE150. The sequencing depth (based on clean read): VCaP-Con is about 157X, VCaP-DHT is about 156X, LNCaP-Con is about 150X, and LNCaP-DHT is about 150X.