scMultiome predicts transcriptional regulators of T _RM _2. (A) UMAP plot depicting the annotation of colonic lamina propria CD4⁺ T cells derived from CD (n = 3, CD Patient 1–3 in Table S1) and control (n = 3, Ctrl-Patient 1-3 in Table S1) samples. The clusters were merged as they were assigned to the same cell population through reference mapping (Fig. S3 D). (B) Distribution of cells originating from CD (red) and control (blue) samples. (C) Feature plot illustrating the predicted expression of CD103 and HLA-DR as determined by the MapQuery function. (D) Feature plot showcasing the expression of IFNG and GZMB. (E) Coverage plot of the IFNG and GZMB loci. (F) Predicted TF binding within DARs of the T_RM_2 cluster. Differential accessibility was computed using Signac and Seurat, while TF binding was analyzed with motif analysis using Signac. (G) Predicted TF binding within DARs of the T_RM_2 cluster. TF binding was analyzed with ChIP-Atlas. (H) Volcano plot depicting differentially expressed TF-coding genes. RUNX2 and BHLHE40 are highlighted in F–H. (I) Venn diagram illustrating the number of TFs identified from the three analyses (F–H). (J) Expression patterns of 15 TFs identified from three analyses. (K) Expression levels of 15 TFs across clusters. The dot size indicates the percentage of cells expressing the gene within each cluster, while color intensity reflects the average expression level.