Question: Can I use Xylene alternatives when performing Tissue Deparaffinization during the Visium CytAssist for FFPE assay?
Answer: To successfully run the Visium CytAssist Spatial Gene Expression for FFPE assay, FFPE sections placed on glass slides must be Deparaffinized to remove the paraffin wax. Insufficient paraffin wax removal can negatively impact the stain's quality and the Visium CytAssist for FFPE assay performance. Thus, complete Deparaffinization of the tissue is critical. Because Xylene can pose health concerns and some facilities have restrictions on using this reagent, we have tested non-toxic alternatives to Xylene with the Visium CytAssist for FFPE workflow.
Limited testing was performed with Neo-Clear (Millipore Sigma, PN:1097435000) and Histo-Clear (VWR, PN:101412-878), as Xylene alternatives during the Tissue Deparaffinization step of the IF and H&E Staining Demonstrated Protocols. Based upon side-by-side comparisons across a subset of mouse and human tissues, both Neo-Clear and Histo-Clear were determined to be acceptable alternatives to Xylene. We recommend for optimal assay performance to use Xylene due to the extensive validation yielding consistent results with this reagent and some variability observed with the use of these alternatives. Because of the variability in results we don’t recommend these alternatives as comparable options.
Note: Xylene alternatives were not tested for Hardset Coverslip removal when processing archived slides.
Products: Visium CytAssist for FFPE