Illumina RNA Prep with Enrichment

A fast, integrated workflow for producing enriched and indexed sequencing libraries from a broad range of sample types and RNA input quantities.

< 9 hr

Assay time

< 2 hr

Hands-on time

10 ng RNA; 20 ng FFPE RNA

Input quantity

See full details in the specifications table

Overview

Illumina RNA Prep with Enrichment uses on-bead tagmentation followed by a simplified, single 90-minute hybridization step to provide an exceptionally fast solution for RNA sequencing (RNA-Seq) applications. 

Fast, simple, and scalable workflow

Prepare and enrich sequence-ready libraries in less than nine hours total time with less than two hours of hands-on time. Combine with an Illumina high-throughput sequencing instrument for significantly more samples per run.

High-quality data from difficult samples

Enable delivery of reproducible results from limited starting material and damaged or degraded samples, such as formalin-fixed, paraffin- embedded (FFPE) tissues.

Affordable and thorough RNA-Seq

Maximize discovery power at a fraction of the sequencing depth. Illumina RNA Prep with Enrichment is designed to provide exceptional capture efficiency and coverage uniformity, minimizing required sequencing depth for accurate detection without bias.

Flexible, modular panel design

Detect and discover allele-specific expression, fusion detection, biomarker screening, and more using a variety of pre-built, validated probes or custom probes for maximum flexibility.


Specifications


Required products

The complete RNA Prep with Enrichment workflow requires use of a library prep, a probe panel, and index adapters (all items sold separately).

Optional components include:

  • Illumina RNA Fast Hyb Enrichment—Includes enrichment reagents only for customers processing at a different plexity from what is recommended

  • Illumina RNA Prep, (L) Tagmentation—Includes pre-enrichment reagents only for customers processing at a different plexity from what is recommended

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Applications

The Illumina RNA Prep with Enrichment enables flexibility in sample type and RNA input amounts in the preparation of targeted sequencing libraries for a wide range of RNA-Seq applications that support detection and discovery studies such as allele-specific expression, fusion detection, biomarker screening, and more.

Example workflow


Project recommendations

Instrument Recommended number of samples Read length
NextSeq 550 System

Illumina RNA Prep with Enrichment + Exome Panel 

Mid output: 5 

High output: 16 

(based on 25M reads per sample) 

2 × 100 bp

NextSeq 1000 System, NextSeq 2000 System

Illumina RNA Prep with Enrichment + Exome Panel

P2: 16

P3: 48 

(based on 25M reads per sample) 

2 × 100 bp

NovaSeq 6000 System

Illumina RNA Prep with Enrichment + Exome Panel

SP: 32

S1: 64

S2: 164 

S4: 384

(based on 25M reads per sample)

2 × 100 bp

MiSeq System

Illumina RNA Prep with Enrichment + Viral Surveillance Panel or Pan-Coronavirus Panel

Up to 25 samples (based on 1M reads per sample)

2 × 150 bp

NextSeq 550 System

Illumina RNA Prep with Enrichment + Viral Surveillance Panel or Pan-Coronavirus Panel

Up to 384 samples (based on 1M reads per sample)

2 × 150 bp



Related applications and methods

Documentation

Product literature

Compare

Illumina RNA Prep with Enrichment TruSeq RNA Exome Illumina Stranded mRNA Prep
Assay time < 9 hr ~2 days
Automation capability Liquid Handling Robots Liquid Handling Robots
Content specifications Captures the coding transcriptome when used with Illumina Exome Panel Captures the coding transcriptome/RNA exome
Description 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 Gives researchers a clear, comprehensive view of the coding transcriptome with precise strand information and a reduced sample input requirement.
Hands-on time < 2 hr ~11 hr
Input quantity 10 ng RNA; 20 ng FFPE RNA 10 ng total RNA from fresh/frozen samples, or 20 ng total RNA from FFPE samples
Instruments 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 Bead-linked transposome Biotinylated capture probes that target coding RNA. Does not require RNA with poly-A tails.
Method Target Enrichment, Targeted RNA Sequencing, mRNA Sequencing mRNA Sequencing, Exome Sequencing
Multiplexing Up to 384 Unique Dual Indexes (UDIs) Up to 24 single, 96 combinatorial (CD) dual
Nucleic acid type RNA RNA
Specialized sample types Blood, Low-Input Samples, FFPE Tissue Low-Input Samples, FFPE Tissue
Species category Human, Virus Human
Strand specificity Non-Stranded Stranded
Technology Sequencing Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants Single nucleotide polymorphisms (SNPs), Novel transcripts, Transcript variants

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Figures

Illumina RNA Prep with Enrichment delivers a fast workflow

On-bead tagmentation and a single, 90-min hybridization step combine to deliver a faster workflow with fewer steps compared to TruSeq RNA Exome.

