Figure 3.

Diversity of Ventricular Zone Cell Types

Single-molecule RNA FISH (RNA smFISH) was performed at three anteroposterior positions and three developmental time points, each with eight genes detected in the same single tissue section by sequential hybridizations. For clarity, the panels of this figure show subsets of markers, but all eight markers were stained for in the same single sections.

(A) Schematic of coronal sections taken in anteroposterior axis over several developmental time points, not to scale.

(B) Representative images of sequential RNA smFISH with eight probes over three cycles and corresponding composite.

(C) The expression of genes selected for RNA smFISH in mouse and human VZ cell types shown as violin plots. The violin plots represent the posterior probability distribution for the expressed number of mRNA molecules per cell type. Grey, enriched over baseline with posterior probability >99.8%. Right axis shows absolute molecule counts.

(D) Diagram showing the spatiotemporal location of cells discovered by RNA smFISH in the sections shown in (A). VZ, ventricular zone; PA, parenchyma. Representative images are shown in Figure S5.

(E) RNA smFISH showing the distribution of Msx2, Ednrb, and Slc6a11 in the E11.5 ventral midbrain.

(F) Signal for Rfx4 on the same section as (E), shown separately for clarity.

(G) Inset as indicated in (E).

(H) Inset as indicated in (E).

(I) Inset as indicated in (E).

(J) RNA smFISH showing the distribution of Rfx4, Msx2, and Slc6a11 in the E13.5 ventral midbrain.

(K) Inset as indicated in (J) with additional markers Pdgfra, Sox10, and Ednrb. ^∗, putative mRgl2 cell; arrow, putative intermediate between Rgl2 and OPC.

(L) Inset as indicated in (J) showing markers in (K) in addition of Cd36.

(M) RNA smFISH showing the distribution of Rfx4, Cd36, and Slc6a11 in the E15.5 ventral midbrain.

(N) Inset as indicated in (M) with additional markers Pdgfra, Sox10, Foxj1, Msx2, and Ednrb. ^∗, putative mRgl2 cell; arrow, putative mOPC located in the parenchyma.

(O) Inset as indicated in (M) with additional markers Pdgfra, Sox10, and Ednrb in the VZ.

(P) RNA smFISH showing Foxj1, Msx2, Slc6a11, and Ednrb. Arrowheads indicate putative ependymal cells in VZ.