Circadian rhythms in mammals are controlled by approximately 20,000 neurons in the suprachiasmatic nucleus (SCN) in the hypothalamus. These pacemaker neurons generate rhythmic output signals that coordinate the daily cycles of physiology and behavior of a whole animal. A collaborative project between Dipesh Chaudhury’s and Justin Blau’s labs is studying how 24 hour rhythms in the excitability of these SCN pacemaker neurons are generated. We are generating single cell gene expression profiles of the mouse SCN at different times of day to identify the molecular mechanisms driving rhythmic excitability and sustained depolarization. Circadian pacemaker neurons offer a powerful paradigm to understand how the transcriptional state of a neuron is transformed into rhythmic neuronal activity and ultimately into behavior.