What is Spatial Transcriptomics and Why Does It Matter?
Spatial transcriptomics combines tissue histology with transcriptome-wide gene expression profiling while preserving the native spatial coordinates of RNA molecules within the tissue section. Unlike bulk or single-cell RNA sequencing that loses tissue architecture, this approach enables researchers to map where specific genes are expressed in relation to cell types, tissue structures, and pathological features. For oncology and immunology, this means visualizing immune cell infiltration patterns, tumor heterogeneity, and clonal architecture directly on the tissue slide.
Our spatial transcriptomics service utilizes advanced platforms (e.g., Xenium Analyzer, Visium, GeoMx) to capture gene expression from FFPE or frozen tissue sections. The workflow integrates histological staining, probe hybridization, high-resolution imaging, and computational reconstruction to generate spatial gene expression maps. We support human and rodent samples, including core needle biopsies, tissue microarrays, and surgical resections. By linking transcriptomic data with morphological context, we enable deep characterization of the tumor microenvironment, identification of rare cell populations, and correlation of spatial gene expression patterns with genomic alterations.
This service is designed for precision oncology firms, pharmaceutical R&D groups, and translational research institutes investigating immune dynamics, biomarker discovery, and mechanisms of immune evasion. With rigorous sample qualification and dedicated bioinformatics support, we deliver actionable insights that bridge molecular profiles with tissue-level biology.
Our Spatial Transcriptomics Service Offerings
Tissue Sample Qualification & Preparation
Expert handling of FFPE and frozen human/rodent samples, including custom sourcing through accredited biobanks. Rigorous quality assessment to ensure optimal RNA preservation and tissue morphology for downstream analysis.
Probe Panel Selection & Custom Design
Flexible choice from pre-designed panels (e.g., Prime 5K covering 5,001 genes, IO panel with 360 immune-focused genes) with the option to add up to 100 custom probes for targets of interest. Panel selection is tailored to your scientific question.
High-Resolution Imaging & Gene Expression Mapping
Analysis of tissue regions up to 472 mm² with single-cell resolution. Pathologist-validated region selection ensures biologically relevant areas are captured. Deep-learning-based cell segmentation enables accurate single-cell assignment.
Comprehensive Bioinformatics & Data Analysis
End-to-end computational pipeline including alignment of transcripts to spatial coordinates, cell type identification, spatial clustering, tumor microenvironment characterization (immune infiltration, signaling pathways), and differential expression analysis across tissue regions.
How Our Spatial Transcriptomics Service Works
Service Scope – Parameter & Typical Project Scope
| Parameter | Typical Project Scope |
|---|---|
| Tissue types | FFPE and frozen sections from human or rodent (tumor biopsies, TMAs, surgical resections, organoids). Custom sourcing available via accredited biobanks. |
| Region of interest analysis | Individual regions mm² are analyzed; multiple regions may be selected per project. Each region is validated by an expert pathologist to ensure biological relevance. |
| Pre-designed probe panels | Prime 5K (5,001 genes) and IO (360 immune-related genes) panels available. Panel selection based on scientific goals and sample quality. |
| Custom probe add-on | custom gene probes can be added to existing panels for targets not covered by pre-designed sets, allowing tailored gene selection per project. |
| Data outputs | High-resolution spatial gene expression maps (single-cell level), cell type identification and localization maps, tumor microenvironment profiles, spatial clustering, and differential expression analysis across regions. |
Why Partner with Us for Spatial Transcriptomics
Immuno-Oncology Expertise
More than a decade of experience processing over 10,000 tissue samples for immuno-oncology research, supported by +30 peer-reviewed publications in the field. Our team understands the nuances of tumor microenvironment analysis and immune evasion mechanisms.
End-to-End Project Management
A dedicated PhD study director oversees your project from experimental design through data discussion. This single point of contact ensures continuity, rapid decision-making, and thorough interpretation of results aligned with your research objectives.
Advanced Technology & Sample Qualification
We deploy cutting-edge in situ single-cell platforms (Xenium, Visium, GeoMx) and enforce rigorous sample QC to guarantee optimal RNA quality and tissue preservation. Our pathologist-reviewed region selection maximizes biological relevance.
Customizable Bioinformatics Pipeline
Our in-house computational solutions go beyond standard clustering. We offer spatial neighborhood analysis, integration with H&E or multiplexed IHC data, and custom downstream analyses (cell–cell communication, pathway activity mapping) tailored to your hypotheses.
Featured Study
Case Study
High-plex spatial transcriptomic profiling reveals distinct immune components and the HLA class I/DNMT3A/CD8 modulatory axis in mismatch repair-deficient endometrial cancer
View articleReady to Map the Spatial Transcriptome of Your Samples?
Partner with our spatial biology experts to design a study that integrates tissue histology, gene expression, and genomic profiling. From sample qualification to advanced bioinformatics, we deliver the spatial insights you need to advance your oncology, immunology, or neuroscience research.