Samples for ChIPseq samples were prepared and sequenced as previously described10 (link), with minor changes. The DNA was sheared using Biorupter Pico (Diagenode), 5 cycles 15 seconds on 90 seconds off. Reads were first trimmed using TrimGalore v0.6.061 , then mapped to hg19 using Bowtie2 v2.3.462 (link) with default settings. Bigwig files were generated with DeepTools v3.1.363 (link) with the following settings: minimum mapping quality of 15, bin length of 10bp, extending reads to 200bp and reads per kilobase per million reads (RPKM) normalization.
Peaks were called for all samples using MACS2 v2.1.164 (link) with default options. Overlaps between the sets of identified peaks across samples were obtained using BEDtools v2.25.065 (link). Heatmaps were generated using DeepTools63 (link) for the different sets of peaks identified in the wild type cell line, excluding those overlapping blacklisted regions of the genome (ENCODE project consortium, 2012).
Peaks were called for all samples using MACS2 v2.1.164 (link) with default options. Overlaps between the sets of identified peaks across samples were obtained using BEDtools v2.25.065 (link). Heatmaps were generated using DeepTools63 (link) for the different sets of peaks identified in the wild type cell line, excluding those overlapping blacklisted regions of the genome (ENCODE project consortium, 2012).
