Expression Profiling Kits

QuantSeq Expression Profiling Library Prep Kits

QuantSeq kits enable cost-efficient sequencing by counting. These kits are an exceptional alternative to standard RNA-Seq and microarrays. Just one fragment per transcript is produced and therefore there is no need for length normalization. This makes data analysis very simple and accurate.

The kits of Lexogen are available in 2 versions and for different platforms. 

The QuantSeq FWD kit generates reads towards the poly-A tail, directly reflecting the mRNA sequence. This version is available for Illumina and IonTorrent platforms.

The QuantSeq REV kit enables exact pinpointing the 3’ end in Read 1, as the first nucleotide of the read corresponds to the very last nucleotide of the mRNA sequence. This requires a Custom

Sequencing Primer (CSP version 2, included in the kit). This version is only available for Illumina platforms.

12nt UDI Indexing kits  are available to increase the number of libraries that can be pooled on a single lane of an Illumina Flow cell.

QuantSeq 3’ mRNA-seq Library Prep Kit FWD (Illumina/IonTorrent)


The QuantSeq FWD kit is designed to generate Illumina or IonTorrent compatible libraries of sequences close to the 3’ end of poly-A RNA
o    Genome-wide analysis of gene expression
o    Cost-saving and streamlined globin mRNA depletion during library prep
o    Cost-efficient alternative to microarrays and standard RNA-seq
o    Down to 100pg total RNA input (5ng for IonTorrent version)
o    Applicable for low quality and FFPE samples
o    Sequencing ready libraries in 4.5hours
o    Free Data analysis on the Bluebee® Genomics Analysis Platform

Analysis of Low Input and Low Quality Samples 

QuantSeq kits are compatible with low input samples, down to 100pg and are suited to work with low quality input material, including FFPE samples.

High Strand Specificity

QuantSeq maintains exceptional high strand-specificity (>99.9%) and allows to map reads to their corresponding strand on the genome, enabling the discovery and quantification of antisense transcripts and overlapping genes.

Mapping of Transcript End Sites (TES)
By using longer reads, QuantSeq FWD allows to exactly pinpoint the 3’ end of poly-A RNA and therefore obtain accurate information about the 3’ UTR.

Unique Molecular Identifiers (UMI)
The separately available UMI Second Strand Synthesis Module for QuantSeq FWD allows unique tagging of individual transcripts with 6nt long UMI’s, located between the partial P5 adapter and the random priming sequence. This enables identifying PCR duplicates and eliminating amplification bias.

Direct Counting for Gene Expression Quantification
QuantSeq kits produce only 1 fragment per transcript. Therefore, no length normalization is required, allowing more accurate determination of gene expression values. This makes QuantSeq the best alternative to microarrays and conventional RNA-seq in Gene Expression studies.

Rapid Turnaround
In only 4.5 hours, including less then 2 hours hands-on time, QuantSeq’s straightforward workflow generates sequencing-ready NGS libraries

Cost Saving Multiplexing
The length restriction in QuantSeq libraries allows a high level of multiplexing by saving sequencing space and enables up to 9.216 libraries being sequenced in a single Illumina lane.

Automation Friendly
The QuantSeq kit is available as an automated version (autoQuantSeq 3’ mRNA-seq Library Prep kit for Illumina) as well to accommodate automated library prep. The protocol has been adapted for automation on several platforms (including Sciclone NGS, Hamilton Microlab STAR, Bravo and Biomek platforms). 

Simple Bioinformatics Analysis
The QuantSeq data analysis pipeline has been integrated on the Bluebee Genomics Analysis Platform and can be used by any user, even without bioinformatics background. The access codes are included in QuantSeq kits and additional codes can be purchased separately.Ordering information

QuantSeq 3’ mRNA-seq Library Prep Kit REV for Illumina


The QuantSeq REV kit is designed to generate libraries at the 3’ end of poly-A RNA. This makes it possible to exactly pinpoint the 3’ end in Read 1 and enables the study of the 3’ UTR and alternative polyadenylation.
•    3’ UTR analysis and study of alternative polyadenylation
•    Down to 10ng total RNA input, including FFPE samples
•    Sequencing ready libraries in 4.5 hours with only 2 hours hands-on time
•    Cost-efficient sequencing of up to 9.216 samples/lane
•    Automation friendly
•    Free Data-analysis via the Bluebee® genomics analysis platform

Depletion of globin mRNAs during QuantSeq Library Prep
Combined with the Globin Block Module, it is possible to generate globin-depleted, sequencing ready 3’ mRNA libraries from as little as 50ng of total RNA frow whole blood. The Globin Block module can be integrated seamlessly in the protocol without additional protocol steps. Using this module, reads mapping to globin mRNA can be reduced to as low as 5%, dramatically increasing gene detection.

figure 4: Increased gene detection in human blood Quantseq libraries using Globin Block. CPM = Counts per million*

High Strand-specificity
While maintaining exceptional strand-specificity of 99,9%, QuantSeq allows to map reads to their corresponding strand on the genome. This enables the discovery and quantification of antisense transcripts and overlapping genes.

