Fig. 5

M. marinum infection of Ly6C⁺MHCII⁺ monocytes alters the transcription profile of individual early and intermediate clusters. (a–d) Transcriptional analysis of infected versus bystander Ly6C⁺MHCII⁺CD64⁺ myeloid cell clusters. (a) Graph depicting number of significantly up and down regulated genes between individual infected and bystander clusters. Differential expression was defined by an average log fold change > 0.5 and a p-value < 0.05, consistent across the two experiments. (b) Scaled heatmap showing the average expression of genes that were commonly enriched in infected cells across all early and intermediate clusters. (c) Expression level of the 114 genes significantly upregulated in infected clusters (left panel) and the 124 genes significantly upregulated in bystander cells (right panel) calculated using AddModuleScore⁶⁸ and overlayed on the scRNA-seq based tUMAP. (d) Radar chart showing selected signaling pathways enriched infected and bystander cells using Gene Ontology Biological Process 2023 (Enrichr) tool.