Fig. 2

Estimated cell type proportions in tissue sections labeled with RNAScope/Immunofluorescence. A Schematic of experimental design for combined single molecule fluorescent in situ hybridization (smFISH) with immunolabeling using RNAScope/immunofluorescence (IF). The “Star” combination of probes/antibodies marked Excitatory Neurons [Excit], Microglia [Micro], and Oligodendrocyte/OPC [OligoOPC] cell types in 13 tissue blocks. The “Circle” combination marked Astrocytes [Astro], Endothelial cells [Endo], and Inhibitory Neuron [Inhib] cell types in 12 tissue blocks. The total RNA expression gene (TREG) [45], AKT3, was also included in each combination to estimate RNA abundance. B Representative fluorescent image of a single field for the “Star” combination showing expression of SLC17A7, TMEM119, OLIG2, AKT3, and the nuclear marker DAPI. C Representative fluorescent image of a single field for the “Circle” combination showing expression of GFAP, CLDN5, and GAD1. D Barplots of estimated cell type proportions from RNAScope/IF data for “Circle” and “Star” experiments. E Scatter plots of cell type proportions estimated from snRNA-seq data (x-axis) vs. RNAScope/IF, annotated with the Pearson correlation (cor), root mean squared error (rmse), and relative rmse (rrmse) against the mean RNAScope/IF proportions