Fig. 1: Transcriptomic profiling of the developing mouse VM identifies a dopaminergic gene coexpression module.
From: Distinct radial glia subtypes regulate midbrain dopaminergic neuron development
a, Schematic overview of the experimental workflow. Embryonic tissue from TH-GFP mouse embryos was collected for bulk RNA-seq at E11.5, E12.5, E13.5 and E14.5. Regions sampled included the VM, DM, ventral forebrain, ventral hindbrain and alar plate (L). Bulk RNA-seq data were used to define the transcriptional network of the dopaminergic (mesDA) module. Contributions of individual VM cell types to this network were inferred using scRNA-seq data from the developing mouse VM6. b, WGCNA of the mesDA module, filtered for the top 5% interactions. Node color represents gene expression changes during development, and node size corresponds to mean expression level. c, Contribution of VM cell types to the transcriptional network in b, based on cell-type-specific expression profiles from ref. 6. d, GO term enrichment for the top four contributing cell types of the mesDA module (Rgl1–Rgl3 and ependymal cells), determined using two-sided Fisher’s exact test with Benjamini–Hochberg correction. Individual cell-type transcriptomes based on data from ref. 6. Top, GO biological process (GO:0008150). Bottom, GO cellular component (GO:0005575). e–g, GSEA for mRgl1 (e), mRgl2 (f) and mRgl3 (g). Selected top-ranking terms based on NES from the MSigDB C2 and C5 gene sets (v5.0) are shown. DM, dorsal midbrain; NES, normalized enrichment scores.
