We recommend ordering the new Illumina DNA/RNA UD Indexes Sets A-D (20091654, 20091656, 20091658, 20091660). The IDT for Illumina DNA/RNA UD Indexes Sets A-D (20027213, 20027214,20042666, 20042667) are obsolete and the last order date is January 30, 2025, as announced in PON2023-1440.
Illumina RNA Prep with Enrichment
Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.
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Library Prep
Index Adapters
Panel
Services
Illumina RNA Library Prep with Enrichment Training
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Product Highlights
Illumina RNA Prep with Enrichment uses On-Bead Tagmentation technology followed by simplified, single hybridization to provide an exceptionally fast workflow for RNA-based library preparation and enrichment.
Learn more about the technology
Rapid, Simple and Scalable Workflow
Prepare and enrich libraries in less than 9 hours total time with less than 2 hours of hands-on time. This workflow results in 50%+ time savings compared to TruSeq RNA Exome. Illumina Qualified Methods are available on a range of automation platforms through our partners.
High-quality Data from Difficult Samples
Get high sensitivity from as little as 10 ng total RNA from fresh or frozen samples or 20 ng total RNA from degraded samples (such as FFPE).
Affordability and Focus
Isolating target transcriptome coding regions maximizes 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. Only 2.5 µL probes are needed per enrichment reaction.
Modular Panel Design for Flexibility
Choose from a variety of pre-built, validated probe pools or customize your own probes for maximum flexibility. Multiplex up to 384 samples in a single run. The modular design supports a wide range of RNA-Seq applications across regions of interest, enabling detection and discovery studies such as allele-specific expression, fusion detection, biomarker screening, and more.
RNA Exome Capabilities
Achieve rapid, targeted interrogation of an expansive number of target genes, including the RNA exome. Illumina RNA Prep with Enrichment can be used with the Illumina Exome Panel, which features a highly optimized probe set that delivers comprehensive coverage of coding RNA sequences. The Illumina Exome Panel includes > 425,000 probes, each constructed against the NCBI37/hg19 reference genome, covering > 98% of the RefSeq exome. The probe set captures > 214,000 targets, spanning 21,415 genes of interest.
Respiratory Virus Detection
The Respiratory Virus Oligo Panel provides highly sensitive detection and characterization of common respiratory viruses, including coronavirus strains. The oligo probes used for hybrid–capture-based target enrichment remain effective even within highly mutagenic regions, allowing targeting of rapidly evolving RNA viruses. Use the Respiratory Virus Oligo Panel with Illumina RNA Prep with Enrichment.
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Specifications
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 2000 System | Illumina RNA Prep with Enrichment + Exome Panel P2: 16 P3: 40 (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 + Respiratory Virus Oligo Panel Up to 25 samples (based on 1M reads per sample) |
2 × 75 bp |
| MiniSeq System | Illumina RNA Prep with Enrichment + Respiratory Virus Oligo Panel Up to 25 samples (based on 1M reads per sample) |
2 × 75 bp |
| NextSeq 550 System | Illumina RNA Prep with Enrichment + Respiratory Virus Oligo Panel Up to 384 samples (based on 1M reads per sample) |
2 × 75 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 |
Product Comparison
| Illumina RNA Prep with Enrichment | TruSeq RNA Exome | Illumina Stranded mRNA Prep | |
|---|---|---|---|
| Assay Time | < 9 hours | ~2 Days | 6.5 hours |
| Automation Capability | Liquid Handling Robots | Liquid Handling Robots | Liquid Handling Robots |
| Content Specifications | Captures the coding transcriptome when used with Illumina Exome Panel | Captures the coding transcriptome/RNA exome | Captures the coding transcriptome with strand information |
| 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. | A simple, cost-effective solution for analysis of the coding transcriptome with precise strand information |
| Hands-On Time | < 2 hours | ~11 hours | < 3 hours |
| Input Quantity | 10ng total RNA from fresh/frozen samples, or 20ng total RNA from FFPE samples | 10 ng total RNA from fresh/frozen samples, or 20 ng total RNA from FFPE samples | 25-1000 ng standard-quality total RNA |
| Mechanism of Action | Bead-linked transposome | Biotinylated capture probes that target coding RNA. Does not require RNA with poly-A tails. | PolyA capture, ligation-based addition of adapters and indexes |
