In order to better understand the forces that drive gene expression diversity in the mammalian nervous system, we next examined the expression of neurotransmitters and neuropeptides. We examined the co-expression of neurotransmitters while retaining information about the tissue compartment (Figure S6A). While glutamate (VGLUT2) was the only neurotransmitter expressed in all compartments, GABA contributed the larger number of cell types and was mostly concentrated in the forebrain. GABAergic and glutamatergic (VGLUT1 and VGLUT2) neurotransmission was mutually exclusive; we did not find a single cell type anywhere in the nervous system that expressed both. Glutamatergic neurons in the telencephalon all used VGLUT1, with some additionally using VGLUT2, whereas in more caudal regions, VGLUT2 dominated. Interestingly, the boundary that separated VGLUT1 dominance from VGLUT2 dominance appeared to be the telencephalon-diencephalon border, analogous to the separation of the two major types of astrocytes at this same boundary (although both were expressed in the thalamus).
