Figure 3.

Nuclear encoded mitochondrial transcripts differentiate neurons by neurotransmitter identity and anatomical location. A, Volcano plots were assembled using the Allen single-cell RNAseq dataset. A total of 50,002 pyramidal glutamatergic neurons were compared with 22,745 GABAergic interneurons. Volcano plots are organized by subunits belonging to the mitochondrial ribosome, electron chain complexes I to V, and the SLC25A family of solute transporters. The mitochondrial ribosome and the SLC25A family of transporters are the most dissimilarly expressed transcripts when comparing GABAergic with glutamatergic neurons. B₁, t-SNE cell atlas generated with the expression levels of all transcripts encoding mitochondrial ribosome subunits. The t-SNE atlas encompasses >20 areas of mouse cortex and hippocampus, totaling 76,307 cells. Color codes denote brain regions annotated by the Allen Brain Atlas. B₂ shows B₁ data after 100 consecutive permutations. Anatomical segregation is lost. C, Diagram explaining strategy for cell type and anatomic callout in t-SNE atlases. GABAergic neurons were color-coded green and glutamatergic neurons were color coded gray. Cell type and anatomic region were marked by a triangle. D, t-SNE atlas shown in B₁ that was layered with the neurotransmitter identity of cells and anatomic location of cells (triangles). GABA, parvalbumin (Pval), somatostatin (Sst), γ-synuclein (Sncg), vasointestinal peptide (Vip), and lysosomal-associated membrane protein family member 5 (Lamp5) denote markers defining specific interneuron subpopulations. E, t-SNE atlas shown in B₁ but layered with the subtype of interneuron (triangles).