Protocol using AGO-APP for isolation and sequencing of argonaute-bound miRNAs in specific neuronal subtypes of the mouse brain

Argonaute protein affinity purification by peptides (Ago-APP) is an immunoprecipitation-based approach that isolates argonaute-bound, putatively active microRNAs (miRNAs) via expression of a T6B peptide. Here, we present a protocol for the application of Ago-APP to olfactory bulb interneurons in mice expressing a Cre-dependent T6B transgene. We outline procedures for maintaining these transgenic mice, performing T6B immunoprecipitation from brain tissue, and preparing miRNA sequencing libraries. This workflow can be applied to specific neuronal subtypes and even subcellular compartments as well as extended to other models, including Drosophila. For complete details on the use and execution of this protocol, please refer to Kapoor et al.1