US Based · Spatial Transcriptomics
10x Genomics Xenium In Situ Spatial Service
Imaging-based spatial transcriptomics at subcellular resolution. Map up to 5,000 genes in situ within individual cells on FFPE or fresh-frozen tissue, with panel selection, slide placement, instrument runs and analysis in our SF Bay Area lab.
Capture area
10.45 × 22.45 mm per slide
Panels
Prime 5K or v1 panels
Species
Human and mouse
Run
2 slides per run
Turnaround
1-4 weeks
Price
Service Highlights
From tissue block to in situ map, all in one lab
Every stage runs in-house with defined QC criteria, from sectioning and Xenium slide placement through imaging, decoding and spatial analysis. Engage us for end-to-end service, or enter at the stage where you need support.
Tissue Prep & QC
- Sectioning and TMA building
- Pre H&E staining
- RNA QC, DV200 ≥30%
PANEL SELECTION
- Prime 5K, v1 or custom gene panels
- Protein and segmentation add-ons
Xenium Processing
- Slide placement and probe hybridization
- Imaging and decoding
- Post-run H&E staining
Analysis
- Xenium Explorer files
- Cell segmentation outputs
- Publication-ready figures
Service Packages
Panel options for all species and sample types
Every package covers 1 run with 2 slides each with a 10.45 × 22.45 mm capture area. Choose the gene capture your study needs, then match it to your starting material.
| Package | Panel | Species | Sample compatibility |
|---|---|---|---|
| Xenium Prime 5K | 5000 gene panel (Add on 1–100 custom genes) Human 5K gene list Mouse 5K gene list | Human or Mouse | FFPE and fresh frozen with DV200>30% (Ship blocks or sections mounted on Xenium slides) |
| Xenium v1 | Smaller gene panels – options below (Add on 1-100 custom genes) | Human or Mouse | FFPE and fresh frozen with DV200>30% (Ship blocks or sections mounted on Xenium slides) |
| Xenium v1 Customized | Fully customized panel – 1–480 genes | Any species with an annotated transcriptome | FFPE and fresh frozen with DV200>30% (Ship blocks or sections mounted on Xenium slides) |
Pre-designed v1 panels · select a panel to download its gene list
EVERY SERVICE INCLUDES
- RNA extraction and QC per slide
- Tissue sectioning and placement
- Xenium run - 2 slides
- Post-run H&E staining
- Xenium Analyzer results
Available as add-ons
- v1 cell segmentation
- Custom gene add-ons
- v1 protein add-ons (tumor, immune checkpoint, proliferation, immune)
- TMA construction and multiple block QC
- Pre-run H&E, tissue morphology
- OCT or paraffin embedding
Need whole-transcriptome discovery?
Technical excellence
Subcellular resolution without sequencing
Padlock probes, rolling circle amplification and on-instrument imaging turn each transcript into a precise signal in its native cell. What that means for your data:
- ✓ Sensitivity comparable to single-cell RNA-seq
- ✓ Low false discovery rate from stringent probe binding
- ✓ Distinguishes closely related transcripts and isoforms
- ✓ Captures short genes and degraded FFPE transcripts
- ✓ Results come straight off the run, with no library prep or sequencing
Multimodal staining assigns each transcript to an individual cell, giving true cell-level expression rather than inferred spots.
Six protein subpanels, 27 markers in total, run alongside RNA on the same human FFPE section. Compatible with every human v1 panel, pre-designed or custom. Run all six or only those you need. Cell segmentation markers are required and included. Not available with Prime 5K.
The section stays intact after the run, so it can go on to IF, H&E or a Visium CytAssist run without cutting a new section.
Analysis Packages
Standard or advanced interpretation
Every run delivers Xenium Analyzer results. Add an analysis package for a more comprehensive analyzed data set run through Seurat and R packages for downstream interpretation.
Xenium Standard Analysis
- Xenium Analyzer output files
- Xenium Explorer file for interactive viewing
- Cell-by-gene expression matrix
- Run QC metrics
Xenium Advanced Analysis
- Quality filtering of cells and transcripts
- Clustering and UMAP on segmented cells
- Cell type annotation
- Neighborhood and cell-cell interaction analysis
- Differential expression between regions or groups
- Interactive data portal with publication-ready figures
Service experience
Working with us
Every project is run by scientists, tracked in one portal, and processed entirely in our own lab.
PhD-Level Project Oversight
A PhD scientist owns your project from design through interpretation.
Dedicated Project Manager
One point of contact from quote through delivery.
Easy Ordering
Register samples, track status, and download results in one portal.
100% US-Based
Every stage runs in-house in Foster City, CA. No outsourcing.
Resources & insights
Technical resources
Brochure
Spatial Transcriptomics Brochure
Spatial transcriptomics with Signios Bio: where gene expression meets precision.
BLOG
Choosing the Best Spatial Service for Your Study
Visium HD vs. Xenium Prime vs. Illumina StrataMap — matching platform to study design.
BLOG
Integrating Single-Cell and Spatial Data
Building multimodal maps for translational research.
Frequently asked questions
Planning your Xenium project
Choosing a panel
Should I choose Xenium or Visium HD?
Xenium targets up to 5,000 known genes at subcellular resolution with direct cell assignment, ideal for hypothesis-driven work. Visium HD captures the whole transcriptome for unbiased discovery. Our scientists help you choose, or combine both on the same study.
What is the difference between Prime 5K and v1 panels?
Prime 5K is a 5,000-gene pre-designed panel for broad coverage. v1 panels are smaller, tissue-specific designs. Both include cell segmentation and accept custom gene add-ons.
Can I design a custom panel?
Yes. v1 custom standalone panels are available at 1–50, 51–100, 101–300 and 301–480 genes, and custom genes can be added to v1 or Prime 5K panels.
Can I detect protein as well as RNA?
Yes, on human FFPE tissue with v1 panels. Run all six protein subpanels (tumor, immune checkpoint, proliferation and differentiation, and immune cell A, B and C) for up to 27 proteins, or only the ones you need. Protein is not available with Prime 5K.
Samples & tissue prep
What sample types do you accept?
FFPE blocks, FFPE sections mounted on Xenium slides, fresh frozen tissue, fresh frozen OCT blocks, and fresh frozen sections on Xenium slides.
What quality do my samples need?
Which species are supported?
Can you section and mount my tissue?
Yes. Sectioning and placement are included, one section per slide and two slides per run. TMA construction, embedding and pre-run H&E are available as add-ons.
Data & logistics
What is included in a package?
Two QCs (RNA extraction and QC per block or slide), tissue sectioning and placement, a Xenium run on two slides, post-run H&E staining, and Xenium Analyzer results.
What data do I receive?
What is your turnaround time?
Approximately 4 weeks from sample receipt to data delivery. Expedited run options are available for as short as 1 week.
How is pricing structured?
Pricing is per run of two slides. Contact us for a quote, including volume pricing for multi-run projects.
Get started with your project
Ready to add spatial context to your study? Contact our team for a technical consultation. We will guide you through panel selection, sample requirements, and add-ons aligned to your analysis goals.
- Volume pricing for multi-run projects
- Results in 1–4 weeks
- Subcellular, cell-level resolution
- 100% in-house at Foster City, CA