ChIP-seq analysis

The raw sequencing data of public ChIP-seq dataset ({"type":"entrez-geo","attrs":{"text":"GSE79899","term_id":"79899"}}GSE79899) was downloaded and decompressed from GEO database by using SRAtoolkit (v3.0.0). The raw sequencing reads were then firstly quality controlled with FastQC and mapped to the human genome (hg38) by using bowtie2 ⁷⁰ (version 2.3.2). After alignments, we used Picard software (version 2.21.1) to mark and discard the PCR duplicates from aligned results. We then estimated the fragment sizes of ChIP-seq libraries with phantompeakqualtools ⁶³ as the parameter “--extsize” of MACS2 and analyzed the significant binding or histone modification regions by utilizing MACS2 ⁵⁶ (version 2.2.7.1) with following parameters: -g hs --mfold 5 50 -p 0.01 --nomodel --shift 0 --keep-dup all -B --SPMR. Finally, the peaks with p-values less than 0.01 were recognized as significantly enriched regions and kept for downstream analysis. The normalized signals of aligned ChIP-seq tags were calculated by deeptools ⁶⁴ (version 3.5.1).