TruSeq RNA Exome

Provides a reproducible, economical solution for sequencing RNA from FFPE tissues and other low-quality samples. Accuracy from as little as 10 ng total RNA.

The product previously known as the TruSeq RNA Access Library Prep Kit (Cat. No. RS-301-2001 and RS-301-2002) is now called TruSeq RNA Exome. The product configuration has changed. In the new configuration, major components such as library preparation, index adapters, enrichment reagents, and exome panels can be purchased separately. If you were previously buying Cat. No. RS-301-2001 or Cat. No. RS-301-2002, purchase the following components: TruSeq RNA Library Prep for Enrichment (Cat. No. 20020189), TruSeq RNA Enrichment (Cat. No. 20020490), Exome Panel (Cat. No. 20020183), and one item from the Index Adapters section below.

Overview

TruSeq RNA Exome, previously known as the TruSeq RNA Access Library Prep Kit, converts total RNA into template molecules of known strand origin, followed by sequence-specific capture of coding RNA. This provides a low-cost solution for analyzing human RNA isolated from formalin-fixed, paraffin-embedded (FFPE) tissues and other low-quality samples.

Key features

  • Affordability and focus - Isolating human transcriptome coding regions maximizes discovery power at a fraction of the sequencing depth

  • High-quality data from difficult samples - Optimized for sequencing RNA from degraded samples, including FFPE tissues

  • Samples with limited starting material - Greatly reduced sample input requirements (as little as 10 ng total RNA from fresh or frozen samples or 20 ng total RNA from degraded samples) while maintaining high sensitivity

TruSeq RNA Exome generates RNA sequencing (RNA-Seq) libraries from degraded samples that focus on the RNA coding regions. Isolating these high-value content regions to help maximize discovery power, while requiring only a fraction of the read depth of total RNA sequencing. The results are low input requirements, high sample throughput, and cost-effective transcriptome analysis. Reagent volumes supplied are sufficient to support 1- to 4-plex enrichment reactions.


Specifications


Required products

Illumina now offers modular product ordering to enable flexibility in your workflows. Please order library prep, enrichment, index adapters, and exome panel components separately.

/ Results

Applications

Example workflow


Project recommendations

Instrument Recommended number of samples Read length
NextSeq 550 System

5 to 16 samples per run (based on 25 million reads per sample)

2 x 75 bp

NovaSeq 6000 System

Samples per run (dual flow cell): S1: 96, S2: 96, S4: 192 (currently limited by available index combinations)

2 × 100 bp

NovaSeq 6000 System

Samples per run (dual flow cell): S1: 96, S2: 96, S4: 192 (currently limited by available index combinations)

2 × 100 bp


Related applications and methods

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TruSeq RNA Exome Illumina RNA Prep with Enrichment Illumina Stranded mRNA Prep
Assay time ~2 days < 9 hr 6.5 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/RNA exome Captures the coding transcriptome when used with Illumina Exome Panel Captures the coding transcriptome with strand information
Description Gives researchers a clear, comprehensive view of the coding transcriptome with precise strand information and a reduced sample input requirement. 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 A simple, cost-effective solution for analysis of the coding transcriptome with precise strand information
Hands-on time ~11 hr < 2 hr < 3 hr
Input quantity 10 ng total RNA from fresh/frozen samples, or 20 ng total RNA from FFPE samples 10 ng RNA; 20 ng FFPE RNA 25-1000 ng standard-quality total RNA
Instruments 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 NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NovaSeq X System, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System
Mechanism of action Biotinylated capture probes that target coding RNA. Does not require RNA with poly-A tails. Bead-linked transposome PolyA capture, ligation-based addition of adapters and indexes
Method Exome sequencing, mRNA sequencing mRNA sequencing, Targeted RNA sequencing, Target enrichment mRNA sequencing
Multiplexing Up to 24 single, 96 combinatorial (CD) dual Up to 384 Unique Dual Indexes (UDIs) Up to 384 Unique Dual Indexes (UDIs)
Nucleic acid type RNA RNA RNA
Specialized sample types Low-Input Samples, FFPE Tissue Blood, Low-Input Samples, FFPE Tissue Not FFPE-Compatible, Low-Input Samples
Species category Human Human, Virus Mammalian, Bovine, Mouse, Human, Rat
Strand specificity Stranded Non-stranded Stranded
Technology Sequencing Sequencing Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Novel transcripts, Transcript variants Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants

Figures

Efficient Gene Fusion Discovery

TruSeq RNA Exome enables detection of expressed fusion transcripts without the need to design probes specific for the fusion junction. The well-characterized BCR-ABL fusion is detected efficiently in the Universal Human Reference RNA (UHRR) sample at 25 M reads.

Resources

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Ebola and sexual transmission

Six months after being discharged from the Ebola treatment, a male survivor of Ebola Virus Disease (EVD) transmitted the virus to his female partner, who died of the disease. The survivor’s semen had tested negative by conventional means, but the authors were able to enrich the semen sample for EBOV RNA with the Illumina TruSeq RNA Access Kit and custom probes.

Library prep (1)

TruSeq® RNA Library Prep for Enrichment (48 Samples)

20020189

Includes reagents for preparing 48 libraries. Purchase index adapters, enrichment panel, and enrichment reagents separately.

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Enrichment (1)

TruSeq® RNA Enrichment (12 enrichments)

20020490

Sufficient for 12 enrichment reactions when paired with TruSeq RNA Library Prep for Enrichment. Purchase library prep, index adapters, and probe panels separately.

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Index adapters (2)

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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Panel (1)

Illumina Exome Panel – Enrichment Oligos Only

20020183

Sufficient for 8 enrichment reactions when paired with Illumina DNA Prep with Enrichment, 12 reactions when paired with TruSeq RNA Exome, and 32 reactions when paired with Illumina RNA prep with enrichment. Purchase library prep and enrichment reagents and index adapters separately.

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Selection summary

Product

Qty

Unit Price

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

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

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