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. 2022 Feb 17;11:e71864. doi: 10.7554/eLife.71864

Figure 2. Common neurogenic lineages in each ganglionic eminence.

(A) UMAP plots displaying all GE-derived cells annotated from left to right by: brain region, putative cell clusters, mouse strain and expression of VZ marker Nestin and SVZ/MZ marker Dcx. (B) UMAP visualizations show transcriptional diversity in each GE region. Several genes are depicted to highlight distinct neurogenic stages: Nestin, Hes5, and Olig2 are indicative of VZ cells (green), Asc1 and Gadd45g label intermediate SVZ cells (blue), and Dcx, Sp9, and Mapt depict postmitotic neuronal precursors (red). (C) UMAP plots of MGE, LGE, and CGE cells annotated via putative cell clusters and including Slingshot analyses depicting developmental progression through neurogenic stages.

Figure 2.

Figure 2—figure supplement 1. Differential gene expression between mouse lines and brain regions.

Figure 2—figure supplement 1.

(A) Violin plots showing expression of pan-VZ-enriched genes from Nes-dVenus mice and expression of SVZ/early postmitotic genes enriched in cells from WT mice. (B–C) Violin plots depicting differential gene expression profiles of cells arising from the LGE (yellow), MGE (blue), and CGE (red). Highlighted genes include those that are predominantly expressed within one GE (B) or display intriguing expression profiles based on scRNAseq and/or in situ hybridization data (C).
Figure 2—figure supplement 2. Integration and visualization of multiple embryonic mouse scRNAseq datasets.

Figure 2—figure supplement 2.

(A–C) Integration of 3 scRNAseq datasets of embryonic mouse ventral telencephalon: This study, E13.5 MGE and E14.5 LGE and CGE dataset acquired via Drop seq from Mayer et al., 2018, and MGE and CGE dataset from two different timepoints (E12.5 and E14.5) acquired via Fluidigm C1 system by Mi et al., 2018. UMAP plots depicting all cells from the three studies annotated by dataset (A), putative cell clusters (B) and expression of Nestin and Dcx (C). (D–E) High Nestin-expressing cells (> 1.5 normalized dataset) were extracted from the combined dataset. UMAP plot annotated by dataset (D) and bar graphs showing the total number of high Nestin-expressing cells present in each study (E).
Figure 2—figure supplement 3. Genes defining common neurogenic cell types between brain regions.

Figure 2—figure supplement 3.

UMAP visualizations highlighting genes that help define VZ (green), SVZ (blue) and MZ (red) cell populations in the MGE, LGE, and CGE. Cells are color-coded according to their levels of expression as per the color scale. Red ovals in LGE and CGE highlight the Ebf1-positive, Mapt-positive, Sp9-negative population of putative immature GABAergic projection neurons.