Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis

We performed comprehensive epigenetic profiling in immune cell samples from patients with ankylosing spondylitis and healthy controls. Note: Due to Zenodo updating their maximum file limit to 100 files, version 4 (v4) of this archive has been split into 5 compressed archive (tar.gz) files containing all previous and additional files. Version 4 of this archive (updated 03/06/2025) adds 4 files to the archive that were omitted in previous versions which have now been made available. These were: RNA_CD8_raw_counts.txt.gz RNA_CD8_normalised_counts.txt.gz RNA_CD14_raw_counts.txt.gz RNA_CD14_normalised_counts.txt.gz -------------------------------------------------------------------------------------------------------------------------- RNA-seq/ATAC-seq/ChIPm/eRNA: Raw and normalised count data for each gene or epigenetic 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. This data can be found in the "Raw_Counts.tar.gz" and "Normalised_Counts.tar.gz" archives. -------------------------------------------------------------------------------------------------------------------------- ChromHMM: We used ChromHMM to integrate epigenomic data into a 14-emission state model detailing chromatin functionality in AS patients and healthy controls. ChromHMM filenames are in the format: "ChromHMM_sampleID_celltype_n.bed.gz" where n is the number of states in the ChromHMM emission model. This data can be found in the "ChromHMM_AS_HV.tar.gz" archive. -------------------------------------------------------------------------------------------------------------------------- Capture-C: 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. This data can be found in the "CapC_Count_Data.tar.gz" and "PeakY_regions.tar.gz" archives.