10x Xenium In Situ Spatial RNA Analysis Service
Mapping the true complexity of tissue microenvironments requires more than just identifying which genes are expressed—it requires knowing exactly where they operate. Our 10x Xenium In Situ Spatial RNA Analysis service provides an end-to-end partnership to help you achieve true subcellular resolution, from strict tissue QC to advanced cell segmentation.
- True subcellular spatial mapping (~15 nm resolution).
- Optimized workflows for challenging FFPE tissues.
- Pre-designed or fully customized gene panels.
- Advanced cell segmentation and spatial bioinformatics.
Unlocking Subcellular Spatial Biology with 10x Xenium
Traditional bulk RNA sequencing loses physical tissue context, and standard single-cell RNA sequencing disrupts vital cell-cell interaction networks. The 10x Xenium platform bridges this gap by enabling targeted, highly multiplexed in situ RNA hybridization directly on tissue sections.
As a dedicated scientific partner for US-based pharma and academic researchers, we manage the entire complexity of the Xenium assay. Whether you are profiling hundreds of targets to understand tumor progression or mapping neurological architectures, our team ensures stable data delivery. We seamlessly integrate this with our broader Spatial Transcriptomics Services to match your specific project phase.
End-to-End Xenium Workflow & QC Checkpoints
Processing sensitive tissues requires a transparent and rigorously controlled workflow. We implement stringent quality control at every critical transition point to safeguard your samples and ensure data reliability.
- Sample Receipt & RNA QC
Upon receiving your samples, we perform physical inspections and RNA integrity assessments (e.g., DV200 profiling for FFPE samples) to identify potential degradation risks early.
- Panel Selection & Optimization
Choose from 10x Genomics' pre-designed panels (such as Human Brain or Mouse Tissue) or collaborate with our team to design custom probe panels tailored to your specific therapeutic targets.
- In Situ Hybridization & Imaging
Tissue sections are carefully placed on specialized slides. The targeted RNA molecules undergo circularization, rolling circle amplification, and cyclic fluorescent imaging to achieve precise spatial coordinates.
- Primary Data Processing & QC
We extract decoding signals, align them to spatial coordinates, and generate initial cell boundaries using DAPI staining.
Sample Submission Requirements
To maximize the success rate of the Xenium assay, proper sample preparation and shipping are critical. We regularly process both Fresh Frozen and FFPE tissues, subject to the following baseline requirements:
| Sample Type | Recommended Thickness | Slide Requirements | Key QC Checkpoints | Shipping Conditions |
|---|---|---|---|---|
| FFPE Tissue Block | 5 µm | 10x Genomics Xenium specific slides | DV200 evaluation; Block age assessment | Dry ice / Cold packs |
| Fresh Frozen (OCT) | 10 µm | 10x Genomics Xenium specific slides | RIN evaluation; Morphology check | Dry ice |
Note: Prolonged storage of FFPE blocks can lead to significant RNA degradation. We recommend submitting recently sectioned tissues or discussing your sample’s history with our experts before shipping.
Advanced Cell Segmentation & Bioinformatics Analysis
A frequent challenge in spatial transcriptomics is the precise assignment of RNA transcripts to overlapping cells in dense tissues. While standard vendor pipelines provide initial decoding, accurate downstream biology relies on refined cell boundaries.
Our bioinformatics team goes beyond basic data generation. We offer layered analysis packages to fit your internal capabilities:
Standard Deliverables
- Raw Image Files & Coordinates: High-resolution images and decoded transcript spatial coordinates.
- Cell-Feature Matrices: Gene expression matrices mapped to initial DAPI-based boundaries.
- Xenium Explorer Files: Readily compatible files for your independent visual review using 10x software.
Advanced Segmentation & Integration
- Refined Cell Segmentation: Utilizing advanced algorithms and multi-modal image integration to improve cell boundary accuracy in complex morphologically regions like the TME.
- Multi-Omics Integration: Mapping previously acquired single-cell RNA-seq datasets onto your new Xenium spatial coordinates to achieve a multi-dimensional tissue atlas.
