This Technical Note provides guidance for designing and using custom probes, including probe pooling and dilution. The document also includes data highlighting custom probe specificity. Additional optimization may be required. Performing a pilot experiment with these unsupported workflow modifications is recommended prior to larger studies. For use with the following probe-based assays: both singleplex and multiplex experiments for Next GEM and GEM-X Flex Gene Expression v1, Visium v2, and Visium HD.

For these assays, 10x Genomics provides a pre-designed whole transcriptome panel of probes for target hybridization. Custom probes may be designed for use with these assays 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.