FFPE tissue refers to biological tissue samples that are preserved by being fixed in formalin and then embedded in paraffin wax. This process helps maintain the structure of the tissue for long-term storage and analysis.

FFPE stands for Formalin Fixed Paraffin Embedded, which refers to the process by which the tissue is preserved.

FFPE tissues are prepared in a way that preserves cellular structure and allows long-term storage of your tissue specimens, making them valuable for histological and molecular analysis – especially in cancer research. FFPE tissues can be used for both immunohistochemistry and in-situ hybridization.

Tissues used in FFPE are fixed in formalin immediately after excision. Later, they are embedded in paraffin wax, which solidifies as it cools. Once this process is complete, the samples can then be subjected to processes such as blocking, sectioning, permeabilization, and antigen revival. 

FFPE tissue samples can be stored for many years if kept in controlled environmental conditions. Some FFPE samples have been successfully stored and used for decades.

FFPE samples are suitable for a wide range of analyses, including histological examination (e.g., H&E staining), immunohistochemistry (IHC), in situ hybridization (ISH), RNA and DNA extractions, spatial genomics and proteomics, molecular techniques like polymerase chain reaction (PCR), and next-generation sequencing (NGS).

Yes, other tissue preservation methods include freezing samples in liquid nitrogen or embedding them in an optimal cutting temperature (OCT) compound. The choice of tissue depends on your specific research or diagnostic needs.

FFPE samples and frozen samples are both common methods of preserving biological tissues for research and diagnostic purposes. Each method has its advantages and disadvantages; the choice between FFPE and frozen samples always depends on the specific requirements of your study. Some general advantages to using FFPE over frozen tissues include longer-term preservation, tissue archiving, tissue availability, easier tissue handling, and storage, cost-effectiveness, easier shipping due to tissue stability, and compatibility with both IHC and ISH.

Whatever the application, the use of FFPE tissues poses some challenges. FFPE tissues may undergo antigen masking during the process of formalin fixation; antigen retrieval methods are often needed to unmask epitopes and enhance antibody binding in IHC. The process of fixation may also lead to the degradation of nucleic acids and proteins, affecting the overall quality of the tissue and potentially interfering with the success of both IHC staining and DNA and RNA extraction. Fixation can also sometimes cause cross-linking of proteins, making it difficult to extract DNA and RNA. 

Other challenges of working with FFPE tissues include fragmentation of nucleic acids, degradation of preserved tissue over time, mild chemical modifications in nucleic acids, and, occasionally, inefficiency of nucleic acid extraction due to the paraffin. Newer techniques and protocols have been developed to overcome these challenges, such as optimization of extraction protocols, or heat-induced epitope removal methods that unmask affected antigens. 

Specialized kits and protocols are available for DNA and RNA extraction from FFPE samples. These methods often involve the steps of deparaffinization, digestion, and purification. BioChain offers kits and reagents to extract NA from FFPE samples, including our xTractPure™ line (for DNA and RNA) and the Membrane Protein Extraction Kit to name a few.

Yes, FFPE samples are commonly used in biomarker discovery. FFPE samples are particularly useful in cancer testing due to their long shelf-life, as archived specimens can provide valuable historical data.

Yes, FFPE tissues can be used for spatial biology research, although fresh-frozen tissues are often preferred. Nevertheless, FFPE tissues are valuable for use in spatial applications such as ISH and Fluorescence ISH, IHC, spatial transcriptomics, and multiplexed imaging. 

Paraffin-embedded tissue sections are commonly used in histology and pathology, but they may pose challenges for RNA ISH. Paraffin embedding involves the use of wax to preserve tissues for sectioning, and this process can lead to RNA degradation and cross-linking of nucleic acids, making it more difficult to detect RNA molecules.

However, researchers have developed methods to overcome these challenges and perform RNA ISH on paraffin-embedded tissues. These methods often include steps to deparaffinize the tissue sections, retrieve the RNA, and minimize RNA degradation. Additionally, using probes that specifically target the RNA of interest, and optimizing the hybridization conditions can improve the sensitivity and specificity of RNA ISH in paraffin-embedded sections.

In summary, while paraffin-embedded tissue sections may not be the first choice for RNA ISH, with appropriate modifications and optimization of protocols, it is possible to perform RNA ISH on such samples. Researchers should carefully consider the specific requirements of their experiment and may need to experiment with different conditions to achieve optimal results.

Positively charged slides play a crucial role in the preparation and mounting of FFPE tissue sections for various laboratory techniques, including histological and immunohistochemical analyses. The positive charge on these slides is typically provided by a coating of a substance such as poly-L-lysine or aminosilane. Positively charged slides promote strong adhesion, minimize tissue folding and rolling, enhance tissue spreading, improve staining quality, facilitate in situ techniques, and increase uniformity in staining protocols. BioChain uses positively charged slides in its FFPE fixation process.

Avoid using any solutions with detergents such as Triton X 100, or Tween 20. These detergents may cause the tissue to fall off the slides.

For matched FFPE tissues for eg-T6235090-PP we carry 5 PT slides and 5 PN slides. There is 1 section of 8um thickness on each slide. We ensure high precision and consistency in thickness across all slide types.

Our FFPE fixation protocol has the following steps:

• Immediately after excision, fix tissue in 10% formalin for 24 hours
• Move tissue to ethanol for gradient dehydration
• Clear tissues using xylene for transparency
• Dip sample into paraffin wax
• Embed

No demineralization of the tissues is performed.

Yes, BioChain can provide decalcified FFPE bone samples.

No, the sections have not been coated with anything.

BioChain’s FFPE tissue samples harvested from cancer patients are fixed immediately after harvest. FFPE tissue samples harvested from cadavers are fixed between 12 and 24 hours after harvest. 

No, our histopathological services are not performed under GLP conform conditions.

No, we do not label the sections with any dyes.

Yes, an IRB certificate can be provided on request for your sample. All samples are collected from informed consented donors.