Fig, 1
Workflow for ATAC-Seq library preparation, analysis, and biomarker selection in circulating CD8+ T cells from IgAN patients. a Schematic of the ATAC-Seq workflow. Circulating CD8+ T cells were isolated from peripheral blood mononuclear cells (PBMCs) of IgAN patients. Genomic DNA from open chromatin regions was fragmented via tagmentation using Tn5 transposase. These constructed ATAC libraries were sequenced and aligned to human reference genome (hg19). Chromatin accessibility for each sample was normalized using a factor derived from 20 control peaks. Normalized enrichment values within ATAC-peaks were converted to area values. DARs were identified by comparing early- and late-stage groups using fold change and Student’s t-test. Schematic created with BioRender.com. b Biomarker selection process. A total of 279 DARs with fold change > 2 and P < 0.05 between the early-stage (blue) and late-stage (red) group were identified (left, middle). Of these, 122 DARs with peak widths < 500 bp were selected as candidate biomarkers (right, top), including 104 early-stage group and 18 late-stage group enriched peak. Biomarkers were ranked based on relative distance and mean area values in the non-enriched group. A heatmap shows normalized area values as Z-scores ranging from ‒2 (navy) to +2 (yellow) (right, bottom).
