Sequence FFPE RNA from degraded tissues

Helping you uncover the critical information in preserved samples

Low-Quality/FFPE RNA-Seq Solutions

RNA sequencing (RNA-Seq) analysis of FFPE and other low-quality samples can offer invaluable insights for disease research. Unfortunately, most of this valuable data was previously inaccessible. Recent FFPE RNA-Seq solutions from Illumina now enable researchers to access critical data, yielding high quality results from degraded samples.

Webinar: FFPE RNA-Seq

Learn how to overcome hurdles in FFPE RNA sequencing.

Access Webinar

mRNA sequencing (mRNA-Seq) is an accurate and cost effective method for analyzing the coding transcriptome. Focusing your sequencing budget on only the messenger RNAs allows for increased sample throughput and lower per sample costs, while enabling discovery of novel features such as alternative splicing, fusion transcripts and coding variants.

TruSeq RNA Access Library Prep Kits overcome the limitation of traditional poly-A based methods for capturing the coding transcriptome; these traditional methods are ineffective for FFPE RNA-Seq analysis. By applying sequence-specific capture that does not rely on the presence of polyadenylated transcripts, TruSeq RNA Access is ideal for mRNA-Seq with FFPE or degraded samples and samples with limited starting material.

Total RNA sequencing (total RNA-Seq) provides the most complete view of the transcriptome, enabling analysis of both coding and multiple forms of noncoding RNA in a single experiment.

Total RNA-Seq provides highly accurate transcript abundance information, and also enables detection of novel features such as gene fusions, transcript isoforms, cSNPs, and allele-specific expression.

TruSeq Stranded Total RNA Library Preparation Kits couple proven sample preparation and ribosomal RNA removal chemistries into a single, streamlined solution for robust whole-transcriptome analysis with RNA-Seq, for FFPE and other low-quality samples as well as normal samples.

QC Recommendations for FFPE RNA-Seq

Extraction methods for FFPE tissue generally yield highly degraded RNA. Read our FFPE quality control recommendations to determine whether your FFPE samples are viable input material for Illumina library preparation kits.

View Tips
QC Recommendations for FFPE RNA-Seq

Targeted RNA sequencing is a highly accurate and specific method for measuring expression of transcripts of interest, offering both quantitative and qualitative information. This allows for differential expression analysis, as well as allele-specific expression measurement and verification of the presence of fusion genes.

The TruSight RNA Pan-Cancer Panel enables comprehensive detection of 1385 gene fusions and gene expression changes, providing researchers with a focused view of the functionally relevant changes occurring in cancer. The panel is compatible with FFPE tissue and accommodates as little as 20 ng of total RNA input from FFPE. The TruSight RNA Pan-Cancer Panel provides a sensitive, reproducible, and economical solution for studies of expression dynamics and functional mechanisms in cancer.

TruSight Tumor 170 is a comprehensive panel that detects fusions and splice variants (as well as other variant classes) that contribute to solid tumor progression from 40 ng of nucleic acid, and is compatible with low-quality FFPE samples.

TruSeq Targeted RNA Expression, a targeted RNA-Seq solution compatible with FFPE and low-quality RNA samples, enables measurement of dozens to thousands of targets simultaneously. The assay leverages proven Illumina sequencing technology to deliver an accurate and powerful method for validating gene expression arrays as well as RNA-Seq studies.

Interested in receiving newsletters, case studies, and information from Illumina based on your area of interest? Sign up now.
Library Prep and Array Kit Selector

Determine the best kit for your needs based on your project type, starting material, and method of interest.

Find the Right Kit
Gain a Complete View of the Transcriptome

See how the NextSeq Series provides a scalable approach for RNA sequencing, with higher sensitivity and accuracy than conventional arrays.

Read Application Note
Easily Analyze RNA-Seq Data

User-friendly BaseSpace Apps simplify data analysis for the most common RNA sequencing study designs.

Find Analysis Tools