The Xenium platform uses targeted panels to detect gene expression at subcellular resolution. The Xenium Prime 5K pan tissue and pathways pre-designed panels were designed to enable comprehensive cell type and cell state identification using publicly available single cell RNA sequencing data. The panels also cover canonical signaling pathways, as well as genes relevant to developmental biology, human immuno-oncology, and genes that are well known in biomedical literature.
Consult the Xenium Prime In Situ Gene Expression with optional Cell Segmentation Staining User Guide (CG000760) to execute the workflow.
The table below provides the following information for available pre-designed Xenium Prime In Situ 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 annotation information in CSV format (see below for details).
- Downloadable
gene_panelJSON 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).
Each pre-designed panel contains 609 negative control codewords, 40 negative control targets, and 21 genomic control probes. 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 for Xenium Prime, with a goal of reaching three probe sets per gene. Add-on custom panels will target five probe sets per gene.
Genomic control probes are designed to bind to intergenic genomic DNA, but not to any transcript sequence present in the tissue. They are not designed to only target non-homologous regions of the genome.
For any custom panel request, 10x generates the negative control targets for the design; customers do not need to specify these in Xenium Panel Designer standard or advanced workflow requests.
Please read the Xenium Panel Designer Workflow Guide page for information about add-on custom or advanced custom gene panel options.
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 Codewords | The number of codewords used to decode each gene. Xenium Prime pre-designed panels are designed with multiple codewords per gene. |
| Number of Probe sets | The number of probe sets targeting each isoform of the gene. |
| Protein name | The full name of the protein encoded by the gene. |
| Location | The predicted subcellular location of the gene from CellChatDB. |
| Cell type | The computational or manually curated cell type from the Chan Zuckerberg Initiative CellGuide. |
| Cell chat pathway | The predicted cell-cell communication pathways that the gene is a member of from CellChatDB. |
References
- Jin, S., MV Plikus, and Q Nie. CellChat for systematic analysis of cell-cell communication from single-cell and spatially resolved transcriptomics. bioRxiv. 2023.