Fig. 2.

Data integration highlights Notch inhibition–induced molecular changes in NSCs.

(A) Low-dimensional embedding of qNSCs after integration of LY-treated and control datasets (Fig. 1, H and I, and fig. S2A). Cells are colored on the basis of the refined cluster annotations derived from integrated analysis; cluster q1 resolves into six clusters (1a to 1f), cluster q4 into two clusters (4a and 4b), and a previously overlooked cluster 8 is identified. (B) Violin plot comparing the expression of ascl1a and ccnd1 across all clusters for control and treated cells (clusters colored as in A). y axis: number of reads normalized for sequencing depth. (C) Depiction of the over or under-representation of distinct subpopulations of qNSCs between control and treated datasets (clusters are color coded as in Fig. 2A). The further a curve is shifted away from the central line, the more a given cluster is enriched (to the right) or depleted (to the left) in the LY-treated dataset. (D) Low-dimensional embedding of cycling cells after integration of LY-treated and control datasets. Cells are colored on the basis of the refined cluster annotations derived from integrated analysis. Cluster 1 in green represents cycling NSCs and clusters 2 to 6 represent IPCs progressively more advanced in the cell cycle. (E) Violin plot comparing the G₁/S and G₂/M scores across all clusters of cycling cells for control and LY-treated cells (clusters colored as in D). Absolute values do not reflect direct expression of genes and comparison must rely on relative values of each score. (F) Depiction of the over or under-representation of distinct subpopulations of cycling cells between control and LY-treated datasets (clusters are color coded as in D). Interpretation as in (C).