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Related Experiment Video

Updated: Jul 17, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
09:20

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue.

Renata A Coudry1, Sibele I Meireles, Radka Stoyanova

  • 1Division of Population Science, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111, USA.

The Journal of Molecular Diagnostics : JMD
|January 26, 2007
PubMed
Summary

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Researchers developed a reliable method for gene expression profiling using RNA from formalin-fixed, paraffin-embedded (FFPE) tissues. This technique enables analysis of archived samples, yielding high-quality microarray data comparable to fresh frozen tissues.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant archival resources.
  • Extracting high-quality RNA from FFPE samples for gene expression analysis is challenging.
  • Laser capture microdissection (LCM) offers a method for isolating specific cell populations from FFPE tissues.

Purpose of the Study:

  • To establish a reliable method for gene expression profiling using RNA from FFPE tissues.
  • To compare gene expression profiles from FFPE samples with matched frozen samples.
  • To provide recommendations for assessing RNA quality from FFPE samples.

Main Methods:

  • Utilized a custom-designed 22,000 oligonucleotide microarray.
  • Isolated colonic epithelial cells from FFPE and matched frozen samples using LCM.

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Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens
12:24

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens

Published on: May 5, 2018

Related Experiment Videos

Last Updated: Jul 17, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
09:20

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens
12:24

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens

Published on: May 5, 2018

  • Extracted, amplified, and labeled RNA from FFPE tissues using the Paradise Reagent System.
  • Assessed RNA quality using Bioanalyzer, RT-PCR, and agarose gel electrophoresis.

    • Main Results:

    • Demonstrated the feasibility of obtaining reliable microarray data from FFPE samples via LCM.
    • Achieved high concordance (Pearson's correlation coefficient 0.80–0.97) between FFPE and frozen samples.
    • Observed high correlation reflecting ribosomal RNA peaks in FFPE-derived RNA compared to frozen samples.

    Conclusions:

    • A reliable method for gene expression analysis using FFPE tissue RNA is established.
    • LCM combined with microarray analysis provides valuable gene expression data from archival FFPE samples.
    • Practical recommendations for RNA integrity and quality assessment in FFPE samples are provided.