Neuronal ensembles are functional units in the brain; ensembles are built by distinct neuron types that contribute differentially to information processing depending on the physiological range allowed by their gene expression and molecular properties. In this chapter, we describe single-nuclei RNA sequencing and biSNE analysis, a key method to characterize the molecular signatures and patterns of gene expression that define distinct subtypes of neurons. These subpopulations often underlie specific brain functions influencing behavioral states, both in health and disease.