10X Xenium In Situ Gene Expression for Fresh-Frozen Kidney v1

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Abstract
This is a protocol for preparing fresh-frozen kidney tissue for in situ spatial transcriptomics using a custom probe panel with the 10X Xenium Analyzer platform. Slide preparation is a multi-day process encompassing cryosectioning, probe hybridization, subsequent ligation and amplification, quenching and nuclei staining, and in situ imaging. Each phase of the workflow is extensively detailed within published 10X User Guides, which are cited throughout this version. After data is collected, slides are H&E stained for histopathological evaluation of healthy and diseased tissue, and used for integrated data registration to neighboring images and modalities. There are sample evaluation and QC measures built into the 10X protocols, which are carefully observed in addition to our own go/no-go criteria.