MCF-7/shCtrl_input
DNA was eluted and crosslinks were reversed at 65C overnight. DNA was treated with RNase A and Proteinase K, then purified using Quick-DNA Microprep Kit (Zymo Research). DNA was amplified with 11 PCR cycles using custom barcoded primers (Nextera), quality control-checked on a Fragment Analyzer (Agilent), quantified by Qubit, and pooled for sequencing on a NextSeq2000 (Illumina). Libraries were sequenced using 50-bp paired-end reads targeting 50M reads per sample. Sequencing reads were processed with the ENCODE Histone ChIP-seq pipeline (v2.2.1) (github.com/ENCODE-DCC) and aligned to the human genome (hg38) using Bowtie2 (v2.5.1) with minimum read length set at 2 (Langmead and Salzberg, 2012). Unmapped/low quality reads were filtered using samtools (v1.16.1) and duplicated reads were removed using Picard (v2.27.5).