Optimized protocols expand your discoveries

One of the challenges many sequencing projects face is extracting enough high-quality nucleic acid for accurate and reproducible results. This challenge can be especially problematic when you’re extracting RNA from FFPE tissue.

At HudsonAlpha Discovery, we focus on the quality and usability of genomic data and have refined all aspects of the RNA-Seq workflow to maximize what you can learn from each sample. For example, our optimized RNA extraction protocols demonstrate that it is possible to extract high quality RNA from FFPE tissue for reliable, reproducible RNA-Seq data and we invite you to give our methods a try.


Learn more with HudsonAlpha Discovery’s RNA-SEQ services.


Analyze a range of RNA types


Optimized sequencing of RNA from FFPE tissue


Quickly scale-up and scale-down any project


  • Transcriptomics
  • Biomarker discovery & profiling
  • Reads per kb million (RPKM), fragments per kb million (FPKM), and transcripts per million (TPM) analyses
  • Differential Expression Analysis
  • Fusion Detection
  • RNA splice site isoform analysis
  • Ingenuity Pathway Analysis (Qiagen)
  • Disease research
  • Personalized medicine
  • All research phases and activities
    •  Basic discovery
    •  Translational and pre-clinical
    •  Clinical

Study a full range of RNAs, even from challenging samples, with our RNA-Seq services.

Highlights of Our RNA-Seq Services

Here are a few examples of what we offer:

Analyze All Types of RNA Utilizing Various Techniques, Including:

  • Total RNA
  • PolyA+/mRNA
  • Ribosomal-reduced (rRNA-reduced) RNA
  • Globin-reduced RNA
  • Long and short non-coding RNA
  • miRNA
  • Extracellular RNA, such as exosomal RNA and RNA in extracellular bodies

Nucleic Acid Extraction and Library Preparation

  • Optimized extraction protocols for a variety of samples
  • Dual concurrent RNA-DNA extraction from challenging sample types such as FFPE tissue—READ THE WHITEPAPER
  • Matched DNA-Seq and RNA-Seq extracted from the same tissues and fluids

RNA Amplification and Library Construction From Low Quantity RNA

  • Takara (Clontech) SMARTer Pico Mammalian RNA Amplification for rRNA-reduced library construction and RNA-Seq from both low and high quality RNA, including RNA isolated from FFPE tissues
  • NuGen RNA amplification and standard cDNA library construction from moderate to high-quality RNA
  • Customer-preferred methods also possible

Illumina TruSEQ RNA Exome (formerly TruSEQ RNA Access) for capturing coding RNAs


  • Illumina TruSight Tumor170 including RNA analysis of 55 genes
  • TruSight Oncology 500 including RNA analysis of 55 genes
  • Additional off-the-shelf options and validation services

Read Length

  • Dual-index 100 base paired-end reads
  • Inquire for custom read-length options

Bioinformatics Analysis and Data Storage

  • Tier 1: FASTQ output and summary report
  • Tier 2: Standard application-specific outputs (BCL, FASTQ, BAM, VCF, gVCF)
  • Tier 3: Standard output as well as interpretation, reports, and flexible data delivery, storage, and consulting time
  • RPKM, FPKM, TPM analyses
  • Differential expression analysis
  • Fusion Detection
  • RNA splice site isoform analysis
  • Ingenuity Pathway Analysis (Qiagen)
  • Flexible data delivery options
  • 90 days storage included with service pricing
  • Long term storage available

Whole genome Sequencing

The HudsonAlpha Discovery Difference

Flexible and creative problem solving with expert scientific guidance


Optimized protocols and automated workflows that reduce technical bias


Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results


Massive scale with 10 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs


A decade of proven experience spanning thousands of projects and hundreds of publications


Leverage the power of the HudsonAlpha Discovery division:

Retaining and extracting longer RNA molecules from FFPE samples


At HudsonAlpha Discovery, we’ve optimized the recovery of RNA from FFPE tissues to yield longer RNA molecules than standard protocols, as demonstrated by the consistently high DV200 scores (Figure 1), which report on the percentage of RNA fragments ≥200 nucleotides in length in any given sample.


Figure 1. Our optimized protocol for extracting RNA from FFPE tissues consistently yields RNA with high DV200 scores (the smaller number of samples processed using the standard protocol is due to limitations in the amount of available tissue).


Featured Paper

RNA-Seq for Biomarker Discovery

Long noncoding RNA, LINC00460, as a prognostic biomarker in head and neck squamous cell carcinoma (HNSCC)

Chaudhary R, et al. Am J Transl Res. 2020; 12(2): 684–696. PMCID: PMC7061833.

In this study, completed when the HudsonAlpha Discovery lab was still the HudsonAlpha Institute Genomic Services Lab, our RNA-Seq services supported an investigation into the possibility of using lncRNAs as a prognostic biomarker of survival in p16-negative HNSCC.

Their findings: “we report LINC00460 is more abundant in tumors compared to adjacent normal tissue and that it may serve as a potential prognostic biomarker in HNSCC.”1

Their findings: “Our finding not only corroborates the previous study but further enhances our understanding of the prognostic value of lncRNAs in HNSCC progression.”1

Recent Publications

  1. Chaudhary R, et al. Long noncoding RNA, LINC00460, as a prognostic biomarker in head and neck squamous cell carcinoma (HNSCC). Am J Transl Res. 2020; 12(2): 684–696. PMCID: PMC7061833.
  2. Dai C, et al. Tacrolimus- and sirolimus-induced human β cell dysfunction is reversible and preventable. JCI Insight. 2020 Jan 16; 5(1): e130770. PMCID: PMC7030815.
  3. Fish EJ, et al. Circulating microRNA as biomarkers of canine mammary carcinoma in dogs. J Vet Intern Med. 2020 May; 34(3): 1282–1290. PMCID: PMC7255679.
  4. Barnhill EC, et al. Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium. RNA Biol. 2019 Nov;16(11):1643-1657. doi: 10.1080/15476286.2019.1653680.

To propel your projects with The Power of Discovery.™

Contact Us Today

Let us know about your project!