| Method | mRNA Sequencing, Target Enrichment, Target Enrichment, Targeted RNA Sequencing | Exome Sequencing, mRNA Sequencing | mRNA Sequencing |
| Multiplexing | Up to 384 Unique Dual Indexes (UDIs) | Up to 24 single, 96 combinatorial (CD) dual | Up to 384 Unique Dual Indexes (UDIs) |
| Technology | Sequencing | Sequencing | Sequencing |
| Variant Class | Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants | Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants | Gene Fusions, Novel Transcripts, Single Nucleotide Polymorphisms (SNPs), Transcript Variants |
Viruses Detected by Respiratory Virus Oligo Panel
- Human coronavirus 229E
- Human coronavirus NL63
- Human coronavirus OC43
- Human coronavirus HKU1
- SARS-CoV-2
- Human adenovirus B1
- Human adenovirus C2
- Human adenovirus E4
- Human bocavirus 1 (Primate bocaparvovirus 1 isolate st2)
- Human bocavirus 2c PK isolate PK-5510
- Human bocavirus 3
- Human parainfluenza virus 1
- Human parainfluenza virus 2
- Human parainfluenza virus 3
- Human parainfluenza virus 4a
- Human metapneumovirus (CAN97-83)
- Respiratory syncytial virus (type A)
- Human Respiratory syncytial virus 9320 (type B)
- Influenza A virus (A/Puerto Rico/8/1934(H1N1))
- Influenza A virus (A/Korea/426/1968(H2N2))
- Influenza A virus (A/New York/392/2004(H3N2))
- Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
- Human bocavirus 4 NI strain HBoV4-NI-385
- KI polyomavirus Stockholm 60
- WU Polyomavirus
- Human parechovirus type 1 PicoBank/HPeV1/a
- Human parechovirus 6
- Human rhinovirus A89
- Human rhinovirus C (strain 024)
- Human rhinovirus B14
- Human enterovirus C104 strain: AK11
- Human enterovirus C109 isolate NICA08-4327
- Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
- Influenza A virus (A/Hong Kong/1073/99(H9N2))
- Influenza A virus (A/Texas/50/2012(H3N2))
- Influenza A virus (A/Michigan/45/2015(H1N1))
- Influenza B virus (B/Lee/1940)
- Influenza B virus (B/Wisconsin/01/2010)
- Influenza B virus (B/Brisbane/60/2008)
- Influenza B virus (B/Colorado/06/2017)
- Influenza B virus (B/Washington/02/2019)
- Human control genes
Illumina RNA Prep with Enrichment delivers a fast workflow
On-Bead Tagmentation and a single, 90-minute 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). UHR RNA libraries were sequenced on a NovaSeq 6000 System, subsampled to 25M clusters per library. Data was analyzed with the BaseSpace RNA-Seq Alignment v 1.1.1 app.
Detection of BCR-ABL1 gene fusion
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.
Gene fusion detection
| 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%) |
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 transcripts (coding and UTRs). Data from TruSeq RNA Exome libraries are shown for comparison.
Product Literature
Brochure | PDF 1 MB
Illumina library preparation solutions
Brochure | PDF 2 MB
Application Note | PDF < 1 MB
Improved detection of circulating transcripts
Application Note | PDF < 1 MB
NextSeq 1000 and NextSeq 2000 RNA sequencing solution
Application Note | PDF < 1 MB
Enrichment of coding transcripts in degraded samples using hybrid probe capture
Application Note | PDF < 1 MB
Surveillance of infectious disease through wastewater sequencing
Application Note | PDF < 1 MB
Application Note | PDF < 1 MB
Application Note | PDF < 1 MB
Rapid detection of respiratory pathogens using the MiniSeq System
Application Note | PDF < 1 MB
Data Sheet | PDF | 5 versions
Manuals and Support Information
Illumina RNA Prep with Enrichment (L) Tagmentation Documentation
Illumina RNA Prep with Enrichment (L) Tagmentation Reference Guide Documentation
Illumina RNA Prep with Enrichment (L) Tagmentation Checklist Documentation
Illumina RNA Prep with Enrichment (L) Tagmentation Consumables & Equipment Documentation
Custom Protocol Selector
Generates customized, end-to-end instructions
All Illumina DNA RNA UD Indexes Support All Illumina RNA Prep with Enrichment (L) Tagmentation Support
NextSeq 500/550 v2.5 Kits
These sequencing reagent kits offer increased stability and robustness over the v2 kit version.
Illumina DNA PCR-Free Prep
A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing.
Illumina RNA Prep with Enrichment
Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.
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.
TruSight Cardio Sequencing Panel
This kit provides researchers with a comprehensive, cost-effective solution for identifying causal variants implicated in inherited cardiac conditions (ICCs).
NextSeq 1000/2000 Reagents
NextSeq 1000/2000 reagent kits contain a reagent cartridge, flow cell, and resuspension buffer. Multiple flow cell configurations offer adjustable output based on project needs.