Fig. 5: Spatially resolved neuronal atlas of the MTN, pre-LC, LC, and Bar.
From: A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution
a Voronoi plots depicting cells of a ROI that includes MTN, pre-LC, LC, and Bar across 9 sequential sections, from −5.2 to −5.8 bregma level. Glia/non-neuronal cells are in gray. b t-SNE plot of 22,358 neurons. c Stacked area chart showing each cluster’s cell frequency (cluster trajectory) across all 9 MERFISH sections. Clusters displayed by the Voronoi, t-SNE, and stacked area chart are color-coded according to the legend in (b). Clusters underlined in the legend represent external-to-the-ROI neuron types/glia contamination. d Dot plot of the top 2 markers for each cluster. e Left: MERFISH image showing the spatial distribution of Prph, Th, and Brs3 at bregma levels −5.5 and −5.6. (scale bar: 75 μm). Right: violin plots depicting the average expression level (y-axis) of 9 genes in clusters at3_8 and at3_24 (x-axis). f Left: MERFISH image showing the spatial distribution for Th, Pdyn, and Tnc in bregma levels −5.6 and −5.3 in the pre-LC (top) and LPBD (bottom). (scale bar: 50 μm). Right: violin plots depicting the expression level (y-axis) of 8 genes in clusters at3_30 (pre-LC) and at2_5 (LPBD) (x-axis). g Voronoi plots depicting LC noradrenergic neurons across 9 sequential MERFISH sections from −5.2 to −5.8 bregma level. Other ROI’s neuronal clusters and glia/non-neuronal cells are in gray. h t-SNE plot of 4,074 noradrenergic neurons. i Stacked area chart showing each cluster’s cell frequency (cluster trajectory) across 9 sequential MERFISH sections in (g). Clusters displayed by the Voronoi, t-SNE, and stacked area chart are color-coded according to the legend in (h). j Dot plot depicting Th, Ddc, Dbh, Slc18a2, Slc6a2, Hcrtr1, and Hcrtr2 genes and the top 2 marker genes for each subcluster. In (i, j), only clusters composed of >200 cells were included. All differentially expressed genes in the dot plot have an average log fold-change >0.25 and an adjusted p-value <0.01. Test used: Wilcoxon Rank Sum two-sided Bonferroni-corrected Test; NA, no marker detected.
