Protocol for characterizing craniopharyngioma subtypes and their microenvironments using single-cell RNA sequencing and immunohistochemistry.

Here, we present a comprehensive protocol for analyzing craniopharyngioma subtypes and their tumor microenvironments at single-cell resolution. We describe tumor tissue dissociation, single-cell isolation, RNA sequencing library preparation, and bioinformatics analysis procedures. We also detail immunohistochemistry procedures for validating findings. This approach enables the detailed characterization of tumor cellular composition, immune cell networks, and molecular signatures that distinguish adamantinomatous from papillary craniopharyngiomas. For complete details on the use and execution of this protocol, refer to Matsuda et al.1.