Question: Can I use Xylene alternatives for Deparaffinization with Visium for FFPE?
Answer: To successfully run our Visium for FFPE assay, FFPE sections placed on the Visium Spatial Gene Expression Slide must be Deparaffinized to remove the paraffin wax. Insufficient paraffin wax removal can negatively impact the stain's quality and the Visium for FFPE workflow. Thus, proper Deparaffinization is critical to the workflow. Because Xylene can pose health concerns and some facilities have restrictions on using this reagent, we have tested non-toxic replacements for Xylene with the Visium for FFPE workflow.
We found that Neo-Clear (Millipore Sigma, catalog #109843) and Xylene performed equivalently for Deparaffinization from side-by-side testing. Furthermore, we did not see any impact on assay performance when using Neo-Clear as compared to Xylene. Therefore, either Xylene or Neo-Clear can be used to perform Deparaffinization when carrying out the Deparaffinization, H&E Staining, Imaging & Decrosslinking, or Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging Demonstrated Protocols for Visium Spatial Gene Expression for FFPE.
We are currently updating our documentation to reflect this alternative.
Products: Visium for FFPE