ChIP-seq and ATAC-seq Analysis of Transcription Factors

ChIP-seq and ATAC-seq were performed as described previously (Ohba et al., 2015 (link)). Briefly, chromatin prepared from 1 × 107 PANC-1 cells was immunoprecipitated with anti-β-catenin (Cell signaling, D10A8), CBP (Abcam, ab2832), p300 (Abcam, ab14984), and c-JUN (Abcam, ab31419) antibodies. Libraries were prepared with ThruPLEX DNA-seq Kit (Takara-bio, R400674). For ATAC-seq, 50,000 nuclei were labeled with TD buffer (Illumina, 15027866) and Tn5 transposes (Illumina, 15027865). Libraries were sequenced with Illumina Hiseq X ten. Sequence reads were mapped to the human genome (hg19) with bowtie (Langmead et al., 2009 (link)). Binding peaks were determined with the CisGenome peak caller (Ji et al., 2008 (link)). Common peaks were determined by intersection with bedtools. De novo motif analysis was performed using the Gibbs motif sampler provided in the CisGenome package (Ji et al., 2008).