Ffpe Samples
Ffpe Samples - Related Videos
07:30
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
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Cited by 19 •
2020
This method describes the steps to improve the quality and quantity of sequence data that can be obtained from formalin-fixed paraffin-embedded (FFPE) RNA samples. We describe the methodology to more accurately assess the quality of FFPE-RNA samples, prepare sequencing libraries, and analyze the data from FFPE-RNA samples.
04:33
Extracellular DNA Staining: A Method to Identify Extracellular DNA in FFPE Tissue Sections
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2023
This video describes the technique of staining extracellular DNA in FFPE tissue sections. The stained extracellular DNA can be quantitated to determine the efficacy of any therapeutic treatment that leads to the death of cancer cells.
04:17
Formalin-Fixed Paraffin Embedded (FFPE) Tissue Preservation: A Method for Studying Tissue Morphology
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2023
The following video describes how to preserve morphology of a tissue with formalin fixation and paraffin embedding.
02:43
Deparaffinization and Rehydration of Tissue Sections: A Two-step Procedure to Remove Paraffin Wax from FFPE Tissue Slides Followed by Tissue Rehydration
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2023
In this video, we demonstrate the processing of FFPE or formalin-fixed paraffin-embedded sections obtained from gastrointestinal tumor tissue. The deparaffinization and rehydration steps allow the processing of the tissue specimen for subsequent analytical applications.
03:53
FFPE Tissue Pretreatment for RNA CISH: A Procedure to Process Formalin-Fixed Paraffin-Embedded Tissue Sections for RNA Chromogenic In Situ Hybridization
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2023
This video demonstrates the steps involved in the pretreatment of FFPE tissue specimens for RNA chromogenic in situ hybridization. The pretreatment process helps maintain nucleic acid integrity within the cells and overall tissue morphology.
FAQs
Formalin creates crosslinks among proteins and other cellular components, stabilizing tissue structure but making biological molecules less accessible. These chemical links contribute to the preservation of morphology needed for microscopy, yet they can interfere with downstream recovery or detection of nucleic acids and proteins. Consequently, molecular assays on archived sections require extraction strategies and assay conditions adapted to fixation-related damage.
Dehydration and paraffin infiltration stabilize the specimen for sectioning and help retain its spatial organization. However, the overall preservation process can fragment nucleic acids, so molecules recovered from archived material may be less intact than the tissue appearance suggests. This difference explains why excellent microscopic morphology does not guarantee equally strong molecular assay performance.
Fixation-related changes can mask epitopes, the molecular regions recognized during antibody-based detection. In immunohistochemistry, that masking may reduce the visibility of a target protein even when the tissue remains structurally well preserved. Researchers therefore interpret protein staining in light of fixation effects and optimize the assay to obtain dependable biomarker evaluation.
Reliable nucleic-acid results depend on more than recovering material from the paraffin-embedded specimen. Researchers must use careful extraction and then optimize assay conditions for the fragmentation and other fixation-related changes present in the sample. This approach helps distinguish a true biological signal from weak or inconsistent detection caused by specimen processing.
They are especially useful when investigators need to study archived clinical material, including specimens collected previously for diagnosis. Because the preserved tissue can support histological examination, immunohistochemistry, and biomarker evaluation, FFPE collections enable retrospective studies that connect tissue morphology with molecular or protein-related findings. Their value is greatest when historical samples are the available research resource.
In pathology, these specimens support histological diagnosis and immunohistochemistry, while in broader biology they provide material for biomarker evaluation and molecular analysis. The combined readout can relate preserved tissue architecture to DNA, RNA, or protein measurements. Interpreting those results requires attention to fixation-related fragmentation, epitope masking, and assay optimization.