FIGURE 2.

VDR ATAC-seq in AA and EA cell lines. A, ATAC-seq was undertaken in triplicate in HPr1AR, LNCaP, RC43N, and RC43T following 1α,25(OH)₂D₃ treatment (100 nmol/L, 4 hours) or vehicle control. FASTQ files were QC processed, aligned to hg38 (Rsubread), sorted and duplicates removed before further processing with ATACseqQC to generate nucleosome free and mononucleosome regions. Differential enrichment of regions was measured with csaw and the significantly different regions (P_adj < 0.1) were then intersected to generate the Venn diagrams of overlapping regions by a minimum of 1 bp (ChIPpeakAnno). B, Motif enrichment in NF regions was undertaken with Homer and ranked by significance to visualize in descending significance. C, Frequency of enriched motifs by TF families’ class. D, Enrichment of circadian rhythm TFs.