“…UMAP dimensionality reduction and combined analysis of all 4 groups (LP WT , TLO WT , LP Csf2-/-, TLO Csf2-/-) yielded 18 clusters from a total of 15,369 cells (Fig S4A). Based on their top 30 cluster-defining genes, we identified clusters corresponding to B cells (clusters 7, 10), T/NK cells (cluster 14), and epithelial and stromal cells (clusters 0, 5, 6, 9, 11, 15-17), which were excluded from subsequent analysis ( Moura Silva et al, 2021). MPs in clusters 0 and 5 co-expressed Cd4 but not Ccr2, consistent with our flow cytometric classification (Fig 5F).…”