Systematic evaluation of RNA quality and microarray data reliability in human formalin-fixed paraffin-embedded and fresh frozen tissue samples

We assessed the feasibility and reliability of microarray studies using formalin-fixed paraffin-embedded (FFPE) tissue-derived RNA compared with transcriptome data from paired fresh-frozen (FF) material. We established a robust workflow to generate highly reproducible microarray datasets from only 2 ng RNA input. For prior quality assessment, inspection of Agilent Bioanalyzer electropherograms, calculation of RNA fragment size distribution (DV200) and routine qPCR for selected references genes were done. The study bases on tissue samples (hippocampus of right hemisphere) from three epileptic patients suffering from Rasmussen encephalitis. After surgical resection, the tissue was coronally cut into two parts. One part was immediately snap-frozen and stored at -80 °C (FF samples). The second half was fixed in 4% PFA and embedded in paraffin (FFPE samples).