Fig. 4

M. marinum infection induces a metabolic shift and alterations in chemokine/cytokine transcription in Ly6C⁺MHCII⁺ monocytes in vivo. (a–f) Transcriptional characterization of Ly6C⁺MHCII⁺CD64⁺ clusters. (a) Expression of indicated genes overlayed on tUMAP. (b) Pseudotime overlay on tUMAP of scRNA-seq data obtained from infected and bystander Ly6C⁺MHCII⁺ CD64 + myeloid cells using cluster 1 as the pseudotime starting point. (c) Scaled heatmap showing the average expression of the top 50 Differentially expressed genes (DEGs) per cluster. (d) Signaling pathway activity within individual clusters as assessed using PROGENy^32,33,34. (e) Radar chart showing selected enriched pathways within indicated clusters using Gene Ontology Biological Process 2023 (Enrichr) tool. (f and g) Scaled heatmap showing the average expression of selected genes within (f) the Cellular Response to Type II Interferon or Interferon-Mediated Signaling Pathway, and (g) the Cytokine-Mediated Signaling Pathway, in indicated clusters.