Protocol for flash-freezing, pooling, and preparing single nuclei suspensions from amniote inner-ear sensory epithelia.

The inner-ear sensory epithelia are characteristically difficult to dissociate into healthy single-cell suspensions, with adult tissue presenting the most challenges. Recent advances in RNA sequencing have allowed for transcriptomic profiling of single nuclei, instead of single cells, offering a valuable alternative for processing sensitive tissue for single-cell genomics. Here, we provide a detailed protocol for flash-freezing, pooling, and preparing single nuclei suspensions from mouse and chicken inner-ear sensory epithelia, with a focus on optimization and quality control.