Extended Data Figure 6. Gene sets corresponding to GABAergic interneurons and proliferating layers also are highly expressed in the ganglionic eminences.

To examine the relationship between genes enriched in the cortical VZ, including gene modules associated with GABAergic interneurons and mitotically active proliferative cells, WGCNA was performed on the combined cortical and GE samples (referred to as the "GE network"). a. Genes from module C31 in the whole cortex WGNCA (GABA neurons) are assigned primarily to three modules in the GE network. GE31a has a similar pattern in cortex as C31, is highly expressed in GE and is enriched in genes associated with GABAergic interneurons. Other genes from C31 were assigned to modules with other cortical patterns and functional ontological associations (GE31b, GE31c). b. Genes from module C38 in the whole cortex WGNCA also divide primarily into three GE modules that are enriched in both the cortical germinal layers and the GE. These modules are enriched for genes expressed in astrocytes, potentially reflecting expression in radial glia, and are associated with cell cycle. For all plots, module eigengene (ME) expression is averaged across brain and layer (as in Fig. 3b of the main manuscript), also including LGE, MGE, and CGE (referred to here collectively as GE). Numbers in parentheses below each plot show the number of genes from module C31 in a, or C38 in b, out of the total number of module genes in the newly-generated network. One representative enrichment category for each module is shown with enrichment p-value.