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 Library Prep Training
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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.
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
Illumina Stranded total RNA Prep supports a broad range of RNA inputs, from 25 ng to 1000 ng.*
This information enables detection of antisense transcription, enhances transcript annotation, and increases alignment efficiency.
Prepare libraries for Illumina sequencing in less than a day. Illumina Qualified Methods are available on a range of automation platforms through our partners.
Multiplex up to 384 samples and sequence in a single run.
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:
*Not compatible with FFPE samples
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 |
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 |
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
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
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