Whole-Mount Visualization of Primary Cilia in the Developing Mouse Brain.

Primary cilia are evolutionarily conserved organelles that play critical roles in brain development. In the developing cortex, neural progenitors extend their primary cilia into the ventricular surface, where the cilia act as key signaling hubs. However, visualizing these cilia in a systematic and intact manner has been challenging. The commonly used cryostat sectioning only provides a limited snapshot of cilia on individual sections, and this process often disrupts the ciliary morphology. By contrast, the previously established whole-mount technique has been shown to preserve ciliary architecture in the adult mouse cortex. Here, we adapt and optimize the whole-mount approach for embryonic and neonatal brain, allowing robust visualization of ciliary morphology at the ventricular surface during development. This protocol describes step-by-step procedures for whole-mounting and immunostaining delicate embryonic and neonatal mouse cortices, enabling direct visualization of cilia in neural progenitors in the developing brain. Key features • This protocol adapts the whole-mount technique and applies it to delicate embryonic samples from embryonic day 12 (E12) to neonatal brain (P3). • This protocol details the necessary steps to achieve intact and direct visualization of cilia in the developing mouse cortex. • This protocol also provides the necessary steps for the dissection and visualization of cilia on the lateral ganglionic eminences (LGE) and medial ganglionic eminences (MGE).