Fig. 2: MERFISH transcriptional profile of the dPnTg.

a Experimental workflow summarized in five main steps: brain dissection, MERFISH assay, signal deconvolution, bioinformatic analyses, and data visualization. In total, 7 animals were used, of which 4 represent a complete series of 10 serial coronal sections. b t-SNE plot of 685,289 cells color-coded according to the legend in (c). c Donut plot depicting the fraction (%) of each cell type identified. d Dot plot of 17 cell markers (y-axis) that univocally identify each cell type (x-axis). For each cell type, 2 markers were plotted, except for VLMC types I and II, where 1 marker was used. e, f t-SNE of 231,103 cells from the “excitatory” group (e) and 110,332 cells from the “inhibitory” group (f) color-coded by cell cluster. The top 2 marker genes specify the identity of each cluster as per (g) and (h), respectively. g, h Dot plot of the expression level of the top marker gene for the “excitatory” (g) and “inhibitory” (h) neuronal clusters. 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. t-SNE, t-distributed Stochastic Neighbor Embedding; OPC, oligodendrocyte progenitor cell; PVM, perivascular macrophages; VSMC, vascular smooth muscle cells; CPE cells, choroid plexus epithelial cells; VLMC1/2, vascular and leptomeningeal cell type 1/2; Diff.OPC, immature oligodendrocytes; NA, no marker detected; CONT, glia contamination.