ChIP-seq peak files

Purified DNA was quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, cat. #Q32854, Waltham, MA, USA), and size and integrity was verified with a Fragment Analyzer (Agilent, Santa Clara, CA, USA). Libraries were prepared as 75 bp paired end reads with the TruSeq ChIP Library Preparation Kit (Illumina, Inc., cat. #IP-202-1012, San Diego, CA, USA) following manufacturer’s instructions. Libraries for H3K4me3, H3K27ac, and Input were sequenced to achieve at least 20 million uniquely mapped reads, and H3K4me1 and H3K27me3 libraries were sequenced to achieve at least 45 million uniquely mapped reads to comply with ENCODE standards for ChIP-seq1. The peaks of H3K4me3, H3K27ac, H3K4me1, and H3K27me3 were called by chipseq model of Nextflow v24.04.247 with Bowtie2 aligner and MACS2 peak caller with ‘-macs_pavalue 0.005’, for narrow histone marks H3K4me3 and H3K27ac with additional parameter ‘--narrow_peak’. The reference genome for alignment was from NCBI (ARS-UI_Ramb_v2.0, GenBank accession GCF_016772045.1).