The Xenium platform uses targeted panels to detect gene expression at subcellular resolution. The panels were designed to cover the major cell types for specific tissues. They consist of genes selected from single cell atlas data, research area experts, and literature searches.
The pre-designed gene panels can accommodate up to 100 additional genes. Contact your 10x Genomics Sales Executive for information about designing custom gene panels that are compatible with pre-designed panels. If you do not know your Sales Executive, please contact customerservice@10xgenomics.com
| Panel | Genes targeted | Metadata CSV file | Gene list XLSX file (read-only) |
|---|---|---|---|
| Xenium Human Breast Gene Expression Panel | 280 | Metadata CSV | Gene list XLSX |
| Xenium Mouse Brain Gene Expression Panel | 248 | Metadata CSV | Gene list XLSX |
Panel metadata
The metadata CSV files linked above provide additional panel information for the pre-designed panels, which may be helpful for designing your experiment or custom add-on genes.
| Column | Description |
|---|---|
| Genes | The gene identifier targeted by the probe. |
| Ensembl ID | The Ensembl gene identifier targeted by the probe. |
| Number of probes | The number of probes targeting each gene. |
| Number of codewords | The number of codewords used to decode each gene. |
| 10x Genomics cell type annotation | The cell type annotation given to each gene based on single cell atlas data, research area experts, and literature searches. |
The Xenium Analyzer outputs directory will include a panel metadata file called gene_panel.json. It contains metadata for the Xenium pre-designed panel genes, as well as any custom add-on genes, in JSON format.