Fig. 6

scRNAseq analysis of HLADR⁺SIRPα⁺ MNPs in inflamed CD colon. a Gating strategy to capture the entire HLADR⁺SIRPα⁺ cell population for scRNAseq analysis. Single cells were sorted across overlapping gates labeled as P1 (brown), P2 (blue), P3 (red), Px (orange), and P4 (green) from 3 patients. b t-SNE visualization of isolated single HLADR⁺SIRPα⁺ cells from all five gates (n = 294 cells that passed QCs), colored by cluster assignment (left) and FACS identity (right). c Heatmap reports scaled expression (log TPM + 1 (Transcripts Per Million) values) of discriminative gene set (AUC cutoff ≥ 0.75; average log fold change expression difference ≥ 1.2) for each cluster defined. Heatmap color scheme is based on z-score distribution from −2.5 (purple) to 2.5 (yellow). Color legend at the top of the heatmap indicates the unbiased cluster assignment as defined in panel (b) and color legend at the bottom of the heatmap indicates the CD patient identity (n = 3; labeled “x”, “y”, and “z”). Violin plots illustrate gene expression level distribution of discriminating surface marker genes (y-axis, (log2(TPM + 1))) across each of the six identified clusters (x-axis)