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of 3’ mRNA-Seq solutions
with the QuantSeq family

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3’ Untranslated region

(noun) /θriː praɪm ˌʌntrænsˈleɪtɪd ˈriːʤən/

The three prime untranslated region, most often referred to as the 3’ UTR, is a region belonging to a messenger RNA, which comes after the termination (STOP) codon. Its sequence and length are highly variable from gene to gene, yet it bears a few common motifs close to the polyadenylation site. The overall sequence being specific to each gene, 3’ UTR can be used to identify each gene, but also for other studies, such as the determination of alternative polyadenylation sites.


QuantSeq – the technology in a nutshell

The patented QuantSeq technology targets the 3’ ends of mRNA molecules, for a quick and cost-effective gene expression analysis by RNA-Seq, as well as other more advanced applications.

QuantSeq comes in different versions:


Watch a short video to learn more about QuantSeq:


QuantSeq is the gold-standard solution for gene expression studies targeting the 3’ end of RNA transcripts. You can work with very low inputs, degraded samples, or blood – QuantSeq will be your companion of choice during your RNA-Seq journey! Please see additional benefits by clicking on each revolving icon below.



QuantSeq allows sequencing less reads than whole-transcriptome approaches: save read space, save money!

Compatible with degraded samples

Do not fear low RIN scores or low DV200 values – with QuantSeq, even degraded FFPE samples can be sequenced.

Scalable for high throughput

With QuantSeq, scale up your experiments to 36,864 samples, while keeping a simplified workflow (QuantSeq-Pool with UDI).

Best-in-class demultiplexing

Rescue your reads with our optimally designed, patented Lexogen 12 nt-long UDI.

Not sure which QuantSeq RNA-Seq product is right for you?

Try the QuantSeq Configurator and find the ideal kit for your application
in less than 2 minutes!

Table 1 | QuantSeq selection table.

QuantSeq with UDI V2
QuantSeq-PoolQuantSeq-Flex V2*
Input RNA quantity1 ng – 500 ng1 ng – 500 ng1 ng – 500 ng10 ng – 120 ng1 ng – 500 ngFlexible input range
RNA typesTotal RNATotal RNATotal RNATotal RNATotal RNANo need for poly(A) enrichment or rRNA depletion
RNA qualityall qualitites, including degraded RNAall qualitites, including degraded RNAall qualitites, including degraded RNARIN ≥ 5all qualitites, including degraded RNAHandles most degraded samples (e.g., FFPE)
Workflow time4.5 hrs4.5 hrs4.5 hrs4.5 hrs4.5 hrsShort protocol – libraries ready to be sequenced within the same day
Kit reaction sizes24, 96, and 38424, 96, and 38424 and 969696Scalable for evaluation, adoption and high-throughput applications
Technologydirect polyA hybridisation, one strand per fragmentdirect polyA hybridisation, one strand per fragmentsame as QS FWD, with additional custom sequencing primersame as QS FWD, with RT pooling and i1 indexing protocolcustom primer options on first and/or second-strand synthesisCount your genes effortlessly, with streamlined multiplexing options
Unique Dual Indexing (UDI)compatible(Add-on needed separately)includedcompatible(Add-on needed separately)compatible(Add-on needed separately)compatible(Add-on needed separately)Take advantage of the best design in industry with Lexogen’s 12 nt UDI
Unique Molecular Identifiers (UMI)compatible(Add-on needed separately)compatible(Add-on needed separately)compatible(Add-on needed separately)includedcompatible(Add-on needed separately)For low input samples – easily identify PCR duplicates
Automation capabilityAll QuantSeq workflows can be automated on liquid handlersSupports high-throughput applications

* The QuantSeq-Flex technology requires the purchase of a core kit (e.g., QuantSeq FWD, QuantSeq with UDI V2, QuantSeq-Pool) and a QuantSeq-Flex module.



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