Question: Can I use Neo-Clear as an alternative to xylene for Deparaffinization with Xenium In Situ Gene Expression?
Answer: To successfully run our Xenium In Situ Gene Expression assay, FFPE sections placed on the Xenium Slides must be deparaffinized to remove the paraffin wax. Insufficient paraffin wax removal can negatively impact assay performance. Thus, proper deparaffinization is critical to the workflow.
For FFPE Sample Preparation, we recommend the following xylene:
Because xylene can pose health concerns and some facilities have restrictions on using this reagent, we have tested a non-toxic replacement for xylene (Millipore Sigma, catalog #214736 or #534056) for Xenium.
We found that Neo-Clear (Millipore Sigma, catalog #109843) and Xylene (Millipore Sigma, catalog #214736) performed equivalently for deparaffinization from side-by-side testing for Xenium In Situ Gene Expression*. Furthermore, we did not see any impact on assay performance when using Neo-Clear as compared to Xylene.
*We have not tested Neo-Clear for:
- Xenium Prime In Situ Gene Expression with Optional Cell Segmentation Staining
- Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide
- Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining
But, Neo-clear is considered a low-risk reagent swap.
Please note that alternative xylene and xylene-substitute reagent part numbers have not been tested in-house for any Xenium In Situ Gene Expression assays and may compromise assay performance.
Products: Xenium In Situ Gene Expression, Xenium Prime In Situ Gene Expression