ChIP-Seq of HES4 in CUTLL_1 human T-ALL cell line
ChIP-Seq libraries were performed in service by Active Motif Enabling Epigenetics Research Biotechnology (Carlsbad, USA). The ChIP-seq data analysis was performed using the nf-core/chipseq pipeline (v2.0.0) implemented in Nextflow (v21.10.6) (Ewels et al., 2020). The ChIP-Seq data were aligned against human genome GRCh37 the Burrows-Wheeler Aligner (BWA, v0.7.17-r1188) with default parameters. MACS2 (v2.2.7.1) was used for identifying enriched regions. Peaks were called with Model-based Analysis for ChIP-seq (MACS2)(Zhang et al., 2008) version 2.1.2 using default parameters after normalization with input as control. The peaks with p-value <0.05 were retained. The ChIP-seq data were visualized using the Integrative Genomics Viewer (IGV). The peak overlaps between different ChIP-seq datasets were determined with the BedTools suit bedtools intersect. Peak annotation and genomic features (transcription starting sites TSS and genes associated with peaks) were found using the annotePeaks function from HOMER (HOMER, v4.11) (Heinz et al., 2010). The deeptools software was used to convert BAM alignment files to bigwig (bamCoverage). To visualize the enrichment of genomic signal on specific target region (TSS) was used the R package Enriched Heatmap (Gu et al., 2018).