Question: Are alternative autofluorescence quenching protocols compatible with Xenium?
Answer: Alternative autofluorescence quenching protocols or modification of the quencher concentration is not currently recommended for any tissue type. The Xenium In Situ Gene Expression autofluorescence quencher is proprietary. We have tested different concentrations of this reagent across a variety of sample types. The current dilution has been carefully optimized to mitigate autofluorescence across a wide variety of supported tissues. In addition, we have calibrated the Xenium Analyzer optics and chemistry to work well with our quencher, for example optimized exposure times. We would not recommend modifying the quenching protocol or making tissue autofluorescence assessments on another microscope platform prior to a Xenium Analyzer run.
Instead, we would recommend performing a pilot experiment to see how well Xenium In Situ Gene Expression works with your sample type. For highly autofluorescent tissues, you may observe lower quality data in highly autofluorescent regions. But these data should still be useable. We are happy to review any pilot datasets you might have.
Product: Xenium In Situ Gene Expression