Question: Can I use PDX/xenograft tissue with Chromium Fixed RNA Profiling?
Answer: At this time, PDX/xenograft models are not supported with any of our assays. Our experience with multi-species data is limited to the characterization of multiplet rates with our single-cell gene expression products using a 1:1 ratio of cells from each species. You can read about this here: How does cellranger count identify multiples?
Concerning Chromium Fixed RNA Profiling 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 actually work on mouse transcripts and vice versa.
In most PDX/xenograft samples, the human tissue is the topic of study, while the mouse tissue is viewed as contamination. Therefore, it might be possible to use the Chromium Human Transcriptome Probe Set v1.0 during the workflow and limit the analysis to only the human cells during the analysis. It may be possible that the mouse cells would cluster on their own in the t-SNE, and researchers could then limit the analysis to the clusters of human cells. However, this requires researchers to identify which clusters are human or mouse by identifying marker genes/probes that are able to differentiate the two populations. We have not tested any approach for this purpose, so this is unsupported and performance cannot be guaranteed.