OVERVIEW: Project Summary A comprehensive understanding of how neural circuits spanning the entire brain generate the full repertoire of perception and behaviors requires a list of brain cell types, as well the means to target each cell type in order to interrogate the functional interactions that give rise to the emergent properties of the whole system. To address these challenges, the “Center for Epigenomics of the Mouse Brain Atlas” (CEMBA) will focus on “epigenetic profiling”, for identification, cataloging, characterization and genetic targeting of mammalian brain cell types, an approach that is complementary to RNA expression analysis. The Center will conduct an integrated set of experiments that together will serve to identify, characterize and make genetically accessible, cell types across the entire nervous system. More than 1 million single neurons across the whole brain will be subjected to single cell epigenetic profiling. Cell types emerging from these profiles will be linked to anatomy for detailed characterization of their locations, morphology, and brain-wide connectivity and projections. And genetic profiling data will be used to generate tools to target gene expression to and interrogate the roles of cell types. By focusing on epigenetic profiling, the Center will harness knowledge of gene regulatory mechanisms to identify cell-type specific genetic enhancers. As has been the case in previous efforts to generate mouse lines on the basis of gene expression profiling, efforts will include both bottom up and top down approaches. Knowledge of differences in the connectivity/anatomy of cell types will be used to allow epigenetic profiles to be linked to anatomy. Knowledge of epigenetic differences between cell populations will be used to identify enhancers, which restrict gene expression to neuronal populations that will be subsequently subjected to detailed characterization. The CEMBA-Data Core will collect, manage, analyze, visualize and distribute brain cell-type and anatomical data. Finally, the Administrative Core will effectively coordinate activities within the center and between cooperating centers in the Brain Cell Census Network.