ChIP-seq library preparation and processing

Libraries were constructed using the manufacturer’s guidelines in the NEBNext Ultra II FS DNA Library Prep Kit for Illumina, using 1ng of starting material. Barcoded libraries were pooled and sequenced with next-generation sequencing. First, raw reads were demultiplexed by barcode. Then the sequences were trimmed with Trimmomatic, aligned with BWA, and normalized by reads per million.^78,79 Then the reads were visualized with IGV. For further analysis peaks were called using MACS2 with -g 12.57e6 in broad mode with a cutoff of 0.05.⁸⁰ Heatmaps were generated using deepTools (v3.5.1).⁸¹