DOI RECORD
Xenium Spatial Transcriptomics with Protein add-on Protocol for Human Tissue v2
Abstract
This is a protocol for performing spatial transcriptomics using 10X Xenium with add-on of protein markers. Here we are using custom panel designed to target cell types in the healthy and disease kidneys and discover their spatial relationships. The protocol has many steps involving selecting tissue, tissue sectioning and mounting on slides, processing to prepare for hybridization with custom panel and in situ imaging. This protocol also includes adding protein marker panels commercially available from 10X to further aid in identifying the marked cells and determine RNA and Protein overlap. Post imaging there are number of analyses that can be performed and these will depend on the biological questions where the methods and tools are still evolving, however, we will focus on key QC parameters to evaluate assay performance. Each of the steps from sectioning to data generation have quality assurance and control steps. Post Xenium assay, slides are stained with hematoxylin and eosin for light microscopy and flanking tissue sections are typically used for light microscopy evaluation or other technologies.