FFPE Tissue Processing Service
Formalin-Fixed Paraffin-Embedded (FFPE) tissue is the gold standard for clinical pathology and archival research. However, standard clinical processing often compromises the delicate molecules required for multi-omics analysis.
Our FFPE Processing service bridges the gap between traditional histology and next-generation spatial biology. We produce high-quality, "omics-ready" FFPE blocks designed to withstand the rigors of antigen retrieval and probe hybridization while maintaining superior morphological detail.
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- Advantages
- Workflow
- Applications
- FAQs
"Omics-Grade" vs. "Pathology-Grade"
While standard pathology focuses on visual staining (H&E), spatial omics requires molecular accessibility. The fixation process creates methylene bridges (cross-links) that stabilize structure but can "lock away" RNA and proteins.
We optimize our workflow to balance structural preservation with molecular recoverability:
- Controlled Fixation Windows: We strictly monitor fixation times (typically 12–24 hours in 10% Neutral Buffered Formalin) to prevent over-fixation, which makes antigen retrieval difficult, or under-fixation, which degrades morphology.
- Standardized Dehydration: We use automated tissue processors with fresh, high-grade ethanol and xylene (or xylene-substitutes) to ensure complete dehydration and clearing. This prevents "mushy" blocks that cause micro-chatter during sectioning.
- RNA-Friendly Protocols: For samples destined for spatial transcriptomics (e.g., Visium CytAssist, Xenium), we adhere to RNase-free handling protocols to maximize the DV200 scores (percentage of RNA fragments >200 nucleotides) required for high-sensitivity mapping.
Our Workflow
From wet tissue to a stable paraffin block, precision is key.
- Grossing & Cassetting: Experienced technicians trim tissue to the optimal size (thickness≤3-4mm) to ensure reagents penetrate the center of the sample evenly.
- Infiltration: Tissue is impregnated with high-quality, low-melting-point paraffin wax, providing the structural support needed for ultra-thin microtomy.
- Orientation & Embedding: We carefully orient the tissue in the mold according to your specific instructions (e.g., "mucosa down" or "en face") to ensure the region of interest is represented in the very first sections.
- Archival Storage: Once embedded, blocks are stable at room temperature for years, making them the perfect solution for longitudinal studies or biobanking.
Applications: Unlocking the Archive
Our optimized FFPE processing workflows are designed to turn your archival blocks into robust data sources. By balancing rigorous structural preservation with molecular accessibility, we ensure your samples are compatible with the industry's leading spatial platforms.
Spatial Transcriptomics: High-Fidelity RNA Mapping
While historical RNA sequencing relied heavily on fresh tissue, recent breakthroughs in probe-based chemistry have made FFPE fully compatible with next-generation spatial transcriptomics. Unlike traditional poly-A capture methods that require long, intact RNA strands, modern platforms (such as 10x Genomics Visium CytAssist, Xenium, and NanoString GeoMx) utilize highly specific probes to target RNA sequences within the fixed tissue. Our team focuses on maximizing the "recoverable" RNA in your blocks, optimizing permeabilization times to allow these probes to penetrate the cross-linked matrix. This allows you to generate rich, whole-transcriptome maps directly from the same archival samples used for your pathological diagnosis.
Spatial Proteomics: The Standard for Protein Profiling
FFPE tissue remains the gold standard for spatial proteomics due to its superior ability to preserve cellular morphology. The formalin fixation process effectively "locks" proteins in place via methylene cross-linking, maintaining the precise subcellular localization of your targets. Our laboratory utilizes specialized antigen retrieval protocols---fine-tuned for temperature and pH---to reverse these cross-links without damaging the tissue. This ensures high-affinity antibody binding for everything from standard Immunohistochemistry (IHC) to high-plex assays, allowing you to visualize complex immune landscapes and tumor microenvironments with exceptional clarity.
FAQs
Q: How old can my FFPE blocks be for spatial transcriptomics?
A: Age is less important than storage conditions, but newer is generally better. We successfully process blocks that are 1–5 years old regularly. For blocks older than 5–10 years, RNA degradation is common. We strongly recommend running a DV200 QC check on any block older than 2 years before committing to a full spatial study.
Q: Can I send pre-cut slides instead of a block?
A: We strongly prefer receiving the whole block. This allows our histologists to cut fresh sections immediately prior to the assay, minimizing oxidation and RNA degradation.
If you must send slides: They must be sectioned onto the specific validated glass required by the platform (e.g., 10x Genomics Visium slides) and shipped immediately in a sealed, desiccated container.
Q: My study involves bone or calcified tissue. Is special processing required?
A: Yes. It is critical that you do not use standard acid-based decalcification if your samples are intended for spatial transcriptomics. Strong acids cause rapid hydrolysis of nucleic acids, resulting in extremely low DV200 scores and failed sequencing libraries.
Instead, we utilize a gentle, EDTA-based decalcification protocol. EDTA acts as a chelating agent to remove calcium slowly without damaging RNA or protein epitopes. While this process takes longer than acid treatment, it is the only method that ensures your calcified samples remain compatible with high-sensitivity platforms like 10x Genomics Visium or Xenium.
Q: Is FFPE tissue compatible with Spatial Lipidomics and spatial metabolomics analysis?
A: Generally, no. The standard FFPE processing workflow requires dehydrating tissue in ethanol and clearing it with xylene or similar organic solvents. These chemicals effectively dissolve and strip away the vast majority of cellular lipids and small metabolites, resulting in severe signal loss and a distorted molecular profile. For these specific applications, we strongly recommend using Fresh Frozen tissue to ensure the true lipidome and metabolome are preserved for analysis.
Q: What is the DV200 score and why do you require it?
A: The DV200 score measures the percentage of RNA fragments that are longer than 200 nucleotides. Because formalin fixation fragments RNA, standard RIN (RNA Integrity Number) scores are not useful.
Requirement: We typically require a DV200 score of >50% for Visium and >30-40% for Xenium/CosMx.
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