The Xenium platform uses targeted panels to detect gene expression at subcellular resolution. The Xenium v1 pre-designed 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.
Consult either the Xenium In Situ Gene Expression - Probe Hybridization, Ligation & Amplification User Guide (CG000582) or Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide (CG000749) to execute the workflow.
Table of contents
Pre-designed panel information
The table below provides the following information for available pre-designed Xenium gene expression panels:
- Panel name and the number of targeted genes
- Downloadable panel metadata with gene name, transcript ID, number of probe sets, number of codewords for each target, and cell type annotation in CSV format (see below for details).
- Downloadable
gene_panel
JSON file for each panel (format described here). - Panel probe sequences in FASTA format and the genomic coordinates of the panel probe sequences in 13-column detailed BED format (see glossary for details).
Panel | Genes targeted | Panel metadata and JSON | Probe genomic target sequences and coordinates |
---|---|---|---|
Xenium Human Brain Gene Expression Panel | 266 | CSV, JSON | FASTA, BED |
Xenium Human Breast Gene Expression Panel | 280 | CSV, JSON | FASTA, BED |
Xenium Human Colon Gene Expression Panel | 322 | CSV, JSON | FASTA, BED |
Xenium Human Immuno-Oncology Profiling Panel | 380 | CSV, JSON | FASTA, BED |
Xenium Human Lung Gene Expression Panel | 289 | CSV, JSON | FASTA, BED |
Xenium Human Multi-Tissue and Cancer Panel | 377 | CSV*, JSON | FASTA, BED |
Xenium Human Skin Gene Expression Panel | 260 | CSV, JSON | FASTA, BED |
Xenium Mouse Brain Gene Expression Panel | 247 | CSV, JSON | FASTA, BED |
Xenium Mouse Tissue Atlassing Panel | 379 | CSV*, JSON | FASTA, BED |
Panel negative controls
Each pre-designed panel contains 40 negative control codewords and 20 negative control targets (except the Xenium Mouse Brain Gene Expression Panel, which has 27).
For negative control targets, multiple probes are designed for each non-biological target sequence. It follows the same design process as for real target sequences, with a goal of reaching eight probe sets per target (for more detail, read the Getting Started with Xenium Panel Design page). An add-on custom panel will have the same number of negative control probe sets as the pre-designed panel it is based upon.
Decoding and negative controls are described on the Xenium Onboard Analysis algorithms page.
Custom panel information
Please read the Getting Started with Xenium Panel Design page for information about supported add-on custom and standalone custom gene panel options.
Panel metadata
For each of the pre-designed panels, a metadata file is provided on this page (CSV format). This file contains additional panel information, which may be helpful for designing your experiment or custom add-on genes.
Column | Description |
---|---|
Gene | The gene identifier targeted by the probe. |
Ensembl ID | The Ensembl gene identifier targeted by the probe. |
Number of Probe sets | The number of probe sets targeting each isoform of the gene. |
Codewords | The number of codewords used to decode each gene. |
Annotation | The 10x Genomics cell type annotation given to each gene based on single cell atlas data, research area experts, and literature searches. |