Question: Can I use PDX/xenograft tissue with Visium for FFPE?
Answer: At this time, PDX models are not fully supported for any of our assays. Our experience with multispecies data is mostly limited to the characterization of multiplet rates with our single-cell products using a 1:1 ratio of cells from each species. You can read about this here: How does cellranger count identify multiples?
Concerning Visium for FFPE specifically, the probes will have difficulty discriminating between mouse and human transcripts when using PDX/xenograft samples. Given that the probes have not been optimized for species specificity, it may be challenging to disentangle the results. We are not sure how many human probes would work on mouse transcripts and vice versa. If there are human probe detections, it may not come from successful detection of human mRNA (as human and mouse references are quite similar).
In most PDX/xenograft samples, the human tissue is the topic of study, while the mouse tissue is viewed as contamination. Therefore, using the Human Transcriptome Probe Panel may be possible during the workflow and limit the analysis to only the human tissue during the tissue selection process. If this approach is taken, there will likely be reads lost due to mouse transcript detection. This approach is untested, unsupported, and performance cannot be guaranteed.
Products: Visium for FFPE