Whole cell extract (ChIP-Seq control) of human colon tumor
ChIP-seq was performed as described previously (Liau et al., 2016). In brief, crosslinked cells were lysed and DNA was sheared to between 400 and 2,000 base pair fragments. Antibodies were as follows: CTCF (Cell signaling #3418), H3K27ac (Active Motif #39133), H3K9me3 (Abcam #8898), H3K27me3 (Cell Signaling #97335). ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3' A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.