Defining cell types that constitute the brain is a critical step towards understanding the relationship between brain structure and function. We are building a state-of-the-art single-cell transcriptomic atlas of adult male and female mouse brains by employing standardized experimental and computational pipelines. I will present a joint analysis of cortical and hippocampal areas based on more than 1 million single cell transcriptomes derived by two experimental platforms. As we reported previously, most GABAergic cell types are shared among cortical areas, whereas glutamatergic types show regional specificity. However, hippocampal GABAergic neurons show distinct gene expression signatures, and glutamatergic neurons in some neighboring cortical regions show gene expression differences that present themselves as continua. I will present new approaches that utilize single-cell transcriptomic and epigenomic information to enable genetic access to cell types and classes for investigating their function.