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Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression

  • CG000709_Post-Xenium_TechnicalNote_RevB.pdf

    Technical Note, CG000709


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Tissue sections processed using the Xenium In Situ workflow remain largely intact post-run and can be used for additional applications. Examples of compatible Xenium post-run workflows include immunofluorescence (IF) staining, H&E staining, and whole transcriptome spatial RNA sequencing using the Visium CytAssist Spatial Gene Expression workflow. This Technical Note highlights the experimental steps and key data metrics obtained downstream of the Xenium (Post-Xenium) workflow on the same FFPE or FF tissue sections, in relation to controls not processed through the Xenium workflow.

Modifications to documentation (Demonstrated Protocols and User Guide) provided here are unsupported. We cannot guarantee assay performance even when implementing the guidance listed in this article and therefore, customers should proceed at their own risk. 10x Genomics Support will not be able to provide additional information beyond this article or replacement reagents.

To import post-Xenium image files to Xenium Explorer, images must be in pyramidal, tiled, OME-TIFF format. Refer to the Xenium Explorer support website for compatible file format details.

Document Type
Technical Note

Last Modified
April 16, 2024