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Species Standalone Custom and Advanced Custom Panel Design for In Situ Xenium v1 Panels

Species Standalone Custom and Advanced Custom Panel Design for In Situ Xenium v1 Panels

  • CG000683_TechNote_Xenium_Custom_Panel_Design_RevD.pdf

    Technical Note, CG000683


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The probe design details in this Technical Note only apply to Xenium v1 In Situ Gene Expression assay chemistry. The guidance in this Note may help to assess feasibility for advanced Xenium Prime In Situ Gene Expression designs, but may not directly apply. Please contact your sales representative to start a conversation about Xenium Prime advanced custom panel experiment feasibility.

Xenium In Situ enables researchers to characterize RNAs in cells and tissues with subcellular resolution. Users can choose among several pre-designed panels, or design add-on custom or standalone custom panels for human and mouse. This Technical Note explains standalone custom panel design for species beyond those currently offered by 10x Genomics ("species standalone custom"), as well as advanced custom designs. Potential advanced custom applications include isoforms, gene fusions, viral or bacterial sequences, protein tags, fluorescent reporters, and transgenes. Types of customization possible, the basic structure of Xenium probes, and how users can select their own RNA-binding domain sequences are covered here. To submit an advanced custom design request, researchers must submit a CSV file, described below, to 10x Genomics. Before creating this file, users are advised to consider these guidelines for probe design. Although pre-designed panels have been extensively tested by 10x, species standalone custom and advanced customization are not fully supported — 10x Genomics will support adding these probes to the panel, but cannot guarantee that these probes will successfully detect their targets.

Design a custom panel with the Xenium Panel Designer app. Either sign in to your existing 10x Cloud account or create a new account to get started today. Guidance is available on the Getting Started with Xenium Panel Design page.

Document Type
Technical Note

Last Modified
May 28, 2024