Figure 5

Gene expression profile of PD-microglia in human midbrain post-mortem samples. The human midbrain microglial expression of 100-plex gene panel was studied with Molecular Cartography from healthy and PD-patient midbrain samples. (a) Detected transcripts can be visualized with ImageJ and the single-cell analysis was carried out with automatic sell segmentation and assignment of transcripts to cells. (b) Visualization of annotated cell types in uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) form. (c, d) Expression of microglial markers in the microglia cluster between different microglial classes presented as distribution percentage of average expression. Expression of genes which were (e) differentially expressed between all three classes, (f) enriched in consensus PD-microglia and (g) decreased expression in non-consensus PD-microglia. (h) Genes that were microglia class-specific. For the midbrain samples, n = 8 controls, n = 7 PD patients, one section per sample. Data presented as distribution percentage of average expression between the microglial classes, differential expression analyzed with the Wilcoxon rank sum test.