Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction.

Quantifying immediate early gene expression as a marker of cellular activity in single-nuclei RNA sequencing data allows for the identification of neurons involved in specific behaviors. Here, we present a protocol for generating single-nuclei libraries from the mouse brain and identifying active cell populations following social interactions. We describe steps for the dissection, preparation, and analysis of the prefrontal cortex, hippocampus, and cerebellum. This protocol has the potential to be modified for any brain region or behavior of interest. For complete details on the use and execution of this protocol, please refer to Walker and Frost.(1).