The Xenium In Situ platform measures gene expression with panels of probes that target genes of interest. The panel design process is described in detail here. In addition to using 10x Genomics pre-design panels, you can request custom panels using the Xenium Panel Designer web app.
Below are several step-by-step videos demonstrating how to use the Xenium Panel Designer and how to interpret design recommendations. These training videos are part of a webinar, the full recording (session 1) is available here.
Table of contents
- Demo 1: Entering gene lists
- Demo 2: Creating an add-on custom panel
- Demo 3: Uploading a single cell reference
- Demo 4: Creating a standalone custom panel
Demo 1: Entering gene lists
This video demonstrates correct and incorrect gene list entries. In this case, we are creating a human panel design. The app flags genes that are not found in the reference (indicating incorrect species gene names) or genes that are already included in a 10x pre-designed panel.
Demo 2: Creating an add-on custom panel
This video demonstrates how to create a 100-gene add-on panel for human colon. In this case, we select a single cell reference provided in the app (Gut Cell Atlas from CELLxGENE), provide a gene list, and describe the results in the panel design summary.
The genes in this design demo are available for download here.
Demo 3: Uploading a single cell reference
This video continues from demo 2 with a modification to the single cell reference step. In addition to selecting the Gut Cell Atlas from CELLxGENE, we also upload our own reference file. This file was downloaded from CELLxGENE, downsampled, and formatted to 10x MEX format (see Creating Single Cell References for Xenium Custom Panel Design from Seurat or AnnData for additional guidance).
The reference used in the demo is available here.
Demo 4: Creating a standalone custom panel
This video demonstrates how to create a standalone custom panel for mouse brain, and in particular how to handle genes with high gene expression. For the demo, several genes are included at the top of the gene list to illustrate how the app handles high expressors in the panel design and how to interpret the panel summary report.
The gene lists are available for download here: