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Dear Customers,

SENSE mRNA-Seq Library Prep Kits (Cat. No. 001.24 and 001.96) are being discontinued. We recommend instead to use our CORALL mRNA-Seq Library Prep Kit.


SENSE mRNA-Seq Library Prep Kit

SENSE is a complete strand-specific mRNA-Seq library prep kit for accurate gene expression profiling, transcriptome sequencing, discovery and quantification of antisense transcripts and overlapping genes.

Superior Strand-Specificity

The strand-displacement stop/ligation technology used in SENSE generates fewer antisense artifacts which can be produced by template-switching in protocols which utilize RNA or cDNA fragmentation. This results in exceptional (>99.9 %) strand-specificity and reduced experimental noise, enabling the detection and quantification of antisense transcripts with high confidence.

Rapid Turnaround

NGS-ready libraries can be produced from total RNA samples in under 5 hours with less than 50 % hands-on time, allowing RNA extraction, library preparation and quality control to be performed in one day.

All-in-One Solution

No additional kits or reagents for poly(A) RNA selection, library amplification, size selection or purification, or barcodes are required.

Low Amount of Input Total RNA

The typical amount of input total RNA is 1 ng – 2 µg.

Efficient rRNA Elimination

SENSE mRNA-Seq Library Prep includes the Poly(A) RNA Selection Kit (Cat. No. 039) which virtually eliminates cytoplasmic ribosomal RNA (<0.001 % of total reads from Universal Human Reference RNA) and removes the need for additional selection or depletion kits, saving you time and money.

Different Sequencing Read Length

For good representation and even coverage of all transcripts in your experiment the library should have a size suitable for the chosen sequencing read length. The size of SENSE libraries for Illumina can be adjusted by simply modulating appropriate buffers during reverse transcription/ligation and purification steps.


SENSE mRNA-Seq Library Prep Kits are available for Illumina sequencing platforms.

Simple Multiplexing

SENSE libraries can be multiplexed with very well balanced barcode sequences, having 9,216 barcode options available for Illumina (single or dual indexing). Learn more about barcodes for multiplexing.


The SENSE kit features an all-in-one mRNA-Seq library preparation protocol. Most of the procedure is performed on magnetic beads, making it amenable to automation and decreasing purification time. The SENSE protocol has a simple workflow consisting of just 3 major steps.
Please find a schematic overview of the workflow for SENSE mRNA-Seq for Illumina below:

Poly(A) Selection
Step 1:
During the poly(A) selection step the total RNA samples are briefly heated
to resolve secondary structures and promote efficient hybridization.


Poly(A) Selection
Step 1:
The denatured total RNA is incubated with the oligodT beads, which

specifically bind polyadenylated RNAs. RNAs lacking a poly(A) tail are
then washed away, leaving only purified poly(A) RNA hybridized to the


Library Generation
Step 2:
As a result of this highly specific bead-based poly(A) selection step almost
all traces of cytoplasmic rRNA, tRNA, and other non-polyadenylated RNAs
are removed.


Library Generation
Step 2:
Library generation is based on Lexogen’s proprietary strand displacement
stop/ligation technology. The starter/stopper heterodimer mix is randomly
hybridized to the poly(A) RNA still bound to the magnetic beads.


Library Generation
Step 2:
A single-tube reverse transcription and ligation reaction extends the starter
to the next
hybridized heterodimer, where the newly synthesized cDNA insert
is ligated
to the stopper.


Library Generation
Step 2:
Distance is modulated by two different buffers resulting in different
conditions for the RT/ligation reaction


Library Generation
Step 2:
During second strand synthesis the RNA is hydrolyzed and the library is
converted to double-stranded DNA. The double-stranded library is purified
to remove magnetic beads and second strand synthesis reaction components.


Library Amplification
Step 3:
The library amplification is performed to add the complete adaptor
sequences required for cluster generation and to produce sufficient
material for quality control and sequencing. i7 and i5 indices can be
added during this step in order to be able to uniquely multiplex your
samples for the sequencing run.


Library Amplification
Step 3:
The finished library is purified from PCR components
which can interfere with quantification.


Library quantification can be performed with standard protocols, e.g., microcapillary electrophoresis or qPCR. Produced libraries are compatible with single-read or paired-end sequencing reagents.

Featured Publications


autoSENSE mRNA-Seq V2 for Illumina

autoSENSE V2 is the automated solution of the SENSE mRNA-Seq Library Prep Kit V2 for Illumina in combination with the software and the Automation Module, which is currently available for the Perkin Elmer Sciclone NGS Workstation in combination with the Zephyr Workstation for the post-PCR step. Please contact if you are interested in automating the SENSE protocol on any other liquid handler.

The main advantage of automating the RNA-Seq library preparation process is in reducing sample tracking errors while dramatically increasing throughput.

Fast and Fully Walk-Away Protocol

The whole autoSENSE V2 workflow is a complete walk-away protocol and 96 samples can be run within 9 hours, including about 2 hours of manual setup time. Since pre- and post-PCR can be run on separate machines the protocol time can be reduced by parallelizing the workflow.

Compatible with SENSE mRNA-Seq V2

The autoSENSE protocol is identical to the manual version of SENSE mRNA-Seq Library Prep Kit V2 and the software is downloadable from our website. With the Automation Module different library size selections can be performed and the workflow can be fully automated.

Flexibility of the Throughput

The autoSENSE kit is appropriate for preparing 9,216 barcoded libraries. The liquid handler program allows for processing of samples in multiples of 8 reactions (full columns of a 96-well plate). The reagents from a single kit can be distributed over several machine runs.

Avoiding Cross Contamination

Pre- and post PCR steps can be programmed on different machines to reduce the risk of cross-contamination of the pre-PCR samples by PCR products.


Frequently Asked Questions

Please find a list of the most frequently asked questions below. If you cannot find the answer to your question here or want to know more about our products, please contact


SENSE mRNA-Seq Library Prep Kit V2 for Illumina

pdf User Guide for Illumina – update 17.07.2019

pdf PCR Add-on Kit for Illumina User Guide – update 03.01.2023
pdf Lexogen i5 6 nt Dual Indexing Add-on Kits (5001-5096) User Guide – update 03.01.2023
pdf SENSE Application Note
pdf Lexogen i7 and i5 Index Sequences – update 05.05.2020

 Library Quantification File

Material Safety Datasheets

MSDS Information can be found in the Documents page.

If you need more information about our products, please contact us through or directly under +43 1 345 1212-41.

SENSE Bioinformatics Data Analysis

Find more about the SENSE Data Analysis here.

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