Fig. 5

RNA seq analysis of pro-vs. anti-inflammatory environment in the model of αsyn cell-to-cell transfer. a MDS plot maintains distance between samples based on normalized CPM expression data for all mapped genes. b Volcano plot of RNA-Seq data where –log10(p-value) is plotted against the log2 fold change expression difference between LPS and IL-4 treatments for every mapped gene. The horizontal dotted red line corresponds to a FDR of 0.05 and the vertical dotted lines correspond to expression changes of 2-fold. Color corresponds to the median gene expression (CPM) in the PBS treatment group. c The top 50 signature genes were given for each of 10 cell types in Gokce et al. 2016. The ratio of genes for each cell type that are also significantly different (IL-4 vs. LPS: FDR < 0.05) are plotted. d Hierarchical clustering (eucledian distance, average linkage) of the RNA-seq results FPKM for the top 50 signature microglial genes with ratio of median LPS/median IL-4 expression. e Hypothesis driven gene ontology enrichment. A subset of biological process gene categories was selected. The enrichment significance measuring the overlap between gene members in these categories and significantly DE expressed genes is plotted. CPM; count per million, FDR; false discovery rate, FPKM; Fragments Per Kilobase Million, MSD; Multidimensional scaling