Fresh Frozen Tissue Spatial Transcriptomics Service
Genome-Wide Spatial Profiling from Fresh-Frozen Tissues
Fresh Frozen Tissue Spatial Transcriptomics enables high-resolution, spatially resolved gene expression profiling while preserving RNA integrity at near-native states. By analyzing freshly frozen tissue sections, this approach captures comprehensive transcriptome information together with spatial context, making it particularly suitable for mechanistic studies, pathway analysis, and discovery-driven research.
This service is ideal for researchers seeking unbiased, genome-wide spatial transcriptomic data with maximal sensitivity and flexibility for downstream bioinformatics analyses.
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- What is
- Workflow
- Deliverables
- Applications
- Why choose
- FAQs
- Sample preparation
What Is Fresh Frozen Tissue Spatial Transcriptomics?
Fresh Frozen Tissue Spatial Transcriptomics is a sequencing-based technology that maps gene expression directly onto tissue sections that have been rapidly frozen after collection, without chemical fixation or paraffin embedding. RNA molecules released from the tissue are captured in a spatially barcoded manner, enabling transcriptomic profiling while retaining the original tissue architecture.
Compared with FFPE-based approaches, fresh frozen tissues maintain higher RNA integrity, allowing efficient poly(A)-based capture and sequencing of a broad range of transcripts. This results in higher gene detection rates, improved dynamic range, and compatibility with advanced analyses such as differential expression, pathway enrichment, and integration with single-cell RNA-seq datasets.
Workflow
The Fresh Frozen Tissue Spatial Transcriptomics workflow is designed to preserve RNA integrity while ensuring reliable spatial mapping and data quality.
Data Deliverables
Customers receive a comprehensive set of data and results tailored for downstream analysis:
- Spatially resolved gene expression matrices
- Tissue images aligned with spatial transcriptomic data
- Quality control metrics and summary reports
- Optional advanced bioinformatics analyses and visualizations
Typical Applications
Fresh Frozen Tissue Spatial Transcriptomics is widely applied across basic, translational, and preclinical research:
- Tissue heterogeneity and microenvironment characterization
- Tumor biology and spatial tumor–immune interactions
- Developmental biology and organogenesis studies
- Neurobiology and brain region–specific expression mapping
- Drug response and mechanism-of-action investigations
- Integration with single-cell RNA-seq or spatial proteomics data
Why Choose Fresh Frozen Tissue?
Fresh frozen samples provide distinct advantages for spatial transcriptomic studies that require depth, sensitivity, and discovery potential:
- High RNA Integrity – Preserves native RNA quality for robust transcriptome-wide profiling
- Unbiased Transcript Detection – Enables genome-wide analysis without predefined probe panels
- Enhanced Sensitivity – Higher gene counts and improved detection of low-abundance transcripts
- Advanced Downstream Analysis – Supports pathway analysis, cell-type deconvolution, and multi-omics integration
- Flexible Research Applications – Suitable for both exploratory and hypothesis-driven studies
FAQs
What types of tissues are best suited for fresh frozen spatial transcriptomics?
Fresh frozen spatial transcriptomics is suitable for a wide range of tissues, including tumor, brain, and other solid tissues. Samples with high RNA quality and well-preserved morphology yield the best results.
Are there species restrictions for this service?
Supported species vary by platform; please contact our technical team for details.
Can fresh frozen samples be combined with other omics analyses?
Yes. Fresh frozen spatial transcriptomics data can be integrated with single-cell RNA-seq, bulk RNA-seq, spatial proteomics, or metabolomics to provide multi-dimensional insights.
Is histological information preserved in fresh frozen samples?
Yes. Although morphology is not as pristine as FFPE samples, fresh frozen sections retain sufficient structural information for spatial annotation and interpretation when properly handled.
What is the typical turnaround time?
Our standard turnaround time is 8-12 weeks from the date we receive your samples.
Learn about other Q&A.
Sample Preparation Guidelines
| Criteria | Recommendation |
|---|---|
| Sample Type | Fresh frozen tissue sections |
| Preservation | Snap-frozen immediately after collection (no chemical fixation) |
| Embedding Medium | OCT (optimal for sectioning) |
| Section Thickness | Typically 5–10 μm |
| Storage & Shipping | Maintained at −80 °C and shipped on dry ice |
Note: Certain spatial transcriptomics workflows may be compatible with chemically fixed frozen tissue sections (e.g., PFA-fixed cryosections). However, fixation can affect RNA integrity and transcriptome coverage. Sample compatibility should be evaluated on a case-by-case basis prior to submission.
Detailed sample preparation and submission guidelines will be provided upon project consultation.
