PRECLINICAL SINGLE-CELL PROFILING
Xenium STAMP single-cell profiling for preclinical studies
Need to resolve how individual cell populations respond to your drug across conditions and time points?
Explicyte applies STAMP (Single-cell Transcriptomics Analysis and Multimodal Profiling), an imaging-based workflow published in Cell, to fixed dissociated cells. Cells are immobilized directly onto Xenium slides and profiled for targeted gene expression at single-cell resolution, without a sequencing step. This enables high-cell-count, multi-condition studies with the mechanistic depth of single-cell transcriptomics.
Up to 48 conditions/run · ~5,000 genes · no sequencing
XENIUM STAMP
Add single-cell transcriptomic depth to functional cell assays
Functional assays tell you whether a drug produces a response. Xenium STAMP helps resolve which cells respond, how their abundance and state change, and which gene-expression programs accompany that response.
Up to 48 conditions within a single run
Two Xenium slides are processed within the same run, allowing multiple treatments, donors, concentrations or time points to be profiled together. This creates economies of scale while limiting inter-run variability.
~1 million cells per run for deep population coverage
High cell capture provides the depth needed to resolve immune and tumor-cell subsets, treatment-induced states, and rare populations within heterogeneous samples.
Transcriptomic depth without sequencing
Profile targeted gene expression at single-cell resolution, with focused panels or Xenium Prime 5K plus custom genes, then resolve differential expression and pathways within defined cell populations.
At a glance
Xenium STAMP: format and readouts
- Samples
- Fixed dissociated cells, including PBMCs, cultured cell lines and cells dissociated from tissues.
- Scale & multiplexing
- Two Xenium slides are processed per run, enabling up to 48 experimental conditions to be profiled together.
- Profiling
- Targeted RNA expression at single-cell resolution using an imaging-based Xenium workflow, without a sequencing step.
- Panels
- Focused Xenium IO panels or Xenium Prime 5K (~5,000 genes), with up to 100 custom add-on genes where required.
- Analysis
- Cell annotation, rare-population analysis, population shifts, differential expression, pathway analysis and treatment comparisons.
- Integration
- Flow cytometry, cytokine profiling and functional assay readouts can be integrated to connect phenotype with mechanism.
WORKFLOW
From functional assay to cell-resolved mechanism
Cells from an in vitro assay or ex vivo sample are fixed after the selected treatment, condition or time point.
Fixed cells are immobilized on Xenium slides and profiled for targeted gene expression at single-cell resolution.
We identify cell populations and states, quantify treatment-induced shifts and analyze differential expression and pathways within relevant populations.
PRECLINICAL APPLICATIONS
Use STAMP where functional readouts need deeper mechanistic resolution
Cell-based efficacy & mechanism of action
Resolve treatment-dependent changes in tumor and immune-cell populations, cell states and gene-expression programs across 2D or 3D models.
Immune activation & safety-related responses
Go beyond secreted cytokines or flow-cytometry readouts to identify the populations and programs associated with immune activation.
Ex vivo pharmacodynamic profiling
Profile fixed dissociated cells collected from preclinical in vivo studies to characterize treatment response and mechanism at single-cell resolution.
CHOOSING THE RIGHT READOUT
Xenium STAMP, flow cytometry or scRNA-seq?
| Approach | Flow cytometry | Xenium STAMP | Chromium X scRNA-seq |
|---|---|---|---|
| Primary readout | Targeted protein phenotyping | Targeted single-cell RNA expression | Whole-transcriptome single-cell RNA profiling |
| Sample format | Dissociated cells | Fixed dissociated cells | Cells or nuclei, with fixed-cell workflows available |
| Gene / marker coverage | Defined protein-marker panel | Targeted RNA — up to ~5,000 genes + custom add-ons | Whole-transcriptome RNA profiling |
| Sequencing required | No | No | Yes |
| Best suited for | Rapid phenotyping and protein-marker analysis | Multi-condition MoA studies, cell states and targeted pathways | Transcriptome-wide discovery and unbiased characterization of cell populations and states. |
| Biological resolution | Cell populations and marker expression | Cell populations, rare states and targeted gene-expression programs | Cell populations, states and transcriptome-wide programs |
| Study scale | Well suited to large sample series | High-cell-count, multi-condition studies; >1M cells and 48 conditions per run | Best suited to focused cohorts requiring broad discovery |
These approaches are complementary. Xenium STAMP is particularly useful when a defined biological question needs to be tested across many cells and experimental conditions, while Chromium X is better suited to broader transcriptomic discovery.
REPRESENTATIVE DATA
Representative Xenium STAMP data
FROM ASSAY TO INTERPRETATION
Why work with Explicyte for Xenium STAMP studies
Preclinical study design
STAMP is integrated into the biological experiment — including treatment conditions, donors, time points and functional readouts — rather than run as an isolated platform service.
Integrated functional & single-cell readouts
Combine Xenium STAMP with flow cytometry, cytokine profiling, tumor-killing assays and other functional measurements within the same program.
In-house biological interpretation
Our bioinformatics team takes the dataset from QC and cell annotation through treatment comparisons, differential expression, pathway analysis and biological interpretation.
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
Contact our team
Discuss your Xenium STAMP study
Tell us your model, cell type, treatment conditions, time points and the biological question you want to resolve. We'll help determine whether STAMP, flow cytometry, Chromium X — or a combination — is the best fit for your study.
XENIUM STAMP FAQ
Frequently asked questions about Xenium STAMP
What is STAMP and how does it work with Xenium?
STAMP stands for Single-cell Transcriptomics Analysis and Multimodal Profiling. It immobilizes fixed dissociated cells on imaging slides so targeted RNA expression can be measured at single-cell resolution using platforms such as Xenium, without a sequencing step. The method was published by Pitino et al. in Cell in 2025.
Which samples can be analyzed with Xenium STAMP
Fixed dissociated cells can be profiled, including PBMCs, cultured cell lines and cells dissociated from tissues.
How is Xenium STAMP different from standard Xenium tissue analysis?
Standard Xenium preserves the spatial organization of cells within a tissue section. STAMP instead profiles dissociated cells immobilized on a slide, making it particularly suited to cell-based assays, perturbation studies and ex vivo profiling where native tissue spatial context is not required.
How is STAMP different from single-cell RNA sequencing?
STAMP uses targeted imaging-based gene-expression profiling and does not require sequencing. It is well suited to high-cell-count studies with predefined biological questions and multiple conditions. Chromium X is more appropriate when broad or whole-transcriptome discovery is required.
Can STAMP be combined with flow cytometry or cytokine profiling?
Yes. Functional, flow cytometry and secretome readouts can be integrated with STAMP to connect an observed phenotype with specific cell populations and transcriptional programs.
Which Xenium panels can be used?
Panel choice depends on the biological question. Xenium Prime 5K provides approximately 5,000 targeted genes with up to 100 custom add-on genes; more focused panels can also be used where appropriate.
Can STAMP resolve rare cell populations?
Its high cell throughput makes STAMP particularly attractive for rare-population analysis, provided the selected gene panel contains appropriate markers. The original publication specifically demonstrated ultra-rare population detection.
Is Explicyte certified for Xenium studies
Yes. Explicyte is a 10x Genomics Certified Service Provider for Xenium, combining platform expertise with preclinical immuno-oncology, functional assays and in-house bioinformatics.