FFPE Spatial Transcriptomics Service

Maximize Archived Tissue Value with FFPE Spatial Profiling

FFPE Spatial Transcriptomics enables spatially resolved gene expression profiling directly from formalin-fixed, paraffin-embedded (FFPE) tissue sections. By leveraging probe-based or imaging-driven technologies optimized for fragmented RNA, this approach unlocks the vast value of archived clinical samples while preserving histopathological context.

This service is particularly suited for translational and clinical research, retrospective studies, and projects where access to fresh frozen tissue is limited.

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What is
Workflow
Deliverables
Applications
Why choose
FAQs
Sample preparation

What Is FFPE Spatial Transcriptomics?

FFPE Spatial Transcriptomics maps gene expression patterns within FFPE tissue sections using targeted probe hybridization or imaging-based detection strategies. Unlike sequencing workflows that rely on intact poly(A) tails, FFPE-compatible spatial transcriptomics is specifically designed to accommodate chemically fixed and fragmented RNA.

By integrating spatial gene expression data with well-preserved tissue morphology and pathological annotations, FFPE Spatial Transcriptomics enables biologically and clinically meaningful insights from archived specimens, including long-term biobank collections.

Workflow

FFPE spatial transcriptomics workflow

Data Deliverables

Customers receive data packages designed for clinical and translational interpretation:

Spatially resolved gene expression profiles
Tissue images aligned with spatial data
Quality control metrics and summary reports
Custom visualizations and region-based expression analyses
Optional advanced bioinformatics and comparative analyses

Typical Applications

FFPE Spatial Transcriptomics is widely used in studies requiring clinical context and sample accessibility:

Retrospective clinical and translational research
Spatial biomarker discovery and validation
Tumor microenvironment and immune profiling
Disease progression and tissue pathology studies
Correlation of gene expression with histological features
Companion diagnostics and therapeutic response research

Why Choose FFPE Spatial Transcriptomics?

FFPE samples offer unique advantages that are critical for many research and translational applications:

Broad Access to Samples – Enables analysis of archived and retrospective clinical specimens
Excellent Morphological Preservation – Maintains histological detail and compatibility with pathology workflows
Clinical Relevance – Well suited for biomarker validation and disease-focused studies
Targeted & Reproducible Profiling – Probe-based detection ensures robust performance with degraded RNA
Seamless Integration with Pathology – Supports co-registration with H&E, IHC, and IF staining

FAQs

Can archived FFPE samples be used?

Yes. Many archived FFPE samples can be analyzed, although RNA quality may vary depending on fixation and storage history. Our team evaluates sample suitability prior to project initiation.

Is FFPE spatial transcriptomics suitable for discovery research?

FFPE workflows are typically targeted and best suited for hypothesis-driven, translational, or validation-focused studies rather than unbiased transcriptome discovery.

Can spatial transcriptomics data be combined with pathology or IHC data?

Yes. FFPE spatial transcriptomics is highly compatible with histological staining, IHC, and IF, enabling direct correlation between gene expression and tissue pathology.

What level of spatial resolution can be achieved?

Resolution depends on the specific platform and assay design, ranging from region-of-interest profiling to near single-cell or subcellular resolution for imaging-based methods.

Which species are supported by your FFPE Spatial Transcriptomics service?

The range of compatible species depends on the technical platform used. For detailed information, please consult our technical team.

Learn about other Q&A.

Sample Preparation Guidelines

Criteria	Recommendation
Sample Type	FFPE tissue sections
Fixation	Neutral buffered formalin
Block Age	Recent or archived blocks (quality dependent)
Section Thickness	Typically 4–5 μm
Storage & Shipping	Room temperature; standard FFPE slide or block handling

Detailed sample preparation and submission guidelines will be provided upon project consultation.

* For Research Use Only. Not for use in diagnostic procedures.

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From Our Clients

"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

"The overall service from Creative Proteomics was outstanding. They made the entire process seamless and efficient, allowing us to focus on our research. We worked with leaf and root samples from various Arabidopsis genotypes for targeted metabolomics analysis. Their thorough profiling of primary and secondary metabolites gave us important insights into how the plants respond metabolically to environmental stress."

Dr. Laura Henderson, Plant Physiologist

"We had a pleasant collaboration with Creative Proteomics on mass spectrometry analysis of lipids. They conducted a detailed analysis of lipid species, providing us with important insights into lipid metabolism and its relationship with metabolic syndrome disease states."

Dr. Sarah Mitchell, Research Scientist

Online Inquiry

Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to for inquiries.

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