The Xenium Panel Designer will check your gene list and provide feedback if any problems or ambiguous genes are encountered for human or mouse samples. You can modify the list based on the feedback before moving to the next step.

Enter a list of gene names and/or Ensembl IDs. Sort the list from most to least important to help us prioritize genes to retain for the final design.

• For add-on custom panels, up to 100 genes can be added to a 10x pre-designed panel.
  • For Xenium v1 designs: The add-on panel list should not include genes that are already in the selected pre-designed panel. These will be flagged for removal during panel review.
  • For Xenium Prime 5K designs: The add-on panel list may include pre-designed genes for which you would like to enhance sensitivity (read more below).
• For standalone custom panels, up to 480 genes are supported.
• Recommended for any panel type: submit ~10-20 additional genes in case any in the main set need to be replaced during the design process.

It is important that the gene symbols and Ensembl IDs match the features in the human or mouse 2020-A reference GTF file exactly. Refer to the relevent GTF file (gene_name, gene_id) or the CSV lists below to check the accepted format.

• If provided, the Ensembl IDs should not include "version decimals" (e.g., "ENSG00000010404" is ok, while "ENSG00000010404.3" is not).
• The Ensembl IDs must be the gene ID (ENSG, ENSMUSG) not the transcript ID.

For Xenium v1 panels, 10x Genomics can design probes for these human and mouse genes, which cover:

• 96.8% of the human transcriptome and 99.7% of the human coding transcriptome
• 85.4% of the mouse transcriptome and 99.8% of the mouse coding transcriptome

For Xenium Prime panels, 10x Genomics can design probes for these human and mouse genes, which cover:

• 99.5% of the human transcriptome and 99.4% of the human coding transcriptome
• 99.7% of the mouse transcriptome and 99.6% of the mouse coding transcriptome

The files below list the genes that are not covered by our existing probes per assay chemistry based on their respective human or mouse 2020-A reference transcriptomes (gene name, Ensembl ID, and gene type). These genes are not available in 10x pre-designed panels and should not be included in custom design requests.

• Xenium v1: Human genes, Mouse genes
• Xenium Prime: Human genes, Mouse genes

Gene boosting is enabled in the Xenium Panel Designer starting December 2024 to increase sensitivity (measured as transcripts per cell) on pre-designed genes from a Xenium Prime 5K panel for custom add-on panel requests (see release notes).

For either the standard or advanced workflows, follow these steps during gene list creation:

1. Gene List: Include the Xenium Prime pre-designed genes you want to boost sensitivity for in your list. We recommend entering these genes at the top of the list to make sure they are included in the next steps.

   Keep in mind that boosted genes count towards the up to 50 or 100 add-on gene total. For example, a 100 add-on panel can be composed of 80 custom add-on genes and 20 boosted pre-designed panel genes.

2. Clean Up Genes: The app unselects pre-designed genes by default ("Include" colummn). Re-select them to follow the gene boosting workflow.

   
   
   

3. Enhance sensitivity for pre-designed genes: Adjust probe set counts to increase the sensitivity of these genes. You can increase the number of probe sets per gene to 20 in total to a pre-designed panel gene. Limits may be lower for some genes and these will be indicated in the app (e.g., "The maximum additional probe sets you can design for (gene name) is (probe set number)").

   We suggest assuming a roughly linear relationship between the number of probe sets and sensitivity when boosting signal. However, this relationship can vary significantly per probe. If boosting a few low-expression transcripts, aim for the maximum number of additional probe sets.

   
   
   

4. Panel generation: After adjusting the probe set values, XPD will regenerate the panel design summary. Review the recommendations in the summary. It may take a few iterations to optimize the design request.

   The number of added probe sets are shown in the Custom Genes Summary table. Check the Panel Utilization for Highly Expressed Genes plot to see the utilization (TP10K) for boosted genes. If there are any concerns (e.g., with optical budget), they will be flagged in the summary. The total number of original plus added probe sets for boosted genes are displayed in the Probe set Summary plot.

Additional information for boosted genes will be available in Xenium Onboard Analysis v3.2 outputs (see release notes) and can be visualized in Xenium Explorer v3.2 (see release notes).