Figure 3.

RNA-Seq analysis revealed cell type-specific gene expression profiles. A, Dendrogram and unsupervised hierarchical clustering heat map (using Euclidean distance) of purified cortical glia, neurons, and vascular cells. The vertical distances on each branch of the dendrogram represent the degree of similarity between gene expression profiles of various samples. Biological replicates showed the highest degree of correlation represented by short vertical distances. Cells in the oligodendrocyte lineage cluster closely together, and the order of the three oligodendrocyte-lineage cell types corresponds to their maturation stages (OPC–NFO–MO). Although astrocytes and oligodendrocytes are both glial cells, their gene expression profiles are as different between each other as they are different from neurons. Consistent with their embryonic origin, mesodermal-derived endothelial cells and microglia cluster farther away from ectoderm-derived neurons, astrocytes, and oligodendrocytes. B, The top 40 enriched genes per cell type are shown in a heat map. Only highly expressed genes with FPKM >20 are included in this analysis. Fold enrichment is calculated as FPKM of one cell type divided by the average FPKM of all other cell types. The majority of these genes showed specific expression by only one cell type, with the exception that some are expressed during more than one maturation stage in the oligodendrocyte lineage.