TruSeq Stranded mRNA

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

~10.5 hr

Assay time

~4.5 hr

Hands-on time

0.1 – 1 ug total RNA or 10 - 100 ng previously isolated mRNA (from species with polyA tails)

Input quantity

See full details in the specifications table

Overview

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.

Cost-efficient

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.

Scalable

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.


Specifications


Required products

Illumina now offers modular product ordering to enable flexibility in your workflows. You may order any of the following library prep products with any of the following indexes. 

/ Results

Applications

Example workflow


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


Related applications and methods


How others use this product

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.

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

Compare

TruSeq Stranded mRNA Illumina Stranded mRNA Prep Illumina RNA Prep with Enrichment
Assay time ~10.5 hr 6.5 hr < 9 hr
Automation capability Liquid handling robots Liquid handling robots Liquid handling robots
Automation details Explore available automation methods Explore available automation methods
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 hr < 3 hr < 2 hr
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 10 ng RNA; 20 ng FFPE RNA
Instruments MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, NovaSeq 6000 System
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, Targeted RNA sequencing, Target enrichment
Multiplexing 1–96 Up to 384 Unique Dual Indexes (UDIs) Up to 384 Unique Dual Indexes (UDIs)
Nucleic acid type RNA RNA RNA
Specialized sample types Not FFPE-Compatible Not FFPE-Compatible, Low-Input Samples Blood, Low-Input Samples, FFPE Tissue
Species category Mammalian, Bovine, Mouse, Human, Rat Mammalian, Bovine, Mouse, Human, Rat Human, Virus
Species details Works with high-quality RNA from any species with polyA tails Works with high-quality RNA from any species with polyA tails
Strand specificity Stranded Stranded Non-stranded
Variant class Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants

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Figures

Technical Replicates

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

Library prep (2)

TruSeq® Stranded mRNA Library Prep (48 Samples)

20020594

Includes RNA purification beads for upfront polyA capture step, PCR master mix to transcript mRNA into cDNA, and reagents for preparing 48 samples. Purchase index adapters separately. Purfication beads are required post polyA capture step and are sold separately.

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TruSeq Stranded mRNA Library Prep (96 Samples)

20020595

Includes RNA purification beads for upfront polyA capture step, PCR master mix to transcript mRNA into cDNA, and reagents for preparing 48 samples. Purchase index adapters separately. Purfication Beads are required post polyA capture step and are sold separately.

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Index adapters (4)

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

20020492

Includes 12 of 24 indexes (Indexes: 2, 4, 5, 6, 7, 12, 13, 14, 15, 16, 18, 19) for preparing 48 individual RNA samples.

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

20020493

Includes 12 of 24 indexes (Indexes: 1, 3, 8, 9, 10, 11, 20, 21, 22, 23, 25, 27) for preparing 48 individual RNA samples.

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

20019792

TruSeq Stranded RNA HT Kit 96 Samples Adapter Plate Box

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

20040871

Includes 96, 8 bp indexes sufficient for labeling 96 samples and is compatible with TruSeq Stranded mRNA and TruSeq Stranded Total RNA Library Prep Kits. Version 2 contains improvements for 8 of the 192 index oligos in plate 20022371, with no changes to the remaining 184. Purchase library preps and probe panels separately.

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Selection summary

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A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

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.

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