ChIPseq of PHF6 in THP-1 cells

The Zymo-Spin ChIP kit (Zymo Research Corp., Irvine, CA, D5209) and anti-PHF6 antibody (SCBT, sc-365237AC) were used for chromatin immunoprecipitation sequencing (ChIPseq) according to the instructions provided by the manufacturer. For ChIPseq, THP-1 cell lines and a total of 5 million THP-1 cells were resuspended in 1 ml of 1× PBS. The high-throughput sequencing was performed by the Cleveland Clinic Sequencing Core on an Illumina 2500 sequencer using 50 bp single-end sequencing. The Bowtie2 alignment tool was used to align ChIPseq reads to the human genome build hg19. We used the HOMER software for finding peaks in aligned data^{40 (link)}. Deeptools was used for generating bigwigs to visualize with the Integrative Genomics Viewer (IGV)^{31 (link),41 (link)}. We downloaded H3K27ac ChIPseq in THP-1 from GEO (GSM5908232) and RUNX1 ChIPseq fastq in THP-1^{42 (link)}. These downloaded data were also aligned and analyzed as described above.