2.9. Chromatin Immunoprecipitation (CHIP) Sequencing

Chromatin immunoprecipitation (CHIP) sequencing was performed following the company’s instructions (SimpleChIP^® Enzymatic Chromatin IP Ki, CST 9003). Chromatin was immune-precipitated with the following antibodies—H3K27ac (CST 4535, 10 μL/sample), H3K27Me3 (CST 9733, 10 μL/sample), Rpb1 (CST 14958, 10 μL/sample) or Rabbit IgG (CST 2729, 2 μL/sample). Following purification, the ChIP DNA was assessed for quality by real time PCR analysis. Libraries were prepared and were subjected to next generation sequencing (Illumina HiSeQ instrument; HiSeq 4000; single read 50 bp (SR50)). Mapping to the human genome (hg38) was performed by bowtie2. Peaks were called and obtained with MACS2 software. The BEDgraph files were converted to the bigwig format and visualized with the Integrated Genome Browser (IGB). The experiment is deposited ({"type":"entrez-geo","attrs":{"text":"GSE124877","term_id":"124877"}}GSE124877 and {"type":"entrez-geo","attrs":{"text":"GSE150395","term_id":"150395"}}GSE150395).