FFPE and low quality samples

Typically RNA isolated from formalin-fixed, or paraffin-embedded (FFPE) tissues is partially degraded and has a low overall quality.

For these samples and other low-quality samples, the Illumina TruSeq RNA Access library prep kit provides a low-cost solution for analyzing (human) RNA. Starting from as little as 10 ng total RNA from intact samples or 20 ng total RNA from degraded samples, it is possible to achieve accurate, sensitive RNA-Seq results. Combining proven RNA library prep chemistry with efficient sequence-specific capture, the TruSeq RNA Access Kit generates RNA-Seq libraries from degraded samples that focus on the RNA coding regions.

Alternatively, we successfully applied Lexogen QuantSeq 3′ mRNA-Seq Library Prep on FFPE samples. This approach is cheaper and ideal for gene expression studies.


Advantages of the TruSeq RNA Access Library Prep

  • Focusing on the (human) transcriptome coding regions
  • High-quality data can be obtained from difficult / degraded samples
  • Sequencing is possible for low input amounts of RNA (10 to 20 ng)


Advantages of the Lexogen QuantSeq 3′ mRNA-Seq Library Prep

  • Affordable: only the 3′ part of each transcript is sequenced
  • Ideal for gene (mRNA) expression studies
  • High-quality data can be obtained from difficult / degraded samples
  • Sequencing is possible for low input amounts of RNA (0.1 ng)



We initiate the process by performing an initial quality check of the total RNA provided by you. During this quality check the concentration and integrity of the RNA is determined. We only continue with samples that passed this initial quality check. If for some reason certain samples did not pass this initial check, we will contact you to discuss on how to proceed.

In the next steps, the RNA is captured (Illumina TruSeq RNA Access library prep kit) and transcribed (Illumina TruSeq RNA Access library prep kit / Lexogen QuantSeq 3′ mRNA-Seq Library Prep) to cDNA. From the cDNA, sequencing libraries are constructed, which are again quality checked. Finally, the libraries are sequenced on one of our Illumina sequencers. The technical quality of the sequencing run is monitored in real time.

Sequencing data can be transferred to you via the Illumina BaseSpace platform or our own server (FTP download).


Feel free to contact us with any questions.



Ghent University,
Faculty of Pharmaceutical Sciences
Ottergemsesteenweg 460
B-9000 Gent


Inside the building

When entering the Ghent University Faculty of Pharmaceutical Sciences through the main entrance, elevators will be located in front of you. NXTGNT is situated on the third floor. When exiting the elevators, NXTGNT is located at your right-hand side.


Contact us


Call: +32 9 264 80 59