title: GSM3693035: EBNA3C-HT 4C-seq AICDA 3C Off Replicate 1; Homo sapiens; OTHER
library_construction_protocol: Cells were treated with 1% formaldehyde to crosslink, and the nuclei were isolated via resuspension in lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and 50 μl protease inhibitors). Then, the nuclei were washed with 1× NEBuffer2 (New England Biolabs) and treated with 0.3% SDS at 65 °C. HindIII digestion was performed at 37 °C overnight, and then, a proximity ligation was performed at 4 °C for 24 h. After reverse cross-linking with a Proteinase K (Ambion, USA) treatment, the DNA was purified using a phenol–chloroform (Solarbio) extraction with ethanol precipitation. The second digestion step was performed using DpnII overnight. Then, we performed a second ligation and ethanol precipitation to extract the DNA. The DNA was finally purified using a QIAquick PCR purification kit (QIAGEN, Germany) according to the manufacturer's protocol. After the PCR reaction, we purified the 4C library using AMPure beads (Beckman, Germany). Libraries were sequenced on the Illumina HiSeq2500 sequencer.
attributes.tag: GEO Accession
attributes.value: GSM3693035