Systematic evaluation of RNA quality and microarray data reliability in rat formalin-fixed paraffin-embedded and fresh frozen tissue samples. Systematic evaluation of RNA quality and microarray data reliability in rat 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. Overall design: The study bases on microdissected striatal areas from rat brain tissue. We included 3 samples derived from FF tissue and 3 samples derived from FFPE blocks.