Fast, simple library prep workflow for RNA exome analysis, combining cDNA synthesis and adapter tagging into a single step.

Illumina Rapid RNA Prep with Exome 2.5 Enrichment

Fast, simple library prep workflow for RNA exome analysis, combining cDNA synthesis and adapter tagging into a single step.

Illumina Rapid RNA Prep with Exome 2.5 Enrichment

Fast, simple library prep workflow for RNA exome analysis, combining cDNA synthesis and adapter tagging into a single step.

Illumina Rapid RNA Prep with Exome 2.5 Enrichment
Data sheet PDF 7 MB

6.5 hr

Assay time

< 1.5 hr

Hands-on time

1–1000 ng RNA

Input quantity

See full details in the specifications table

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Overview

Illumina Rapid RNA Prep with Exome 2.5 Enrichment offers the fastest and easiest RNA-Seq exome library prep solution in the Illumina portfolio. A streamlined, 30-minute one-tube reaction combines cDNA synthesis and on-bead tagmentation. The rapid workflow supports low-input or degraded RNA samples and delivers high-accuracy targeted data.

Learn about on-bead tagmentation

Key features

Fast, simplified library prep

The entire simplified workflow, including enrichment, requires as little as 6.5 hours and less than 1.5 hours hands-on time to generate a sequencing-ready exome-enriched RNA library.

Optimized enrichment performance

Focused coverage of the coding transcriptome using the comprehensive and up-to-date Twist Bioscience for Illumina Exome 2.5 Panel with a 90-min hybridization.

High-quality data from low input samples

Reproducible results from as little as 1 ng of high-quality RNA or 20 ng FFPE* RNA while achieving excellent target coverage.

*FFPE, formalin-fixed, paraffin-embedded samples.

Specifications

Assay time	6.5 hr
Automation capability	Liquid handling robot(s)
Automation details	Explore available automation methods
Description	A fast and easy workflow for RNA exome analysis
Hands-on time	< 1.5 hr
Input quantity	1–1000 ng RNA or 20–1000 ng FFPE RNA
Instruments	NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System, MiSeq i100 Plus System
Mechanism of action	Bead-linked transposome tagmentation, hybrid-capture enrichment
Method	Exome sequencing, mRNA sequencing, Targeted RNA sequencing, Target enrichment
Multiplexing	Up to 384 Unique Dual Indexes (UDIs)
Nucleic acid type	RNA
Specialized sample types	Low-input samples, FFPE tissue
Species category	Human
Strand specificity	Non-stranded
Technology	Sequencing
Variant class	Single nucleotide polymorphisms (SNPs), Gene fusions, Transcript variants, Single nucleotide variants (SNVs)

Required Products

Illumina Rapid RNA Prep with Exome 2.5 Enrichment kits includes the Illumina Rapid RNA Prep kit, the Twist Bioscience for Illumina Exome 2.5 Panel, hybridization reagents, and Illumina Purification Beads. Index sets are sold separately.

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Applications

Illumina Rapid RNA Prep with Exome 2.5 Enrichment enables preparation of sequencing-ready RNA-Seq libraries for whole-transcriptome analysis in as little as 6.5 hr with less than 1.5 hr hands-on time.

Example workflow

Prep

Illumina Rapid RNA Prep with Exome 2.5 Enrichment

Sequence

Analyze

Project recommendations

Instrument	Recommended number of samples	Read length
MiSeq i100 Plus System	Samples per flow cell: 25M clusters per sample; 25M: 1, 50M: 2, 100M: 4	2 × 100 bp
NextSeq 2000 System	Samples per flow cell: 25M clusters per sample; P1: 4, P2: 16, P3: 48, P4: 72	2 × 100 bp
NovaSeq X System	Samples per flow cell: 25M clusters per sample; 1.5B: 60 (30/lane), 5B: 200 (25/lane), 10B: 400 (50/lane), 25B: 1000 (125/lane)	2 × 100 bp

Related applications and methods

RNA Exome Capture Sequencing

Sequence-specific capture of RNA exome generates high-quality RNA-Seq libraries from difficult samples for cost-effective, high-throughput transcriptome analysis.

Low-Quality/FFPE RNA-Seq Solutions

Find FFPE RNA sequencing solutions that yield high-quality results from degraded FFPE tissues and other low-quality samples.

Cancer RNA Sequencing

Detect cancer gene expression and transcriptome changes and identify novel cancer transcripts with RNA next-generation sequencing (RNA-Seq).

