GSM9474713: HDMB03 HiC; Homo sapiens; Hi-C
Chromatin crosslinking was conducted using a final concentration of 2% formaldehyde (Sigma Aldrich, F8775) for 10 minutes and was quenched with Arima Stop Solution 1 at a final concentration of 8.7%. The assay was performed on one million cells. Hi-C data were generated using the Arima-HiC+ kit (P/N A101020), according to the manufacturer's protocols. Hi-C DNA was sheared using the Covaris M220 focused ultrasonicator (PIP: 50 W, DF: 25 %, CPB: 200, Treatment time: 65 seconds, Setpoint Temperature: 6 °C) in 100μL cold Elution Buffer. Fragments were size-selected to 200 bp-600 bp prior to biotin enrichment. Before library construction, size-selected fragments were incubated at room temperature for 15 min with Dynabeads™ MyOne™ Streptavidin T1 beads (Invitrogen, 65601) previously washed three times with 200 µl of Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl). Bead-bound samples were resuspended in 50 µl of Elution Buffer for library preparation using the KAPA HyperPrep Kit (Roche Sequencing Solutions, KK8505) and IDT for Illumina–TruSeq DNA Indexes (Illumina, 20022370), with 6 amplification cycles and DNA cleanup performed using 0.85X AMPure XP Beads (Beckman Coulter, A63881). Libraries were sequenced as 151 bp paired end on the Illumina NovaSeq X Plus system.