Question: Is it possible to design Xenium advanced custom probes for my target?
Answer: Advanced custom probe design is enabled for both Xenium V1 and Xenium Prime chemistries but their requirements differ. For Xenium V1, design of the advanced custom probe is possible if a target yields at least one 40 base unique sequence that is specific to the target. We allow the target region to go down to 32 bases. For Xenium Prime, please allow for 70-80 base genomic target regions.
The odds of successful advanced target detection increases if the target can yield multiple unique sequence contexts that then also allow for good probe metrics (Tm, preferred-ligation junction etc). We recommend BLAST to see if the sequence has any off-target hits.
- Exogenous targets such as GFP are generally amenable to advanced probe design. Same goes for exogenous species genes, e.g. a human gene in mouse tissue.
- We have reports of success of SNV probes that distinguish single nucleotide variants. The key is to place the SNV at the ligation junction.
- For Xenium V1, we provide guidance on advanced custom probe design in the tech note here. At this time, we do not have similar guidance to offer for Xenium Prime.
- See Support site documentation here for details on how to specify advanced custom target information.
The 10x Applied Bioinformatics team can look into designing advanced custom probes only if researchers submit an advanced custom design request. We outline the steps for submission here.
When researchers submit the advanced custom design request, this will generate a support ticket for the 10x Applied Bioinformatics team. Researchers can then share FASTA format cDNA sequences of the advanced custom targets to this ticket if they would like assistance deriving probes.
Product: Xenium In Situ Gene Expression
Last modified: September 12, 2024