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. 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.