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We recommend ordering the new Illumina RNA UD Indexes Sets A-D (20091655, 20091657, 20091659, 20091661). The IDT for Illumina RNA UD Indexes Sets A-D (20040553, 20040554, 20040555, 20040556) are obsolete and the last order date is January 30, 2025, as announced in PON2023-1440.

Illumina Stranded mRNA Prep

A simple, scalable, cost-effective, rapid single-day solution for analyzing the coding transcriptome leveraging as little as 25 ng input of standard (non-degraded) RNA. Read More...
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Library Prep

Illumina® Stranded mRNA Prep, Ligation (16 Samples)

20040532

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Illumina® Stranded mRNA Prep, Ligation (96 Samples)

20040534

Price
 
 
Index Adapters

Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples)

20091655

Price
 
 

Illumina® RNA UD Indexes Set B, Ligation (96 Indexes, 96 Samples)

20091657

Price
 
 

Illumina® RNA UD Indexes Set C, Ligation (96 Indexes, 96 Samples)

20091659

Price
 
 

Illumina® RNA UD Indexes Set D, Ligation (96 Indexes, 96 Samples)

20091661

Price
 
 

IDT® for Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples)

20040553

Price
 
 

IDT® for Illumina® RNA UD Indexes Set B, Ligation (96 Indexes, 96 Samples)

20040554

Price
 
 

IDT® for Illumina® RNA UD Indexes Set C, Ligation (96 Indexes, 96 Samples)

20040555

Price
 
 

IDT® for Illumina® RNA UD Indexes Set D, Ligation (96 Indexes, 96 Samples)

20040556

Price
 
 
Services

Illumina Stranded mRNA Library Prep Training

20044765

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Product Highlights

Illumina Stranded mRNA Prep offers a streamlined RNA-Seq solution for clear and comprehensive analysis across the transcriptome. It offers extraordinary flexibility for input type and supports low input amounts, down to 25 ng total RNA. Illumina Stranded mRNA Prep enables precise measurement of strand orientation, uniform coverage, and high-confidence discovery of features such as novel isoforms, gene fusions, and allele-specific expression.

Exceptional Performance

Illumina Stranded mRNA Prep is optimized to provide exceptional polyA capture efficiency and coverage uniformity. It minimizes the required sequencing depth for accurate, unbiased detection of the coding transcriptome. Illumina Stranded mRNA Prep is based on TruSeq ligation technology, which has been cited in over 9,926 publications since 2011.

Learn more about the technology

Flexibility for Many Study Designs

Illumina Stranded total RNA Prep supports a broad range of RNA inputs, from 25 ng to 1000 ng.*

Precise Measurement of Strand Orientation

This information enables detection of antisense transcription, enhances transcript annotation, and increases alignment efficiency.

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.

Sequencing Scalability

Multiplex up to 384 samples and sequence in a single run. 

The Power of RNA-Seq

RNA-Seq is increasingly the platform of choice for thought leaders, providing a detailed snapshot of the transcriptome at a given point in time. It offers numerous advantages over quantitative PCR, including:

  • Hypothesis-free experimental design, requiring no previous knowledge of the transcriptome 
  • Higher discovery power to detect known and novel transcripts 
  • Higher throughput capability to quantify hundreds to thousands of regions in each assay 
  • Broader dynamic range, providing more accurate measurement of gene expression 
  • More data per assay, providing full sequence and variant information

*Not compatible with FFPE samples

Frequently Purchased Together

Specifications

Project Recommendations

Instrument Recommended Number of Samples Read Length
NextSeq 550 System Mid Output: 5
High Output: 16
(based on 25M reads per sample)		 2 × 75 bp
NextSeq 2000 System P2: 16
P3: 40
(based on 25M reads per sample)		 2 × 75 bp
NovaSeq 6000 System SP: 32
S1: 64
S2: 164
S4: 384
(based on 25M reads per sample)		 2 × 75 bp