Direct Counting for Gene Expression Quantification
Since only 1 fragment per transcript is produced, QuantSeq allows more accurate determination of gene expression values. Therefore, QuantSeq kits are the best alternative to microarrays and conventional RNA-seq in Gene Expression and eQTL studies.

Cost Saving Multiplexing
Since the length restriction in QuantSeq saves sequencing space, the libraries are intended for a high degree of multiplexing. With up to 96 i7 indices included in the kit and the additionally available 96 i5 indices, up to 9.126 samples can be multiplexed and loaded on a single lane, resulting in a substantial saving on sequencing costs.

Simple Bioinformatics analysis
The QuantSeq data analysis pipeline has been integrated on the Bluebee Genomics Analysis Platform and can be used by any user, even without bioinformatics background. The access codes are included in QuantSeq kits and additional codes can be purchased separately.

Automation Friendly
The QuantSeq kit is available as an automated version (autoQuantSeq 3’ mRNA-seq Library Prep kit for Illumina) as well to accommodate automated library prep. The protocol has been adapted for automation on several platforms (including Sciclone NGS, Hamilton Microlab STAR, Bravo and Biomek platforms). 

QuantSeq-Flex Targeted RNA-seq Library Prep Kit V2 for Illumina

The QuantSeq-Flex kit is a library preparation kit, designed to make Illumina compatible liraries from any RNA sample, using custom primers.  Whether it is gene expression analysis, targeted sequencing, adapter-ligation based RNA-seq or any other experiment where a certain region needs to be sequenced, QuantSeq-Flex can be used together with user-supplied primers.

The following types of libraries can be generated:
1.    OligodT primed in reverse transcription, random primed in second strand synthesis (QuantSeq 3’ mRNA-seq)
2.    OligodT primed in reverse transcription, target-specifically primed in second strand synthesis (targeted 3’ mRNA-seq)
3.    Target-specifically primed in reverse transcription, random primed in second strand synthesis (Targeted RNA-seq, allowing identification of novel fusions)
4.    Target-specifically primed in reverse transcription, target-specifically primed in second strand synthesis (targeted RNA-seq; detecting known targets only

•    Flexible kit for targeted sequencing and molecular barcoding
•    Identification of known and unknown Fusion Transcripts
•    Use of custom-designed gene-specific primers for first and/or second strand synthesis
•    Cost-efficient and flexible alternative to pre-designed sequencing panels
•    Multiplexing of up to 9.126 samples per lane

A RNA-Seq Experiment Tailored to your needs
Quant-Seq Modular Kits give the needed flexibility to enable implementation of RNA-seq as part of the experimental pipeline. One Fragment per transcript produced and the use of custom primers makes this kit a perfect solution for cost-saving high-throughput gene expression analysis. Quant-Seq Flex is suitable for targeted sequencing of gene panels, enrichment, detection of fusion genes and various other types of transcripts.

Rapid Turnaround
The straightforward protocol allows generating sequencing-ready libraries in only 4.5 hours, including a hands-on time of less than 2 hours.

Cost Saving Multiplexing
QuantSeq Libraries are intended for a high degree of multiplexing. When combining the 96 i7 indices, included in the kit, with the separately available 96 i5 indices, up to 9.216 samples can be combined on a single lane of an Illumina Flow Cell. This allows substantial sequencing cost saving, as the length restriction in QuantSeq saves sequencing space. 

Contact us for prices of more information

QuantSeq-Pool Sample Barcoded 3’mRNA-Seq Library Prep Kit 

The QuantSeq Pool is the best of both worlds by combining sample barcoding and early pooling. This mRNA-Seq library prep kit is ideal for screening projects, as up to 36.864 samples can be measured. By performing this early pooling and batch processing both time and money is saved. Up to 95% less consumables are needed, such as PCR plates and pipette tips. Sample-barcodes and Unique Molecular Identifiers (UMIs) are included with the kit.

This sustainable mRNA-Seq library Prep kit reduces technical variation between samples. It detects 7.500 to 9.000 highly expressed genes at shallow read depts of 100K to 1M reads per sample. The recommended total RNA input is 10-120ng.

For the 96 sample barcodes the i1 indices are included. If you need more than 96 samples the i5 and i7 indices are necessary, Unique Dual Indexing Sets (Cat. No. 101 – 105, 156). Ready to sequence libraries are obtained within 4.5 hours.

Benefits of the QuantSeq Pool

  • Flexible
  • Cost- and time-efficient
  • Low technical variation

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