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.

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