SureSelectXT RNA Direct Protocol Provides Simultaneous Transcriptome Enrichment and Ribosomal Depletion of FFPE RNA

The ability to extract RNA and prepare RNA sequencing (RNA-Seq) libraries from Formalin Fixed Paraffin Embedded (FFPE) tissues allows researchers to identify and validate new biomarkers of disease onset, progression, and therapy resistance. However, the typically poor quality of RNA derived from FFPE samples has previously limited use of this tissue source as a resource for transcriptome profiling and research by next generation sequencing (NGS)1. Recently, when performing targeted enrichment of cDNA libraries, we have found that with protocol modifications of the Agilent Strand-Specific RNA Library Prep kit we can generate RNA-Seq data with minimal ribosomal contamination and good sequencing coverage. In this study, we used a set of matched fresh frozen (FF) and FFPE-derived RNA from tumor/normal samples to demonstrate that high-quality data can be derived from FFPE samples using a protocol that does not require upfront ribosomal depletion or poly(A) selection. When using the SureSelectXT RNA Direct protocol and the reagents from the SureSelectXT RNA Direct Kit, we found that transcripts were up regulated and down regulated to similar degrees with similar confidence levels in both the FF and FFPE samples, demonstrating the utility for meaningful gene expression studies with RNA stored in FFPE blocks. SureSelectXT RNA Direct Protocol Provides Simultaneous Transcriptome Enrichment and Ribosomal Depletion of FFPE RNA