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 key insights for disease research. Unfortunately, much of this data used to be inaccessible. FFPE RNA-Seq solutions from Illumina now enable researchers to obtain this valuable data, yielding high-quality results from challenging samples.

Webinar: FFPE RNA-Seq

Learn how to overcome hurdles in FFPE RNA sequencing.

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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 relative to total RNA-Seq, while enabling discovery of novel features such as alternative splicing, fusion transcripts and coding variants.1,2

TruSeq RNA Exome overcomes 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 Exome is ideal for mRNA-Seq with FFPE or degraded samples and samples with limited starting material.

Total RNA sequencing provides a comprehensive 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 library preparation and ribosomal RNA removal chemistries into a single 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.

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QC Recommendations for FFPE RNA-Seq

Targeted RNA sequencing is a highly accurate and specific method for measuring expression of transcripts of interest, offering researchers 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.

TruSight Tumor 170 is a comprehensive research 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.

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.

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Sequencing the coding regions or the whole cancer transcriptome can provide researchers with valuable information about gene expression changes in tumors.

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References
  1. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63.
  2. Wilhelm BT, Landry JR. RNA-Seq—quantitative measurement of expression through massively parallel RNA sequencing. Methods. 2009;48:249–57.