TruSeq Stranded mRNA

Prepare sequencing libraries from mRNA to get a clear view of the coding transcriptome with strand-specific information. Read More...
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Library Prep

TruSeq® Stranded mRNA Library Prep (48 Samples)



TruSeq Stranded mRNA Library Prep (96 Samples)



Index Adapters

TruSeq RNA Single Indexes Set A (12 Indexes, 48 Samples)



TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples)



TruSeq RNA CD Index Plate (96 Indexes, 96 Samples)



IDT for Illumina – TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples)



Product Highlights

TruSeq Stranded mRNA offers a streamlined, cost-efficient, and scalable solution for coding transcriptome analysis. It is compatible with a wide range of samples.

Strand Orientation Detection

Get precise measurement of mRNA strand orientation for detection of antisense transcription, enhanced transcript annotation, and increased alignment efficiency. High coverage uniformity enhances the discovery of features such as alternative transcripts, gene fusions, and allele-specific expression.


Stranded information identifies from which of the 2 DNA strands a given RNA transcript was derived. This information provides increased confidence in transcript annotation, particularly for nonhuman samples. Identifying strand origin increases the percentage of reads that align, reducing sequencing costs per sample.


The workflow enables robust interrogation of both standard and low-quality samples, and workflows compatible with a wide range of study designs.

Fast, Automation-friendly Workflow

Prepare libraries for Illumina sequencing in less than a day. Illumina Qualified Methods are available on a range of automation platforms through our partners.

Read a comprehensive assessment of Illumina’s ribosomal RNA depletion protocol

Frequently Purchased Together


Project Recommendations

Instrument Recommended Number of Samples Read Length
NextSeq 550 System RNA Profiling: 13–40 samples per run (based on 10 million reads per sample)
Transcriptome Analysis: 5–16 samples per run (based on 25 million reads per sample)
2 x 75 bp
2 x 75 bp
NovaSeq 6000 System RNA Profiling (samples per run, dual flow cell): S1: 320, S2:384, S4:768. Limited by index combinations (dual). Based on 10 million reads.
Transcriptome Analysis (samples per run, dual flow cell): S1: 128, S2: 256, S4: 768. Limited by index combinations (dual). Based on 25 million reads. 
≤ 2 × 100 bp
≤ 2 × 100 bp

Product Comparison

TruSeq Stranded mRNA Illumina Stranded mRNA Prep Illumina RNA Prep with Enrichment
Assay Time ~10.5 hours 6.5 hours < 9 hours
Automation Capability Liquid Handling Robots Liquid Handling Robots Liquid Handling Robots
Content Specifications Captures the coding transcriptome with strand information Captures the coding transcriptome with strand information Captures the coding transcriptome when used with Illumina Exome Panel
Description Gives researchers a clear, comprehensive view of the coding transcriptome with precise strand information. A simple, cost-effective solution for analysis of the coding transcriptome with precise strand information A reproducible, economical solution enabling targeted transcript detection and discovery from a broad range of sample types and inputs including formalin-fixed, paraffin- embedded (FFPE) tissues and other low-quality samples
Hands-On Time ~4.5 hours < 3 hours < 2 hours
Input Quantity 0.1 – 1 ug total RNA or 10 - 100 ng previously isolated mRNA (from species with polyA tails) 25-1000 ng standard-quality total RNA 10ng total RNA from fresh/frozen samples, or 20ng total RNA from FFPE samples
Mechanism of Action Oligo-dT beads capture polyA tails PolyA capture, ligation-based addition of adapters and indexes Bead-linked transposome
Method mRNA Sequencing mRNA Sequencing mRNA Sequencing, Target Enrichment, Target Enrichment, Targeted RNA Sequencing
Multiplexing 1–96 Up to 384 Unique Dual Indexes (UDIs) Up to 384 Unique Dual Indexes (UDIs)
Specialized Sample Types Not FFPE-Compatible Low-Input Samples, Not FFPE-Compatible Blood, FFPE Tissue, Low-Input Samples
Species Category Bovine, Human, Mammalian, Mouse, Rat Bovine, Human, Mammalian, Mouse, Rat Human, Virus
Strand Specificity Stranded Stranded Non-Stranded

The product previously known as the TruSeq Stranded mRNA Library Prep Kit (Cat. No. RS-122-2101, RS-122-2102, and RS-122-2103) is now called TruSeq Stranded mRNA. The product configuration has changed. In the new configuration, the library preparation and index adapters can be purchased separately. The list of components available for individual purchase can be found in the “Select Product(s)” section.

Method-Specific Workflow Example


Customer Stories

Unraveling Disease Mechanisms With The NextSeq 500 System

Researchers at the Icahn School of Medicine at Mount Sinai are studying mtDNA, piRNA, and TCR repertoire diversity to unlock the secrets of cancer, infertility, and autoimmune disease.

Read More
Precision Immunotherapies Using Tumor-Specific HLA Ligands

RNA-Seq and HLA typing are increasing the power and efficiency of a target discovery platform.

Read More

Supporting Data and Figures

Technical Replicates
Supporting Data and Figures

Figure 2 from TruSeq Stranded mRNA and Total RNA Library Prep Kits Data Sheet, December 2015

Technical replicates of FFPE tissue show high concordance, indicating robust library prep performance. Axes are log2(FPKM). R2 value is shown.

Find the Right Kit

Determine the best library prep kit or array for your needs based on your starting material and method of interest.

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Related Products

This product and its use are the subject of one or more issued and/or pending U.S. and foreign patent applications owned by Max Planck Gesellschaft, exclusively licensed to New England Biolabs, Inc. and sublicensed to Illumina, Inc. The purchase of this product from Illumina, Inc., its affiliates, or its authorized resellers and distributors conveys to the buyer the non-transferable right to use the purchased amount of the product and components of the product by the buyer (whether the buyer is an academic or for profit entity). The purchase of this product does not convey a license under any claims in the foregoing patents or patent applications direct to producing the product. The buyer cannot sell or otherwise transfer this product or its components to a third party or otherwise use the product for the following COMMERCIAL PURPOSES: (I) use of the product or its components in manufacturing; or (2) use of the product or its components for therapeutic or prophylactic purposes in human or animals.