ChIP-seq analysis of wild-type and PML KO mESCs

Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate roles of PML bodies in transcriptional regulation, we conducted ChIP-seq analysis for histone modifications, including H3K4me3, H3K27ac, H3K27me3, and H3K9ac with wild-type and PML knockout mESCs. Overall design: Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive. Multiple mapped reads were filtered out using XS tag. PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools. BigWig files were generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY.