ATAC-seq analyses with 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 functional roles of PML bodies in chromatin organization, we conducted ATAC-seq with wild-type and PML KO mESCs. ATAC-seq profile of wild-type and PML-/- mouse embryonic stem cells. 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 a MAPQ threshold of 30. 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