Extended Data Figure 4 : Analysis of human NPCs.

From: Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

Extended Data Figure 4

ad, Differentiation potential of human SVZ NPCs. Human SVZ NPCs isolated from 19-week-old fetuses form neurospheres in culture (a), and can be differentiated to neuronal (neurofilament, b), oligodendrocytic (OLIG2, c), or astrocytic (GFAP, d) lineages in vitro. Scale bars, 25 μm (a), 10 μm (bd). We note that although OLIG2 can represent different cell types, it is expressed at a low level in the fetal NPCs before differentiation (an average log2(TPM + 1) of 0.82, compared to a threshold of 4 that we use to define expressed genes in our analysis, and with zero cells with expression above this threshold). Thus, the undifferentiated NPCs do not express OLIG2, and we interpret the expression of OLIG2 as a sign of oligodendroglial lineage differentiation. e, f, Single-cell RNA-seq analysis of NPCs. e, NPCs have an expression program similar to the oligodendroglioma stemness program. Heat map shows the expression of genes (rows) most positively (top) or negatively (bottom) correlated with PC1 of a PCA of RNA-seq profiles for 431 single NPCs, across NPC cells (columns) rank ordered by their PC1 scores. Selected genes are indicated, and a full list of correlated genes for PC1 and PC2 is given in Supplementary Table 2. f, NPC cell scores for PC1 (y axis) and PC2 (x axis). PC2 correlated genes are associated with the cell cycle. Cells with the highest PC1 scores tend to be non-cycling (low PC2 score), indicating that while the stemness program is coupled to the cell cycle in oligodendroglioma, it is decoupled from the cell cycle in NPCs.