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FFPE-seq service

Massively multiplexed full-length
RNA-seq for heavily degraded samples.

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Ideal for degraded RNA samples

Compatible with FFPE RNA and samples with RIN values as low as 1.


Bulk RNA sequencing at scale

Massively multiplexed RNA-seq offers unparalleled cost and throughput scalability.


Fast turnaround times

From samples to data in as fast as 1.5 months.

Experimental workflow at a glance

FFPE-seq workflow

What we do


FFPE-seq service

The MERCURIUS™ FFPE-seq service is designed to cope with degraded RNA samples, such as FFPE samples, offering a convenient and streamlined solution for transcriptomics projects. Clients can send us directly purified RNA samples. During the process, we always keep clients informed at defined checkpoints so that we can decide together how to best proceed to the next steps.

Next generation sequencing and data pre-processing (including alignment to the genome of choice) are part of our standard service as well. As a result, we provide our clients raw data, sequencing and alignment reports, and gene count matrices which can be used for downstream gene expression analysis.


How does it work

  • Client prepares the samples

    Sample preparation guidelines for FFPE-seq
  • Client sends submission form

    Sample submission form for MERCURIUSTM FFPE-seq service
  • Client ships samples to Alithea

  • 2 days

    MERCURIUS™ FFPE-seq library preparation for Illumina®

  • 1 week

    Library QC - Client Checkpoint

    (Qubit, Fragment analyzer, shallow sequencing)
  • 1.5 weeks

    Deep sequencing - Illumina

  • 1 week

    Data analysis and reporting - Client Checkpoint

    Example of sample report
  • Data

  • Optional: Alithea performs Differential Gene Expression analysis​


Read more about the FFPE-seq on our blog.


  • We recommend that each sample contains  500ng of total RNA to guarantee high-quality data.
  • The service is validated with the purified RNA samples from various source and RIN values ranging from 1 to 10.  

  • We normally recommend sequencing between 10-20 million reads for each sample.
  • As part of our standard service pipeline, we align the generated data to the genome of choice, provide a detailed report on the alignment and gene counting statistics and, finally, provide ready-to-use gene count matrices for downstream analysis.

    Optionally, we can include differential gene expression analysis.

See our products

Our BRB-seq and DRUG-seq kits make it possible to process virtually any number of RNA samples in one single tube, which helps reduce technical variation, turnaround times and costs.

Experience sample to sequencing-ready library in one day.

Discover our kits

Speak with our RNA sequencing experts

Need guidance or have questions about FFPE-seq and our service?

Easily book a call with our RNA-seq experts.