Documentation

Product literature

Illumina Rapid RNA Prep with Exome 2.5 Enrichment
Data sheet PDF 7 MB

Support documentation

Illumina Rapid RNA Prep with Exome 2.5 Enrichment Product Documentation

All Illumina Rapid RNA Prep with Exome 2.5 Enrichment Support

Compare

	Illumina Rapid RNA Prep with Exome 2.5 Enrichment	Illumina RNA Prep with Enrichment	TruSeq RNA Exome
Assay time	6.5 hr	< 9 hr	~2 days
Automation capability	Liquid handling robot(s)	Liquid handling robot(s)	Liquid handling robot(s)
Automation details	Explore available automation methods		Explore available automation methods
Description	A fast and easy workflow for RNA exome analysis	A reproducible, economical solution enabling targeted transcript detection and discovery of splice variants, gene fusions, and small nucleotide variants from a broad range of sample types and inputs including formalin-fixed, paraffin-embedded (FFPE) tissue sections 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	< 1.5 hr	< 2 hr	~11 hr
Input quantity	1–1000 ng RNA or 20–1000 ng FFPE RNA	10 ng RNA, 20 ng FFPE RNA, up to 1000 ng high-quality RNA	10 ng total RNA from fresh/frozen samples, or 20 ng total RNA from FFPE samples
Instruments	NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System, MiSeq i100 Plus System	NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System, MiSeq i100 Plus System, MiSeq i100 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 tagmentation, hybrid-capture enrichment	Bead-linked transposome	Biotinylated capture probes that target coding RNA. Does not require RNA with poly-A tails.
Method	Exome sequencing, mRNA sequencing, Targeted RNA sequencing, Target enrichment	mRNA sequencing, Targeted RNA sequencing, Target enrichment	Exome sequencing, mRNA sequencing
Multiplexing	Up to 384 Unique Dual Indexes (UDIs)	Up to 384 Unique Dual Indexes (UDIs)	Up to 24 single, 96 combinatorial (CD) dual
Nucleic acid type	RNA	RNA	RNA
Specialized sample types	Low-input samples, FFPE tissue	Low-input samples, FFPE tissue	Low-input samples, FFPE tissue
Species category	Human	Any species, Human, Virus	Human
Strand specificity	Non-stranded	Non-stranded	Stranded
Technology	Sequencing	Sequencing	Sequencing
Variant class	Single nucleotide polymorphisms (SNPs), Gene fusions, Transcript variants, Single nucleotide variants (SNVs)	Single nucleotide polymorphisms (SNPs), Gene fusions, Transcript variants, Single nucleotide variants (SNVs), Insertions-deletions (indels)	Single nucleotide polymorphisms (SNPs), Novel transcripts, Transcript variants

Figures

illumina-rapid-total-rna-exome-2.5-figure2

Efficient enrichment of coding transcripts

Mapping metrics for Illumina Rapid RNA Prep with Exome 2.5 Enrichment show over 98% on-target reads across a range of inputs: 1 ng, 10 ng, and 100 ng universal human reference (UHR) RNA and 25 ng each of FFPE RNA reference and fusion RNA mix commercial samples.

illumina-rapid-total-rna-exome-2.5-figure3

Equivalent enrichment metrics for long and short hybridization times

Percent aligned reads, padded unique read enrichment, median fragment length, duplicate rate, and mean target coverage for Illumina Rapid RNA Prep with Exome 2.5 Enrichment with hybridization durations of 90 min (orange) and 12 hr (blue) across a range of inputs: 1 ng, 10 ng, and 100 ng universal human reference (UHR) RNA. Picard enrichment metrics generated by DRAGEN Enrichment v4.3.13.

illumina-rapid-total-rna-exome-2.5-figure4

High reproducibility across high and low RNA inputs

Illumina Rapid RNA Prep with Exome 2.5 Enrichment shows high correlation of normalized gene counts between 1 ng and 100 ng universal human reference (UHR) RNA input amounts (R² = 0.99). Transcripts per million (TPM) generated by DRAGEN RNA v4.4.

Resources

On-bead tagmentation

Learn more about on-bead tagmentation, a novel chemistry that integrates DNA extraction, fragmentation, library preparation, and library normalization into a streamlined workflow. This approach supports a wide range of input amounts, delivering flexibility across diverse sample types.

Library prep (1)

Illumina Rapid RNA Prep with Exome 2.5 Enrichment, (S) Tagmentation (96 samples)

20158825

Includes reagents for preparing and enriching 96 samples of Rapid RNA libraries (32 hybridization reactions with 3 libraries each), with Twist Bioscience for Illumina Exome 2.5 Panel, and Illumina Purification Beads. UD Indexes sold separately.

List Price:

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Index adapters (4)

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.

List Price:

Discounts:

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.

List Price:

Discounts:

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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Discounts:

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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Accessory products (3)

Illumina Purification Beads 30 ml

20119944

Illumina Purification Beads 30 ml

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Illumina Purification Bead, 100mL

20060057

Includes one, 100-ml container of beads for library clean-up and size selection. Purchase library prep and enrichment reagents, probe panels, and indexes separately.

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Illumina Purification Bead, 400mL

20060058

Includes four, 100-ml container of beads for library clean-up and size selection. Purchase library prep and enrichment reagents, probe panels, and indexes separately.

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FAQ

Step 1— Illumina Rapid RNA Prep combines cDNA synthesis and on-bead tagmentation in a single-tube, 30-min reaction

Step 2—Index PCR and clean up

Step 3—Enrich for RNA exome with 90-min hybridization

Step 4—PCR amplify and clean up

Illumina Rapid RNA Prep with Exome 2.5 Enrichment is available in a 96-sample configuration. These kits are designed for 32 reactions of 3-plex enrichments.

Illumina Rapid RNA Prep with Exome 2.5 Enrichment includes the Twist Bioscience for Illumina Exome 2.5 Panel and has a 30% faster total assay time compared to Illumina RNA Prep with Enrichment.

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