Utilization of FFPE Derived Total RNA for Targeted or Whole Transcriptome RNA-seq using SureSelect Strand Specific RNA Library Preparation Kit

In this application note, we present modifications that should be considered when processing FFPE RNA using Agilent’s SureSelect strand specific RNA library preparation kit for targeted RNA-seq. These guidelines were used to process two very low-quality FFPE RNA samples in parallel with matched snap-frozen controls using a custom SureSelect capture < 3 Mb in size. Our data shows that with a few minor adjustments to the protocol, the SureSelect strand specific library preparation kit can be successfully used to generate libraries from highly fragmented FFPE samples.