Question: How were the Transcriptome Probe panels designed?
Answer: We designed our FFPE Transcriptome probe sets to target conserved regions of the protein-coding transcriptomes of humans and mouse. We designed the probes to be specific for their target transcript. Probes were validated in silico, in vitro, and in tissue.
- To limit sequencing requirements, we have not included probes against mitochondrial or ribosomal genes in the assay.
- A subset of probes targeting highly homologous genes is not directly specific for a single gene target. To maximize flexibility for the assay, we have included these probes but separated them in analysis. By default, SpaceRanger will exclude these probes; customers will have the option to include them in the analysis if relevant for their experiment.
- If included, these probe pairs should be treated as measuring the presence of at least one of the homologous genes targeted.
- No-target, negative control probes were tested in the development of this assay. No specific ligation events were detected using these negative controls during development. These probes were therefore excluded from the final panel sets.
Products: Visium for FFPE