Additional file 6 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 6. Pseudotime trajectory analysis. a UMAP plot of microglia showing all eleven Louvain clusters. b UMAP density plot showing the density of TMEM119 expression. Red star indicates root node for cell ordering. c UMAP plot showing pseudotime trajectories, where cells are colored by pseudotime score. Red star indicates root node for cell ordering. d Ridge plot displaying the pseudotime score of cells in each microglia cluster

Additional file 8 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 8. Nanostring GeoMx workflow and ROI segmenting. a Schematic detailing the workflow of the GeoMx digital spatial profiler platform. b 20x micropictographs displaying single channel CD45 and IBA1 images, the combined image, and how a typical ROI containing a microglial nodule was segmented by intensity thresholding

Additional file 2 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 2. Overlap of DEGs in RE relative to FCD and CTRL. a,b Venn diagrams showing the number of overlapping genes expressed differentially high (a) and differentially low (b) in RE vs CTRL and FCD. c Four-way plot showing FCD expression relative to RE vs CTRL expression relative to RE for each gene

Additional file 10 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 10. CD45+ ROI segment protein expression. Heatmap showing protein expression of 42 protein targets in each CD45+ ROI segment for each sample

Additional file 11 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 11. DEP gene expression in microglia snRNA-Seq. a Volcano plot of significant abundantly expressed proteins detected in microglial nodules versus unaggregated microglia. Red shape and labels highlight DEPs selected for single-nucleus microglia analysis. b tSNE density plots displaying gene expression density in microglia of markers selected in a. c tSNE density plot showing the expression density in microglia where all selected markers are expressed

Additional file 3 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 3. Microglial markers and DEGs in microglial Louvain clusters. a tSNE plot of microglia showing all eleven Louvain clusters. b Violin plots of top five most abundant differentially expressed genes in each microglial cluster, if applicable. c Violin plots illustrating the per-cluster expression of microglia-specific and homeostatic microglial markers

Additional file 5 of Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Additional file 5. Immune modulation and inflammation marker expression differs by disease condition. Ridge plots showing the expression of immune and inflammation markers highlighted in Figure 3, separated by disease condition with accompanying tSNE of microglia for reference