Single-cell RNA-seq (10X Genomics Chromium) of LGE, MGE, CGE, and Cortex from mouse embryonic forebrain

We performed single-cell RNA sequencing to characterize transcriptional heterogeneity of neural progenitors within the ventricular zone and subventricular zone of E12.5 and E14.5 mouse cortex and ganglionic eminences. By using a transgenic mouse line (Nestin-d4-Venus) to enrich for VZ cells, we detect significant transcriptional heterogeneity within VZ and SVZ progenitors, both between forebrain regions and within spatial subdomains of specific GEs. Overall design: LGE, MGE, CGE, and cortex from E12.5 and E14.5 mouse embryos.