You can choose full‑service processing or undertake training to run the system independently—contact the Genome Core to discuss your project needs. If you choose the training option, the Genome Core will provide detailed instructions and protocols for all workflows and will work closely with you to guide the processing of your own samples.
- To learn more about these technologies visit the Instrument section
- If you want to inquire about a project, request a quote or you need help sectioning your samples please send us an email at XXX
- Visit the section How to get started to review the Core guideline
Spatial Biology at True Subcellular Resolution
Xenium (10X Genomics)
Xenium Analyzer is a cutting-edge imaging-based platform for single‑cell spatial transcriptomics. Xenium can profile expression of hundreds of RNA targets and up to 27 proteins at subcellular resolution directly within fresh-frozen or FFPE tissue sections (check protein list here).
Users are responsible for providing all 10X Genomics reagents required for their experiments. The core does not supply these materials.
Please download here the Xenium intake form and send it back to the core. (repeated info)
What you need to bring to the core for a Xenium experiment XXXX (link) ?
H&E Post-Run: The core does not provide post-run H&E staining as part of its standard services, and it is not included in the provided quote. For special requests, please contact us at XXXX.
Useful links:
General Q&A (create a link)
Intake form (link)
FFPE: Best practices for handling tissue samples and Xenium slides before and after sectioning
Fresh Frozen: Tissue Preparation Handbook
- Xenium Overview
- Discover Xenium panel
- Download grant resources
- Explore support hub
- Analysis Guides
- Explore interactive dataset
- Explore publications
Visium HD (10X Genomics)
High-definition spatial transcriptomics at single-cell resolution
Visium Spatial Gene Expression platform is a sequencing-based solution for unbiased, whole-transcriptome spatial profiling directly within tissue sections near to single-cell spatial resolution that reveals gene expression in its native morphological context. Visium HD 3' species-agnostic is now available including feasibility for isoform, TCR/BCR, and SNV detection.
Please download here the Visium intake form and send it back to the core.
H&E: The core does not provide H&E staining as part of its standard services, and it is not included in the provided quote. For special requests, please contact us at XXXX.
What you need to bring to the core for a Visium experiment XXXX (link)
Useful links:
- Intake form (link)
- HD Spatial Gene Expression
- HD 3’ Spatial Gene Expression
- Explore support hub
GeoMx Digital Spatial Profiling (Bruker Spatial)
Unlocking spatial insights for RNA and protein analysis.
GeoMx®: The GeoMx enables highly multiplexed protein and RNA profiling within spatially defined regions of interest on tissue slides. This non‑destructive technology works with whole transcriptome and >570‑target protein panels, using UV‑cleavable indexing oligos and automated capillary collection.
Useful links:
- General Q&A (create a link)
- Intake form (link)
- GeoMx Overview
- What are morphology markers?
- Nanostring Unversity Learning Center: NanoString University is a cloud-based educational and support platform designed to help researchers effectively use NanoString and spatial biology technologies. It offers product manuals, video tutorials, training resources, data analysis tools, and other helpful documentation—all tailored for ease of use and without requiring coding skills.
- Identifying and Troubleshooting Sequencing Data Flags
Which Approach Best Aligns with the Goals of My Study?
Here is a clear comparison table highlighting key features of Xenium, Visium HD, Visium HD 3', and GeoMx technologies:
|
Feature |
Xenium |
Visium HD |
Visium HD 3’ |
GeoMx DSP |
|
Provider |
10x Genomics |
10x Genomics |
10x Genomics |
NanoString (Bruker Spatial Biology) |
|
Technology Type and detection method |
Probed-based gene expression. in situ Hybridization. Imaging-based |
Probed-based gene expression. NGS readout |
3’poly(A) capture-based gene expression. NGS readout |
Probed-based gene expression using UV cleavable barcodes. NGS readout |
|
Target Molecules |
Multiomic- RNA (up to 5000+ targets) + 27 proteins |
Whole transcriptome |
Whole transcriptome |
Multiomic- WTA and up to 570 proteins |
|
Transcriptome coverage |
Protein coding genes |
Protein coding genes |
Whole transcriptome with de novo discovery |
Protein coding genes |
|
Resolution |
Subcellular—< 30 nm precision (XY), < 100 nm (Z) |
~2 µm spots (HD), near single-cell
|
~2 µm spots (HD), near single-cell |
ROI-based (tens to hundreds of µm), not single-cell |
|
Sample Types and compatibility |
FFPE and fresh-frozen; post-run H&E/IF and Visium-compatible |
FFPE, Fresh Frozen |
FFPE, Fresh Frozen |
FFPE, Fresh Frozen |
|
Detection Method |
imaging |
Imaging +NGS |
Imaging +NGS |
Imaging +NGS |
|
Capture Area / Run Throughput |
~472 mm² per run (2 slides), 480 genes <3 days, 5,000 genes <6 days |
Two or four 6.5 × 6.5 mm capture areas, ~5,000 spots per area |
Two or four 6.5 × 6.5 mm capture areas, ~5,000 spots per area |
Variable; depends on number/size of ROIs selected |
|
Sequencing/ Imaging Time |
<3 to 6 days imaging-based depending on panel size |
check |
High sequencing (275–700M reads/area) |
Variable depending on ROIs and panel complexity |
|
Analysis Tools |
Xenium Explorer |
Space Ranger, Loupe Browser |
Space Ranger, Loupe Browser |
GeoMx DSP Software, Q3/Nimbus |
|
Use Case Highlights |
High-res subcellular RNA + protein profiling. Biomarker discovery |
Whole transcriptome discovery with high spatial detail |
Whole transcriptome profiling for broader contexts |
Targeted spatial profiling of RNA and proteins
|
|
Species |
Human and Mouse |
Human and Mouse |
Agnostic |
Human and Mouse |