Product Comparison

Illumina Stranded mRNA Prep TruSeq Stranded mRNA TruSeq RNA Library Prep Kit v2 Illumina RNA Prep with Enrichment Illumina Stranded Total RNA Prep with Ribo-Zero Plus or Ribo-Zero Plus Microbiome
Assay Time 6.5 hours ~10.5 hours ~10.5 hours < 9 hours ~7 hours
Automation Capability Liquid Handling Robots Liquid Handling Robots 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 (without strand information) Captures the coding transcriptome when used with Illumina Exome Panel Captures coding RNA plus multiple forms of non-coding RNA
Description A simple, cost-effective solution for analysis of the coding transcriptome with precise strand information Gives researchers a clear, comprehensive view of the coding transcriptome with precise strand information. A simple, cost-effective research solution for analysis of the coding transcriptome. 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 For whole-transcriptome sequencing studies of multiple sample types. Includes Ribo-Zero plus module for single-tube depletion of abundant transcripts from multiple species
Hands-On Time < 3 hours ~4.5 hours ~4.5 hours < 2 hours < 3 hours
Input Quantity 25-1000 ng standard-quality total RNA 0.1 – 1 ug total RNA or 10 - 100 ng previously isolated mRNA (from species with polyA tails) 0.1 - 1 ug total RNA or 10 - 400 ng previously isolated mRNA (from species with polyA tails) 10ng total RNA from fresh/frozen samples, or 20ng total RNA from FFPE samples 1-1000 ng total RNA for standard-quality RNA samples. 10ng total RNA minimum recommended for optimal performance and FFPE samples
Mechanism of Action PolyA capture, ligation-based addition of adapters and indexes Oligo-dT beads capture polyA tails Oligo-dT beads capture polyA tails Bead-linked transposome Enzymatic rRNA depletion, ligation-based addition of adapters and indexes
Multiplexing Up to 384 Unique Dual Indexes (UDIs) 1–96 Up to 24-plex per lane Up to 384 Unique Dual Indexes (UDIs) Up to 384 Unique Dual Indexes (UDIs)
Strand Specificity Stranded Stranded Non-Stranded Non-Stranded Stranded
Technology Sequencing Sequencing Sequencing Sequencing Sequencing
Variant Class Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants

Method-Specific Workflow Example

 
Prepare Library for:
mRNA Sequencing
 
Sequence Efficiently with:
NextSeq 550 System
NextSeq 2000 System
NovaSeq 6000 System
 
Analyze Your Data with:
DRAGEN RNA Pipeline
RNA-Seq Differential Expression
RNA-Seq Alignment App
 

Supporting Data and Figures

 

Product Literature

Workflows for RNA sequencing

Brochure | PDF 1 MB

Illumina library preparation solutions

Brochure | PDF 2 MB

NextSeq 1000 and NextSeq 2000 RNA sequencing solution

Application Note | PDF < 1 MB

NextSeq 550 RNA-Seq solution

Application Note | PDF < 1 MB

Best practices for read trimming for Illumina Stranded mRNA and Total RNA workflows

Technical Note | PDF < 1 MB

Illumina Stranded mRNA Prep, Ligation

Data Sheet | PDF < 1 MB

Manuals and Support Information

Illumina Stranded mRNA Prep Ligation Consumables & Equipment Documentation

Illumina Stranded mRNA Prep Ligation Checklist Documentation

Illumina Stranded mRNA Prep Ligation Reference Guide Documentation

Illumina Stranded mRNA Prep Ligation Documentation

Custom Protocol Selector
Generates customized, end-to-end instructions

All Illumina DNA RNA UD Indexes  Support   All Illumina Stranded mRNA Prep Ligation Support  

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Illumina Stranded Total RNA Prep with Ribo-Zero Plus or Ribo-Zero Plus Microbiome
Illumina Stranded Total RNA Prep with Ribo-Zero Plus or Ribo-Zero Plus Microbiome

Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with exceptional study flexibility.


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Not for use in diagnostic procedures (except as specifically noted).

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