GSM5134439: ChIPseq_HK4me3_KO_rep2; Homo sapiens; ChIP-Seq
RNA-seq: RNA extraction was performed using RNeasy mini-kit (Qiagen) followed by Turbo DNA-free kit (Ambion).  ChIP-seq: Cells were collected with or without formaline fixation. Chromatin was fragmented by MNase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies. DNA was purified using MinElute columns from Qiagen.  Hi-C: Cells were fixed with 2% of formaldehyde, chromatin was digested with DpnII, DNA ends were biotinylated and re-ligated in situ. DNA was purified by reverse-crosslinking, followed by phenol/chloroform extraction, ethanol precipitation and additional purification using AMPure XP magnetic beads. DNA was sheared by sonication, ligation junctions were enriched by Biotin pull-down. RNA-seq: Libraries were constructed using Truseq stranded total RNA kit (Illumina).  ChIP-seq: Libraries were prepared using the MicroPlex V2 library preparation kit (Diagenode).  Hi-C: Libraries were prepared with standard protocol using TruSeq adapters (Illumina).