Single-Cell Spatial Transcriptomics Service
Mapping Gene Expression at Single-Cell Resolution
Our Single-Cell Spatial Transcriptomics service reveals gene expression patterns at single-cell resolution while preserving their spatial context within tissues. By combining high-resolution imaging with molecular barcoding, this technology enables researchers to map cell types, states, and interactions across complex tissue architectures.
With this service, you can explore cellular heterogeneity and tissue organization, identify spatial biomarkers, investigate cell-to-cell interactions and microenvironment influences, and generate spatially resolved gene expression data to support hypothesis-driven research and translational studies.
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- What is
- Workflow
- Platforms
- Applications
- Why choose
- FAQs
- Sample preparation
- Case study
What is Single-Cell Spatial Transcriptomics?
Single-Cell Spatial Transcriptomics is a cutting-edge approach that combines high-resolution spatial mapping with single-cell RNA sequencing. This technique enables the precise localization of gene activity within tissue samples, offering a powerful tool to explore the interactions between cells in their native environments. By analyzing the gene expression of individual cells within the context of their spatial locations, researchers can gain deeper insights into tissue heterogeneity, developmental biology, and the molecular basis of diseases like cancer and neurodegeneration.
Workflow
Platform
At the heart of our Single-Cell Spatial Transcriptomics service is Xenium, a cutting-edge technology platform designed to deliver high-resolution, spatially mapped gene expression data. Xenium enables the precise analysis of gene activity at the single-cell level within tissue samples, allowing us to capture the spatial organization of cells and their molecular interactions with exceptional accuracy. With Xenium, we can provide unparalleled insights into complex biological processes, including tumor microenvironments, developmental biology, and neural tissue organization.
Deliverables
| Category | Specific Deliverables |
|---|---|
| Comprehensive Data Package |
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| Spatial Visualization |
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| Biological Interpretation |
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Applications
- Cancer Research: Study the heterogeneity of tumor, tumor microenvironments, and spatially localized gene expression changes that drive malignancy.
- Neurodegenerative Diseases: Explore how gene expression varies in different regions of the brain and identify potential biomarkers for diseases like Alzheimer's and Parkinson's.
- Developmental Biology: Investigate how cells organize and differentiate within developing tissues, revealing key insights into embryonic development and tissue regeneration.
- Immune Microenvironment: Assess immune cell localization and activation within tissues, facilitating the development of targeted immunotherapies.
- Precision Medicine: Discover cell-specific gene expression patterns that can guide personalized treatments and drug development.
Why Choose Us?
- True Subcellular Resolution: Unlike older spatial technologies that average signals over 50µm spots, our Xenium platform detects individual RNA transcripts with<1µm precision, allowing for accurate cell segmentation.
- Expert Analysis: Our team of experienced scientists and bioinformaticians provides thorough analysis and interpretation of your data, translating complex results into actionable insights.
- Comprehensive Service: From tissue preparation to data interpretation, we offer end-to-end solutions for your spatial transcriptomics research.
- Multi-omics Integration: Combine our spatial transcriptomics with your scRNA-seq data for a holistic view of cell types, states, and interactions within their native tissue context.
FAQs
What types of tissue samples can I use for Single-Cell Spatial Transcriptomics?
We accept a variety of tissue samples, including fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues. For optimal results, fresh frozen tissues are preferred, but FFPE tissues can also be processed depending on your research needs.
Are there any specific requirements for FFPE tissue samples?
FFPE samples require careful handling during sample collection and sectioning to ensure RNA preservation. We will guide you through best practices for submitting these types of samples.
Can you help with the bioinformatics analysis of the data?
Absolutely! We provide full bioinformatics analysis, including data integration, spatial mapping, and biological interpretation. Our team will guide you through the process and help you extract meaningful insights.
What is the typical turnaround time?
Our standard turnaround time is 3-4 weeks from samples receipt. Please note that turnaround time may vary based on the unique requirements of each project. We recommend contacting our technical team to discuss your specific needs and obtain a tailored timeline.
Learn about other Q&A.
Sample Preparation Guidelines
For optimal results, please follow the guidelines below when submitting your samples. We will perform quality control upon receiving the samples to ensure they meet the experimental requirements.
| Sample Type | Required Quantity | Preparation Instructions |
|---|---|---|
| Fresh Frozen Tissue | 10-20 mg per sample | Collect tissue immediately and snap-freeze it in liquid nitrogen. Store at -80℃ until submission. |
| FFPE Tissue (Formalin-Fixed, Paraffin-Embedded) | 10-20 tissue sections (4-6 μm thick) | Tissue should be fixed in 10% formalin and embedded in paraffin. Send in properly sealed slides or blocks. |
Important: Please contact us before beginning the project to obtain detailed sample preparation instructions tailored to your specific needs.
Single-Cell Spatial Transcriptomics Case Study
Title: Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy
Journal: Biomarker Research
Published: 2024
- Background
- Methods
- Results
- Conclusion
- Reference
Temporal lobe epilepsy (TLE) is a prevalent form of focal epilepsy often associated with hippocampal sclerosis (HS), characterized by neuronal loss, gliosis, and altered neural circuits. The underlying mechanisms of TLE-HS, particularly the reactive changes in neurons and glial cells, remain poorly understood. Mapping these changes at high spatial and single-cell resolution is critical to understanding epileptogenesis and inflammation in the hippocampus.
Hippocampal tissues from TLE and control mice were analyzed using single-cell RNA sequencing (ScRNA-seq) for glial cells and single-nucleus RNA sequencing (SnRNA-seq) for neurons, complemented by Xenium-based spatial transcriptomics to map 247 genes at high resolution. Sequencing data were processed to remove low-quality cells and batch effects, followed by dimensionality reduction, clustering, and differential gene expression analysis. Functional enrichment, pseudotime trajectories, and cell–cell communication analyses were then applied, and integration with spatial transcriptomics allowed the mapping of transcriptional changes across specific hippocampal regions.
In Figure 6, the Xenium-based spatial transcriptomics data reveal the high-resolution spatial organization of 27 hippocampal cell types in both control and TLE mouse brains. The analysis highlights substantial shifts in cellular composition and morphology within the TLE hippocampus, with clear differences in the localization of glial cells and neurons. Dimensionality reduction further demonstrates distinct clustering of cell types, and marker gene mapping shows altered spatial expression patterns in TLE, reflecting the reactive glial proliferation and region-specific neuronal changes induced by epileptic activity.
Figure 6. Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections.
Liu et al. combined single-cell, single-nucleus, and Xenium spatial transcriptomics to create a high-resolution atlas of the hippocampus in mice with temporal lobe epilepsy. They found inflammatory activation in glial cells and altered neuronal–glial interactions, with excitatory neurons showing region-specific transcriptional changes.
This integrated atlas highlights how cell-type–specific and spatial transcriptomic changes contribute to hippocampal dysfunction, providing a valuable resource for studying epileptogenesis and potential therapeutic targets.
Reference
- Liu Q, Shen C, Dai Y, et al. Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy. Biomark Res. 2024;12(1):103. Published 2024 Sep 13. doi:10.1186/s40364-024-00636-3
