This Technical Note provides guidance for custom probe design, spike-in, and analysis for Visium Spatial Gene Expression for FFPE, Visium CytAssist Spatial Gene Expression, and Chromium Single Cell Gene Expression Flex for Singleplexed Samples (Fixed RNA Profiling). Additional optimization may be required. Performing a pilot experiment with these unsupported workflow modifications is recommended prior to committing to larger studies.
For both platforms, 10x Genomics provides a pre-designed whole transcriptome panel of probes for target hybridization. Custom probes may be designed for use with either assay using the guidance provided in this document. While no impact on assay performance is anticipated, the use of custom probes in these assays is not supported or validated by 10x Genomics. 10x Genomics cannot guarantee that custom probes will yield data comparable to that from the whole transcriptome panel.