Fig. 5
Astrocyte-plated and micro-isolated cultured microglia are marked by a culture shock gene set. a Volcano plot of the pseudo-bulk analysis comparing all astro-plated cells to freshly isolated cells. Genes significant with adjusted p-value < 0.01 and abs (average logFC) > 1 are highlighted in red. Meeting our strict criteria, we found 9 genes significantly decreased in the cultured microglia and 231 genes significantly increased. b Pseudo-bulk analysis of Micro-isolated in vitro cells compared to freshly isolated microglia. Genes with adjusted p-value < 0.01 and abs (average logFC) > 1 are highlighted in red. We see similar genes upregulated in this comparison as in the astro-plated in vitro comparison, though at relatively higher p-values. c Pseudo-bulk differential expression volcano plot of a direct comparison between the two culturing methods, micro-isolated in vitro cells compared to astro-plated in vitro cells. Highlighted in red are genes with adjusted p-value < 0.01 and abs(average logFC) > 0.5. d Heatmap showing the individual cell expression of the top 20 up- and downregulated genes found in a. 2000 downsampled cells are used for visualization purposes. e Venn diagram set comparison of the differentially expressed genes (DEG) with abs (average logFC) > 0.5 in the pseudo-bulk micro-isolated versus freshly-isolated microglia, compared astro-plated in vitro versus freshly-isolated microglia