FFPE Human Brain Tissue Quality Control for Xenium v1

The Xenium In Situ Gene Expression platform from 10x Genomics enables high-plex, targeted RNA detection at subcellular resolution, supporting spatially resolved cell typing and molecular profiling. While an optimized workflow has been provided by 10x, formalin-fixed paraffin-embedded (FFPE) post-mortem human brain tissue presents unique challenges due to its heterogeneity and lipid-rich composition. In particular, the quality and integrity of FFPE tissue blocks vary considerably across donors and brain regions. Rigorous quality control prior to Xenium assays is necessary. In this protocol, we describe a standardized pre-assay QC and region of interest (ROI) selection workflow for FFPE human brain tissue. Tissue sections undergo deparaffinization followed by histological and molecular quality checks, including hematoxylin and eosin (H&E) staining to assess morphology, DAPI staining to evaluate nuclear integrity, and immunofluorescent staining to identify ROI regions. These QC steps enable the identification of regions with preserved morphology and targeted protein markers, ensuring that selected ROIs are biologically relevant and suitable for high-quality Xenium analysis.