Figure 4. Integrating developmental scRNA-seq datasets to link embryonic heterogeneity to adult interneuron subtypes.

A) Graph-based clustering of interneurons from the adult mouse visual cortex (Data from Allen Cell Types Database (2015)^22,23).

B-D) Integration of P10 (B), E18.5 (C), E13.5 (D) precursors with P56 cortical interneurons based on shared sources of variation. Upper panel: adult cells colored by subtype and precursors cells in grey. Lower panel: precursor cells colored by adult subtype to which they are assigned.

E) Differentially expressed genes between CGE and MGE derived subsets, that are conserved in both developmental and adult cells (left). Each conserved gene is placed on the heatmap when it is first observed to be differentially expressed during development. Same analysis for Pvalb vs. Sst subsets (middle), and Vip vs. Id2 subsets (right).

F) Conditional deletion of Mef2c in inhibitory neurons using Dlx6a-Cre;Mef2c^loxp/loxpRCE . Immunostaining of P20-P22 somatosensory cortex using anti-GFP (green) and anti-Pvalb (red) (DAPI counterstaining shows cortical layers). Scale = 200 μm.

G) Density quantification of cIN subtypes in the P21 somatosensory cortex using antibodies for Pvalb, Sst, Vip, Npy, and calretinin (CR). Error bars reflect s.e of the mean; Two-tailed unpaired t-test, P < 0.01** n= 3 brains each for cKO and control. Error bars reflect s.e of the mean; Two-tailed unpaired t-test, P < 0.01** n= 3 brains each for cKO and control.

H) Scatter plot comparing average expression of GABAergic single nuclei from post-mortem human neurons after segregation into Pvalb and Sst types. Each dot represents the expression of a human gene. Markers of embryonic cardinal types are shown in green or blue dots, with a subset of gene names annotated.