Xenium - 10x
Xenium is imaging-based spatial transcriptomics at sub-cellular resolution, on FFPE or fresh frozen tissue. It images individual RNA transcripts in intact tissue and, with the multi-omics add-ons, protein on the same section. First-generation and Prime chemistries are available.
Specification
| Vendor | 10x Genomics |
|---|---|
| Modality | imaging-based spatial transcriptomics |
| Tissue | FFPE, fresh frozen |
| Capture area | 2.35 cm2 |
| Targets / plex | module max 500 targets, full custom tiers 500, 1000 targets, custom add-on max 100 targets, Prime 5000 targets, protein max 27 targets |
| Resolution | sub-cellular |
| Species | pre-made panels human and mouse; custom any species a panel can be designed against |
| Minimum | 2 slides (one instrument run) |
| Billing | slide |
Accreditations & experience
The Spatial Technologies Unit is an accredited service provider and among the first facilities worldwide certified through 10x Genomics' Core Lab Training program. See the Accreditations page.
Panels
Xenium supports pre-made modules that reduce the cost and time to start an experiment, and full custom panels at different sizes.
- Pre-made modules are available for human and mouse.
- Full custom panels are offered at 500 and 1,000 targets.
- Pre-made modules can be extended with up to 100 custom genes (the add-on attaches to a module or to Xenium Prime, not to a full custom panel).
Xenium Prime
Xenium Prime brings discovery-scale capture to imaging-based spatial transcriptomics, with 5,000-gene panels for human and mouse. The 5,000-gene pan-tissue module can be extended further with up to 100 custom genes.
Prime also supports a custom panel of 1,000 to 2,000 targets (Xenium Prime Custom), on the Prime chemistry.
Multi-omics
Xenium runs several readouts on the same section.
- RNA + protein: protein measured alongside RNA using protein modules, up to 27 protein targets. Multiple protein modules can run together.
- Protein-based segmentation add-on: antibody-based cell-boundary staining for accurate segmentation; prerequisite for the protein modules, also available with RNA alone.
- Mutations in situ: known mutations added to the panel as probes; clones tracked in situ at single-cell resolution.
- TCR/BCR: probes designed against known T- and B-cell receptor sequences, read at single-cell resolution (probe-based, known-sequence).
Additional capabilities
Same-sample H&E is supported after a Xenium run. The assay is non-destructive: the section survives the experiment, so it can be paired with additional spatial tissue-profiling assays afterward - multiplexed immunofluorescence (up to 100 antibodies), sequencing-based spatial transcriptomics, and others.
What you receive
- morphology images (DAPI and any protein channels)
- cell-feature matrix and transcript coordinate table
- cell and nucleus segmentation masks
- Xenium Explorer bundle (.xenium) and OME-TIFF images
- H&E of the same section where applicable
- QC metrics report; raw files immutable, MD5 checksums at transfer
Access and priority
Internal clients (BIDMC, DF/HCC), external academic and non-profit clients, and industry clients all have equal priority. Projects begin upon sample receipt.