Spatial Transcriptomics Mapping whole transcriptome profiles within tissue
Use spatial transcriptomics to map the whole transcriptome with morphological context.
Our move into spatial
Single Cell Discoveries is the market leader in single-cell RNA sequencing. Single-cell RNA sequencing measures gene expression in individual cells, revealing cellular heterogeneity that is hidden in bulk RNA sequencing. But cells don't exist in isolation — their position and interactions within tissues are crucial to understanding biology. That's why we've expanded into spatial transcriptomics.
Why spatial transcriptomics?
Biology happens in context
Many biological processes depend on the spatial organization of cells and their gene expression. Spatial transcriptomics captures this vital layer of information, showing how cells work together inside tissues — something traditional single-cell RNA sequencing alone cannot do.
Complementing single-cell data
Our deep expertise in scRNA-seq positions us uniquely to harness the powerful combination of single-cell and spatial data. By integrating these datasets, we can more precisely identify cell types, map cellular interactions, and reconstruct the tissue landscape with greater fidelity than either method could achieve alone.
Experience and expertise
Leveraging our extensive knowledge in transcriptomics, sample preparation, and workflow optimization, Single Cell Discoveries is ideally equipped to deliver spatial transcriptomics at the highest standards.
Experience with sample logistics
Spatial transcriptomics demands exceptional sample handling, from tissue preservation to processing, to maintain RNA integrity and spatial information. Our expertise in optimizing sample workflows ensures researchers receive high-quality, reliable spatial data.
Platform agnostic, solution-focused
No single spatial platform fits every research question. We work across multiple technologies, allowing us to match the best method to each specific experiment, tissue type, and resolution need, without bias toward a single provider.
By adding spatial transcriptomics, Single Cell Discoveries offers a complete solution for understanding cells, not just as individual units, but as part of the living tissue environment. We aim to empower researchers with more meaningful biological insights.
We currently provide the 10x Genomics Visium HD service for whole transcriptome spatial discovery at single-cell resolution.
Single-cell RNA sequencing vs. Spatial Transcriptomics
Single-cell RNA sequencing and spatial transcriptomics each offer unique insights: scRNA-seq profiles gene expression at the single-cell level but loses spatial context, while spatial transcriptomics preserves tissue architecture. Researchers often use scRNA-seq for high-throughput screening to identify interesting samples, then apply spatial transcriptomics for deeper, location-specific analysis.
Single-cell RNA sequencing
- High sample throughput — process many samples quickly
- Identify samples with interesting single-cell profiles for follow-up spatial analysis
- Reveals cellular heterogeneity (different cell types and states)
- No spatial context (cells are dissociated)
- Highly flexible — can add modalities like epigenome (ATAC-seq), TCR/BCR sequencing, etc.
Spatial Transcriptomics
- Preserves tissue structure and cellular positioning in data
- Reveals spatial heterogeneity — differences between regions (e.g., primary tumor vs metastasis)
- Lower sample throughput compared to scRNA-seq
- Limited multi-omics integrations (currently RNA-focused)
- Ideal for mapping cell organization, tissue architecture, and microenvironment
How can we help?
Our team can help you design the right strategy.
Book a meeting with our experts today to discuss all our solutions, from single-cell screening to spatial mapping.