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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Updated: Jan 5, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
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FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.

Jeffery M Vahrenkamp1, Kathryn Szczotka2, Mark K Dodson2

  • 1Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA.

Genome Research
|October 26, 2019
PubMed
Summary

We developed FFPEcap-seq, a new method for RNA sequencing from challenging formalin-fixed paraffin-embedded (FFPE) cancer samples. This technique accurately measures mRNA and enhancer RNA expression from degraded FFPE specimens.

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Formalin-fixed paraffin-embedded (FFPE) samples are the standard for clinical cancer specimens.
  • Accurate RNA quantification from FFPE is difficult due to low yields and degradation.
  • Clinical molecular tests require methods applicable to FFPE material.

Purpose of the Study:

  • To develop a method for high-quality RNA sequencing from FFPE samples.
  • To enable accurate measurement of mRNA and enhancer RNA expression from FFPE specimens.
  • To facilitate the clinical application of molecular tests on FFPE samples.

Main Methods:

  • FFPEcap-seq combines enzymatic enrichment of 5' capped RNAs.
  • Template switching is used to create sequencing libraries.
  • The method is designed for FFPE-derived RNA.

Main Results:

  • FFPEcap-seq faithfully captures mRNA expression levels in FFPE specimens.
  • The method detects enhancer RNAs from distal regulatory regions.
  • FFPEcap-seq generates high-quality 5' end RNA-seq libraries.

Conclusions:

  • FFPEcap-seq is a fast and straightforward method for 5' end RNA sequencing.
  • This method overcomes challenges associated with RNA analysis in FFPE samples.
  • FFPEcap-seq has the potential to broaden the impact of clinical molecular tests.