Fig. 1

Meta-analysis of mouse gene expression datasets from microglia and peripheral monocyte/macrophage populations derived from bone marrow, blood, spleen and peritoneum. (a) Venn diagram representing commonly expressed genes across the analyzed RNA sequencing and microarray datasets for microglia (red) and peripheral monocytes/macrophages isolated from bone marrow, blood, spleen or peritoneum (blue). Bioinformatic analysis of the five different expression studies identified 143 microglia-specific genes and 145 genes specific for peripheral monocytes/macrophages. The number of microglia and peripheral monocyte/macrophage genes exclusively expressed in each of the datasets is represented. (b) Heat map representing gene expression (Z-score) of the identified 143 microglia-specific and 145 peripheral monocyte/macrophage-specific genes in each of the analyzed gene expression datasets. Hierarchical clustering identified modules of microglia-specific and of peripheral monocyte/macrophage-specific genes based on the dendrogram. For microglia, the module with the highest differential gene expression of identified microglia marker genes containing St3gal6, P2ry13, P2ry12, Sparc, Slco2b1, Gpr34, Slc2a5, Sall1, Siglec-H, Olfml3, Tmem119, Hpgds and Fcrls was selected for further analysis. For peripheral monocytes/macrophages, the two modules with highest differential gene expression containing the genes F10, Emilin2, F5, Slpi, Fn1, C3, Anxa2, Gda, Mki67, Cd24a, S100a6, Mgst1, Sell and Hp were selected for further analysis. (c) Representation of the expression levels for each of the selected microglia- and peripheral monocyte/macrophage-specific genes in different CNS cell types, including microglia/macrophages, neurons, astrocytes and oligodendrocyte precursor cells (OPCs), newly formed oligodendrocytes, myelinating oligodendrocytes and endothelial cells. FPKM values were extracted from the online database Brain-RNA-Seq (Zhang et al. 2014). The threshold FPKM expression value for excluding genes as microglia markers was set to 25, leading to elimination of St3gal6, Sparc, Slco2b1, Sall1 and Hpgds as microglia markers for further validation. Threshold FPKM expression value for excluding genes as peripheral monocyte/macrophage markers was set to 10, leading to elimination of Slpi, Fn1, Anxa2, Cd24a, S100a6 and Mgst1 as monocyte/macrophage markers for further validation