This document outlines the protocol for executing the Xenium In Situ Gene Expression workflow from probe hybridization to the Xenium Analyzer sample.

Xenium In Situ Gene Expression - Probe Hybridization, Ligation & Amplification

Prepare tissue sections on Xenium slides for on-instrument analysis by following our step-by-step User Guide/Protocols.

Assay

The Xenium In Situ enables high-throughput subcellular mapping of 100s of RNA targets, revealing new insights into cellular structure and function. The platform includes a versatile and easy-to-use instrument, sensitive and specific chemistry, and a diverse menu of customizable panels.

Plan ahead by referring to the list of equipment, kits, and reagents needed for the Xenium Gene Expression.

Experimental Design

Experimental Design & Planning

Learn about the pre-designed Gene Expression panels and engage with 10x design experts to design, order, and manufacture Xenium Custom Genes.

Panel Design

For proper tissue handling and preparation techniques to preserve the morphology, quality, and integrity of tissue sections, refer to our Demonstrated Protocols for FFPE.

Tissue Prep for FFPE

For proper tissue handling and preparation techniques to preserve the morphology, quality, and integrity of tissue sections, refer to our Demonstrated Protocols for Fresh Frozen.

Tissue Prep for FF

Tissue Prep for Fresh Frozen

Refer to instrument-specific documents for seamless instrument operation.

Instruments

Details about the algorithms used in the Xenium onboard analysis pipeline and the generated output files.

Onboard Analysis

Analyze your Xenium data using our visualization tools.

Xenium Explorer

Xenium Explorer Software

Safety Data Sheets

Xenium Analyzer

In Situ Gene Expression

Overview

Documentation

Datasets

Videos

What is In Situ Gene Expression?

Find resources, from protocols to free-to-use analysis tools. Workflow varies based on your sample type. Xenium In Situ Gene Expression currently supports both fresh frozen and FFPE samples.

Access free, publicly available data from a number of different sample types generated with Xenium In Situ solutions.

Xenium In Situ Tissue Preparation

Xenium In Situ Assay Protocols - Best Practices

Find answers to common technical questions, from sample prep through data analysis, about In Situ workflows. 

Xenium In Situ Gene Expression - Probe Hybridization, Ligation & Amplification

User Guide, CG000582

CG000582_XeniumInSitu_GeneExpression_UserGuide_RevA.pdf