FFPE RNA Quality Assessment with Agilent Systems

This technical overview presents a comparison of the analysis of formalin-fixed paraffin-embedded (FFPE) RNA samples using the Agilent 2100 Bioanalyzer and the Agilent Fragment Analyzer systems. The document outlines the challenges associated with RNA extraction from FFPE samples, particularly the degradation caused by formalin fixation. It details the use of the DV200 quality metric, which assesses the percentage of RNA fragments above 200 nucleotides, to determine the suitability of samples for next-generation sequencing. The results section compares the DV200 scores obtained from both systems across various FFPE RNA samples, including cow liver, cow cerebellum, mouse liver, and pig spleen. The findings indicate that both systems provide comparable DV200 measurements and demonstrate high precision, with coefficients of variation below 5.7%. This comparison supports the interchangeability of the two systems for FFPE RNA quality assessment, allowing researchers to confidently incorporate the DV200 metric into their workflows.