- Cell-Cell Communication: Specialized computational modeling to identify localized interaction networks between malignant cells and infiltrating immune populations.
Demo Results & High-Resolution Delivery
Our goal is to provide publication-ready visualization and biologically actionable data matrices. Depending on your analysis tier, typical data outputs include:
- Transcript Spatial Maps: Visualizations of discrete RNA transcripts mapped accurately within specific tissue architectures.
- Cell Segmentation Masks: High-accuracy boundary overlays (often built upon DAPI nuclear staining) defining individual cells for correct transcript assignment.
- Spatially Resolved Clustering: Spatial UMAP or scatter plots identifying distinct cell states localized within the tissue.
- Target Expression Heatmaps: In situ visualization highlighting the expression gradients of specific therapeutic targets across the tissue cross-section.
Key Applications of Xenium Spatial Transcriptomics
The subcellular resolution and high throughput of the Xenium platform make it an essential tool for several core biomedical research areas:
Oncology & Tumor Microenvironment (TME)
Mapping the spatial distribution of immune infiltrates, identifying exhausted T cells in situ, and accurately analyzing highly complex and heterogeneous tumor margins.
Neuroscience
Charting distinct neuronal and glial cell populations across brain slices to understand complex structural organization, mapping cellular changes associated with neurodegenerative disease progression.
Infectious Diseases & Immunology
Tracking host-pathogen interactions directly at the site of infection and measuring the localized immune responses within affected organ tissues at the single-cell level.
Case Study: High-Resolution Target Mapping in Complex Tissues
Source: High resolution mapping of the tumor microenvironment using in situ transcriptomics (Nature Communications, 2023)
Background
Traditional bulk sequencing and standard spatial methods often lack the subcellular resolution required to fully dissect the intricate architecture of the tumor microenvironment (TME). Researchers needed a way to map specific epithelial, stromal, and immune cell states directly within archival breast cancer tissues without losing critical spatial and morphological context.
Methods
The study utilized the 10x Genomics Xenium platform to perform targeted in situ spatial RNA analysis on human breast cancer FFPE sections. Using a highly multiplexed gene panel, the team captured the precise spatial coordinates of discrete RNA transcripts. Advanced cell segmentation algorithms were then applied, leveraging nuclear staining to accurately assign these transcripts to individual cells across the dense tissue landscape.
Results
The subcellular mapping successfully delineated discrete cell populations and their exact spatial distributions. It revealed the precise localization of exhausted T cells and distinct macrophage phenotypes in relation to the tumor boundary, providing a highly granular view of localized immune interactions that standard aggregation methods obscure.
Conclusion
Utilizing Xenium’s subcellular spatial transcriptomics enables the precise validation of specific cell states within complex tissues. This proves the platform's vital role in deeply profiling the TME and identifying localized therapeutic vulnerabilities in standard archival FFPE samples.
10x Xenium vs. Visium: Selecting the Right Spatial Strategy
Choosing the appropriate spatial technology depends heavily on your project phase. We provide comprehensive support across multiple platforms to ensure you use the right tool for your specific question.
| Comparison Dimension | 10x Xenium In Situ | 10x Genomics Visium | Visium HD |
|---|---|---|---|
| Resolution | Subcellular (~15 nm) | 55 µm spot size (Multi-cellular) | 2 µm bin size (Single-cell scale) |
| Target Scope | Targeted Panels (Hundreds of genes) | Whole Transcriptome (Unbiased) | Whole Transcriptome (Unbiased) |
| Primary Application | Targeted validation, TME mapping, detailed cell segmentation | Biomarker discovery, spatial mapping of unknown targets | High-res whole transcriptome discovery |
Selection Strategy:
- Opt for Visium or Visium HD during the early discovery phase when you need unbiased, whole-transcriptome profiling without prior hypotheses.
- Transition to Xenium for the validation phase, where analyzing specific targets across a large cohort of clinical-grade FFPE samples at subcellular resolution is critical.
Frequently Asked Questions
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