The Xenium In Situ Gene and Protein Expression assay uses targeted panels to simultaneously detect RNA and protein markers at subcellular resolution in formalin fixed & paraffin embedded (FFPE) tissue samples. Consult the Xenium In Situ Gene and Protein Expression with Cell Segmentation Staining User Guide (CG000819) to execute the workflow.
The Xenium Protein assay is compatible with all Xenium v1 chemistry human pre-designed and custom gene panel options (both standard and advanced workflows).
Xenium Protein subpanel part numbers (PN) are listed below.
| Kit PN | Xenium Protein subpanel product name and markers |
|---|---|
| 1000833 | Xenium Protein Immune Cell Subpanel A (2 rxn): CD4, CD20, CD8A, CD3E |
| 1000834 | Xenium Protein Immune Cell Subpanel B (2 rxn): CD138, HLA-DR, CD11c, CD68 |
| 1000846 | Xenium Protein Immune Cell Subpanel C (2 rxn): CD16, GranzymeB, CD163 |
| 1000835 | Xenium Protein Proliferation & Differentiation Subpanel (2 rxn): CD45RA, PCNA, CD45RO, Ki-67 |
| 1000836 | Xenium Protein Immune Checkpoint Subpanel (2 rxn): PD-1, VISTA, PD-L1, LAG-3 |
| 1000837 | Xenium Protein Tumor Subpanel (2 rxn): Beta-catenin, CD31, PTEN, PanCK |
As you plan your Xenium In Situ experiment, it may be useful to know the overlap between protein markers per subpanel and genes per Xenium v1 pre-designed gene panel.
In the tables below:
- Column 1: The gene(s) that correlates to each protein marker in a given Xenium Protein Subpanel.
- Columns 2 - 8: The pre-designed Xenium v1 human gene expression panels; names are abbreviated. Complete product names and part numbers are provided here.
- indicates the gene is present in a pre-designed Xenium v1 human gene expression panel.
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| CD3E: CD3E | - | ||||||
| CD4: CD4 | - | - | |||||
| CD8A: CD8A | - | ||||||
| CD20: MS4A1 | - | - |
The HLA-DR protein marker correlates to the HLA-DRA gene, which is not included in any of the pre-designed human v1 panels.
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| CD68: CD68 | - | ||||||
| CD11c: ITGAX | - | - | - | - | |||
| CD138: SDC1 | - | - | - | - | - | - |
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| GranzymeB: GZMB | - | - | - | - | |||
| CD163: CD163 | - | ||||||
| CD16: FCGR3A | - | - |
The CD45RA and CD45RO protein markers are isoforms and do not have a gene equivalent. They may correlate with the PTPRC gene (see below).
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| PCNA: PCNA | - | - | - | - | |||
| Ki-67: MKI67 |
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| PD-1: PDCD1 | - | - | - | ||||
| PD-L1: CD274 | - | - | - | ||||
| VISTA: VSIR | - | - | - | - | - | - | |
| LAG-3: LAG3 | - | - | - |
The PanCK protein marker correlates with these keratin genes: KRT4, KRT7, KRT13, and KRT18. It may correlate with other keratin genes.
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| PanCK: keratin genes | - | - | - | ||||
| CD31: PECAM1 | - | - | - | - | |||
| Beta-catenin: CTNNB1 | - | - | - | - | - | - | |
| PTEN: PTEN | - | - | - | - | - | - |
If Xenium Multi-Tissue Stain Mix markers are imaged individually on-instrument, these are the genes that correlate with each protein marker:
| Protein marker: Gene name | Brain | Breast | Colon | Immuno-Oncology Profiling | Lung | Multi-Tissue and Cancer | Skin |
|---|---|---|---|---|---|---|---|
| E-cadherin: CDH1 | - | - | - | - | |||
| Vimentin: VIM | - | - | - | - | - | - | |
| alphaSMA: ACTA2 | - | - | - | ||||
| CD45: PTPRC | - | - | - |