High-quality data from low input samples

Illumina RNA Prep with Enrichment achieves high data concordance between input amounts of 10 ng and 100 ng total RNA from universal human reference (UHR).

Detection of BCR-ABL1 gene fusion from low-input samples

Libraries prepared from 10 ng RNA from the K-562 cell line using Illumina RNA Prep with Enrichment and the Illumina Exome Panel resulted in successful detection of the BCR-ABL1 gene fusion. Top alignment track shows all reads, bottom track shows only reads supporting the BCR-ABL1 fusion gene.

Coverage of coding regions with Illumina RNA Prep with Enrichment

Libraries prepared from 10 ng UHR RNA and 20 ng FFPE RNA using Illumina RNA Prep with Enrichment and the Illumina Exome Panel show more than 85% of the data generated aligned to coding transcripts and UTRs. Data from TruSeq RNA Exome libraries are shown for comparison.

Gene fusion detection from low-input and FFPE samples

100% call rate for BCR-ABL1 and TPM3-NTRK1 gene fusions across six replicates of the K-562 cell line (RNA integrity number, RIN = 7.4, DV200 = 90%) and a colorectal cancer cell line (RIN = 2.5, DV200 = 85%).

Fusion (source) RIN RNA input Detection
BCR-ABL 1 (K-562) 7.4 10 ng 6/6 replicates (100%)
TPM3-NTRK1 (colorectal cancer) 2.5 20 ng 6/6 replicates (100%)

Resources

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Library prep (2)

Illumina® RNA Prep with Enrichment, (L) Tagmentation (16 Samples)

20040536

Includes reagents for preparing and enriching 16 libraries (16, 1-plex enrichment reactions). Purchase enrichment probe panel, Purification Beads and index adapters separately.

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Illumina® RNA Prep with Enrichment, (L) Tagmentation (96 Samples)

20040537

Includes reagents for preparing and enriching 96 libraries (32, 3-plex enrichment reactions). Purchase enrichment probe panel, Purification Beads and index adapters separately.

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Index adapters (8)

Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

20091654

Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

20091656

Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

20091658

Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

20091660

Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

20027213

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

20027214

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

20042666

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

20042667

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Panel (4)

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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Respiratory Virus Oligos Panel V2

20044311

Sufficient for 32, 3-plex enrichment reactions when paired with Illumina RNA Prep with Enrichment (96 samples) kit. Purchase library prep and enrichment kit and index adapters separately.

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Viral Surveillance Panel, RUO 96 Rxns

20088154

Includes Viral Surveillance Panel sufficient for 32, 3-plex enrichment reactions when paired with Illumina RNA Prep with Enrichment kit. Purchase library prep and enrichment kit and index adapters separately.

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Pan-Coronavirus Panel, RUO 96 Rxns

20088155

Includes Viral Surveillance Panel sufficient for 32, 3-plex enrichment reactions when paired with Illumina RNA Prep with Enrichment kit. Purchase library prep and enrichment kit and index adapters separately.

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Services (1)

Illumina RNA Prep with Enrichment – Customer Site

20044763

2 day on-site training for the Illumina RNA Prep with Enrichment Kit. Hands-on training includes quantification of RNA input as well as best practices, troubleshooting tips, and training on Illumina-supported analysis tools specific to the application workflow.

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Accessory products (2)

Illumina RNA Fast Hyb Enrichment (16 Samples)

20040540

Includes fast hybridization enrichment reagents from the Illumina RNA Prep with Enrichment kit for 16, 1-plex enrichment reactions. Supports customers processing at a different plexity from what is recommended. Pre-enrichment reagents not included. For complete prep with enrichment order the Illumina RNA Prep with Enrichment kit.

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Illumina RNA Prep, (L) Tagmentation (16 Samples)

20040542

Includes pre-enrichment module from the Illumina RNA Prep with Enrichment kit for 16 libraries. Supports customers processing at a different plexity from what is recommended. Enrichment reagents and Purification Beads not included. For complete prep with enrichment order the Illumina RNA Prep with Enrichment kit.

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Selection summary

Product

Qty

Unit Price

FAQs

Illumina recommends using Agilent Technologies Universal Human Reference RNA (UHR) (Catalog no. 740000) as a positive control sample.

The Illumina Exome Panel, Respiratory Virus Oligos Panel V2, Viral Surveillance Panel, and Pan-Coronavirus Panel can be used with the Illumina RNA Prep and Enrichment kit.

 eBLTL are enrichment Bead-Linked Transposomes that tagment cDNA by fragmenting and adding adapter tag sequences in a single and rapid reaction step.

The 16-reaction kit enables a 1-plex workflow while the 96-reaction kit enables a 3-plex workflow. Additional accessory products can be added to either workflow to process at a different plexity from what is recommended.
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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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