title: GSM8483895: HiC-A375-Control-R1; Homo sapiens; Hi-C
library_construction_protocol: Biological replicates of Hi-C were performed on two independent samples of A375 cells, both untreated and with 2 hr treatment of 0.5 µM TSA.  The first biological replicate was processed with the protocol described in (Golloshi et al., 2018). Briefly, 10 million cells were crosslinked with 1% formaldehyde for 10 min. Crosslinked cells were then suspended in lysis buffer to permeabilize the cell membrane and were dounce homogenized. Chromatin was then digested in-nucleus overnight using the DpnII restriction enzyme. Digested ends were filled in with biotin-dATP, and the blunt ends of interacting fragments were ligated together. DNA was then purified by phenol-chloroform extraction. For library preparation, the NEBNext Ultra II DNA Library prep kit (NEB) was used for libraries with size ranges from 200-400bp. End Prep, Adaptor Ligation, and PCR amplification reactions were carried out on bead-bound DNA libraries.  The second biological replicate was processed using the Arima-HiC+ Kit from Arima Genomics following the protocol for Mammalian Cell Lines (A160134 v01) and preparing the libraries using Arima recommendations for the NEBNext Ultra II DNA library prep kit (protocol version A16041v01). Library amplification was performed using the NEBNext Ultra II kit (NEB;E7645S).