Abstract
Multiplexed immunohistochemistry enables analysis of cellular and signaling events in the context of an intact organ. Here, we describe protocols for applying multiplexed immunohistochemistry to the mouse thymus. In particular, we describe how to identify cells at the specific differentiation stage known as β-selection, and to monitor pre-TCR signaling and the cellular response at that stage. For complete details on the use and execution of this protocol, please refer to Allam et al. (2021).