Figure 4.

scRNA-seq characterization of the E13.5 cortex prenatally exposed to MeHg

(A) Schematic of prenatal exposure of MeHg to pregnant mice, created with BioRender.com. 0ppm (control) and 0.2ppm MeHg were administered through drinking water to pregnant mice starting at E0 until E13.5 at which point the dorsal cortical cells were collected for multiplexing. Two technical replicates from both 0 and 0.2ppm MeHg treated groups were tagged and pooled for multiplexing RNA-seq. Following demultiplexing, downstream analysis and trajectory inference were performed.

(B) Visualization cells from 0 to 0.2ppm MeHg groups after PCA and UMAP, colored by Seurat clustering and annotated by cell type.

(C) UMAP visualization of 0.2ppm MeHg (red) and 0ppm (blue) treatment groups.

(D) Visualization of the total cell population after PCA and UMAP, colored by expression of key marker genes (Mki67, Pax6, Neurod1, Bcl11b, Reln, GAD2, Clnd5, Rgs5).

(E) Proportion of cells in each cluster for 0 and 0.2ppm MeHg.

(F) Visualization of subclusters of the transitional cell population after PCA and UMAP, colored by Seurat clustering and annotated by cell type.

(G) UMAP visualization of 0.2ppm MeHg (red) and 0ppm (blue) treatment groups in transitional cell population subclusters.

(H) Heatmap of top ten differentially up-regulated genes over four clusters within the transitional cell population.

(I) Proportion of cells in each subcluster within the transitional cell population for both 0 and 0.2ppm MeHg. See also Figure S4 and Tables 1 and 2.