Single-cell transcriptomic reveals heterogeneity within neutrophil populations with disease-specific difference. (A) Neutrophil (n = 2,963) subclustering reveals three subclusters (left), also colored by patient ID (middle) and disease condition (right). (B) Volcano plot of differential gene expression results of each neutrophil subcluster compared with the rest. Y axis shows −log10 (BH-adjusted P value); x axis shows log2 fold change between cells in subcluster and outside the subcluster. (C) Heatmap of subtype top 10 differentially expressed (DE) genes in each of the neutrophil subcluster. (D) Expression of marker genes in neutrophil subclusters by disease conditions. (E) Fisher’s exact test on abundance of detailed neutrophil subclusters between TB conditions. Statistical annotations: fold-change >2 (ΔΔ). (F) Cell2loc imputed neutrophil abundance distribution on the Visium dataset grouped by TB and granuloma status (Materials and methods). The 5% quantile of the estimated posterior distribution of cell abundance at each Visium spot is displayed, representing the value of cell abundance that the model has high confidence in. Two-sided Mann–Whitney U test without correction were used for statistical testing. ****: P < 0.0001.