Question: Can slides be further processed with H&E staining or another stain after a Xenium Analyzer run?
Answer: It is possible to perform optional staining of Xenium slides post Xenium Analyzer run. We have a validated H&E staining demonstrated protocol outlined in Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining.
Prior to post-Xenium Analyzer run H&E staining, we have found removal of Autofluorescence Solution can improve assay performance as the purple color may make H&E stain darker than anticipated. This utilizes Sodium hydrosulfite (Sigma, 157953). Additional details about this can be found in H&E Staining Demonstrated Protocol.
Additional staining methods are not officially supported, but theoretically possible. For example, antibody-based detection methods (immunofluorescence labeling, IF) are described in “High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue”. This paper details how one might perform IF staining on a breast cancer FFPE tissue assayed with Xenium. We do not recommend quencher removal prior to IF staining.
Products: Xenium In Situ Gene Expression