US Based · Degraded & Archived Samples

FFPE RNA Sequencing Service

High-quality transcriptomic data from FFPE and heavily degraded archived specimens. Takara SMART-Seq Total RNA with ZapR depletion and UMIs, end-to-end in our SF Bay Area lab.

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At a glance

Library prep

Takara SMART-Seq Total RNA

RNA input

250 pg–1 µg, DV200 >20%

Sequencing

NovaSeq X+ PE150

Read depth

20M paired reads

Turnaround

3–4 weeks with expedited options

Price

$265/sample
Volume pricing available

Service Highlights

From FFPE to results, all in one lab

Every stage is performed in-house with defined QC criteria and validated Takara chemistry built for degraded material.

Extraction & Sample QC

Extraction & Sample QC
  • 250 pg total RNA, DV200 >25%
  • 250 pg total RNA, DV200 >25%
  • Blocks, slides or purified RNA
Check Compatibility

Library prep

Library prep
  • Takara SMART-Seq Total RNA
  • Random hexamer priming
  • ZapR rRNA depletion
Explore Chemistry

Sequencing

Sequencing
  • Illumina NovaSeq X+ PE 150
  • 20M paired reads
  • UMI-corrected duplicate removal
Need Deeper Coverage?

Analysis

Analysis
  • 3–4 week turnaround
  • >90% reads on transcripts
  • Secure FTP, S3 or BaseSpace
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Sample Requirements

Check your sample compatibility

Validated for eukaryotic organisms with poly(A) — human, mouse, rat and more.

Sample type SAMPLE REQUIREMENTS
Total RNA >250 pg total RNA in15µl, DV200 >25%.
FFPE blocks Intact blocks shipped at room temperature. We handle deparaffinization and extraction in house.
FFPE slides / scrolls/ curls 5-10 scrolls or unbaked slides at 5–10 µm.
Core biopsies Archived core needle biopsies
Alternative workflows

Samples outside these thresholds are still compatible with other services below.

mRNA-Seq Service (RIN >7)
Low-Input, high quality RNA-Seq (>250 pg)

Need spatial, immune profiling, or tumor microenvironment analysis?

Technical excellence

Built for degraded and cross-linked RNA

Automated deparaffinization and optimized proteinase K digestion recover RNA from blocks, scrolls and slides. Send raw tissue and we handle it, or send purified RNA and we start at library prep.
When RIN drops below 5, the ribosomal peaks are no longer present, so DV200 becomes the quality measurement — we require >25% of fragments longer than 200 nucleotides to ensure a quality library prep. QC results are reviewed with you before we proceed if any sample is marginal or failed, and you can opt to omit it or send a replacement.

Automated liquid handling removes operator variance, so your samples stay comparable.

Degraded RNA has broken or missing poly(A) tails, so oligo-dT capture loses most of it. Random hexamer priming copies every fragment into cDNA regardless of where it sheared, which is why archived tissue still yields usable data.
Mammalian ZapR probes hybridize to abundant ribosomal cDNA and the ZapR enzyme cuts it away, so over 90% of your reads land on informative transcripts. 8-nt UMIs tag each original molecule before amplification, so the pipeline strips PCR duplicates — critical when low input forces extra cycles.

Illumina NovaSeq X Plus with 2x150 bp paired-end chemistry. 30–40M reads suits moderately preserved samples at DV200 >50%; 50–60M compensates for heavier degradation between DV200 25% and 50%.

Service experience

Working with us

Every project is run by scientists, tracked in one portal, and processed entirely in our own lab.

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PhD-Level Project Oversight

A PhD scientist owns your project from design through interpretation.

Dedicated Project Manager

One point of contact from quote through delivery.

Easy Ordering

Register samples, track status, and download results in one portal.

100% US-Based

Every stage runs in-house in Foster City, CA. No outsourcing.

Resources & insights

Technical resources

Whitepaper - icon

Spec Sheet

Takara SMART-Seq Total RNA Spec Sheet

ZapR depletion chemistry, input ranges, DV200 thresholds, and deliverables.

Blog - icon

BLOG

Beyond the RIN Score: Why DV200 Is the Only Metric That Matters for FFPE

Audit biobank inventory with TapeStation or Fragment Analyzer data to predict prep success.

Blog - icon

BLOG

Poly(A) Selection vs. Ribosomal Depletion: Which Approach Fits Your Samples?

Poly(A) for intact mRNA; ZapR ribo-depletion for lncRNAs, bacteria, or degraded FFPE.

More resources
Frequently asked questions

Planning your FFPE RNA-Seq project

Samples & service

RIN is calculated from the 28S/18S ribosomal bands. In FFPE those bands are almost completely shattered, so nearly every sample returns an uninformative RIN of 1 to 2. DV200 measures the percentage of fragments longer than 200 nucleotides, which actually predicts whether library prep will succeed.

The reverse transcriptase and amplification enzymes in the Takara SMART-Seq workflow need magnesium as a cofactor. EDTA chelates magnesium, and even trace amounts can halt first-strand synthesis and fail the entire library prep. Samples must be in clean, nuclease-free, EDTA-free water.

Intact FFPE blocks and cut slides are stable at room temperature and ship by standard overnight delivery — no ice needed. Purified RNA extracted from FFPE is fragile and must ship in a microcentrifuge tube on a generous amount of dry ice.

Yes. Send 5 to 10 freshly cut scrolls or unbaked slides at 5–10 µm, wrapped tightly in parafilm. Our team runs an optimized deparaffinization and extraction protocol designed to maximize yield and limit cross-linking damage.

Data & delivery

Degraded samples contain fewer unique molecules, so they need more PCR cycles and generate more technical duplicates. Tagging each original molecule with an 8-nucleotide barcode before amplification lets the pipeline identify and remove those copies, so the final counts reflect true biological expression.

FASTQ files and a QC report via secure FTP, S3, or BaseSpace.
30–40M reads per sample suits moderately preserved specimens at DV200 >50%, covering medium-to-high expression genes and differential expression. 50–60M compensates for heavier degradation between DV200 25% and 50%, expanding dynamic range to capture rarer transcripts.
 
Cost-effective profiling, accurate quantification of medium-to-high abundance transcripts, and standard differential expression.
50 M+ reads/sample
Alternative splicing analysis, low-abundance transcript detection, and gene fusion mapping.
100 M+ reads/sample
Novel isoform discovery and comprehensive allele-specific expression analysis.

Your data is available on our secure FTP for 2 weeks after delivery, and we retain it in storage for 60 days. Extension options are available — ask your project manager, or request a direct transfer to your own AWS, Globus, or cloud storage.

Yes. Analysis can be added any time. If within the 60-day data retention window you will not need to resubmit the data. Contact your project manager and we will quote the additional analysis.

Ordering & logistics

Submit your inquiry below and our team will help create an account and walk you through submitting your samples.

FFPE extraction, DV200 assessment, and UMI processing add steps to the standard pipeline, so turnaround is typically 4 to 5 weeks. Your project manager provides updates as samples clear each QC milestone.

There is no order minimum. We do recommend at least three biological replicates per condition for reliable differential expression, and per-sample pricing improves with batch size.

Get started with your project

Ready to unlock the transcriptomic data inside your archived tissue inventory? Contact our team for a technical consultation. We will guide you through sample submission, extraction logistics, and the sequencing depth that suits your DV200 range.

  • $265/sample, with volume pricing available
  • Data in 4 to 5 weeks
  • UMI-corrected duplicate removal
  • 100% in-house at Foster City, CA
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