Comprehensive epigenomic profiling reveals disease-specific chromatin states and enhances therapeutic target discovery in ankylosing spondylitis

We performed comprehensive epigenetic profiling in immune cell samples from patients with ankylosing spondylitis and healthy controls. <strong>RNA-seq/ATAC-seq/ChIPm/eRNA: </strong>Raw and normalised count data for each gene or peak in CD4+ T cells, CD8+ T cells, and CD14+ monocytes from AS patients and healthy controls. File name is in the format modality_cell-type_raw/normalised_counts.txt.gz. Table S2 shows which experiments were performed on which samples. <strong>ChromHMM: </strong>We used ChromHMM to integrate epigenomic data. ChromHMM filenames are in the format ChromHMM_sampleID_celltype_n.bed.gz where n is the number of states in the ChromHMM emission model. <strong>Capture-C; </strong>We performed Capture-C to detect chromosome looping interactions between gene promoters and SNPs associated with ankylosing spondylitis. Capture-C count data are shown in the format: CaptureC_celltype_gene_Pro/SNP_normalised.unionbdg. We used PeakY to calculate a score for each interaction. PeakY scores are given in the following format: PeakY_AS/HV_celltype_tier_chrloc_gene_Pro/SNP.txt. gene_Pro and gene_SNP relate to the baitsets given in Table S8.