A fast, integrated workflow for producing enriched and indexed sequencing libraries from a broad range of sample types and RNA input quantities.
Assay time
Hands-on time
Input quantity
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.
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.
Enable delivery of reproducible results from limited starting material and damaged or degraded samples, such as formalin-fixed, paraffin- embedded (FFPE) tissues.
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.
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.
| Assay time | < 9 hr |
|---|---|
| Automation capability | Liquid Handling Robots |
| Content specifications | Captures the coding transcriptome when used with Illumina Exome Panel |
| 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 |
| Hands-on time | < 2 hr |
| Input quantity | 10 ng RNA; 20 ng FFPE RNA |
| Instruments | MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, NovaSeq 6000 System |
| Mechanism of action | Bead-linked transposome |
| Method | Target Enrichment, Targeted RNA Sequencing, mRNA Sequencing |
| Multiplexing | Up to 384 Unique Dual Indexes (UDIs) |
| Nucleic acid type | RNA |
| Specialized sample types | Blood, Low-Input Samples, FFPE Tissue |
| Species category | Human, Virus |
| Strand specificity | Non-Stranded |
| Technology | Sequencing |
| Variant class | Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants |
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
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.
Illumina RNA Prep with Enrichment
| 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 |
Use NGS to discover novel microbes, monitor outbreaks, analyze food sources, and more.
Detect cancer gene expression and transcriptome changes and identify novel cancer transcripts with RNA-Seq.
Drug response RNA biomarker analysis
Assessment of RNA-based biomarkers predictive of therapeutic response is increasingly becoming an integral part of the drug development process.
| Illumina RNA Prep with Enrichment | TruSeq RNA Exome | Illumina Stranded mRNA Prep | |
|---|---|---|---|
| Assay time | < 9 hr | ~2 days | 6.5 hr |
| 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 hr | ~11 hr | < 3 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 | 25-1000 ng standard-quality total RNA |
| 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 | 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. | PolyA capture, ligation-based addition of adapters and indexes |
| Method | Target Enrichment, Targeted RNA Sequencing, mRNA Sequencing | mRNA Sequencing, Exome 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) |
| Nucleic acid type | RNA | RNA | RNA |
| Specialized sample types | Blood, Low-Input Samples, FFPE Tissue | Low-Input Samples, FFPE Tissue | Not FFPE-Compatible, Low-Input Samples |
| Species category | Human, Virus | Human | Mammalian, Bovine, Mouse, Human, Rat |
| Strand specificity | Non-Stranded | Stranded | Stranded |
| Technology | Sequencing | Sequencing | Sequencing |
| Variant class | Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants | Single nucleotide polymorphisms (SNPs), Novel transcripts, Transcript variants | Single nucleotide polymorphisms (SNPs), Gene fusions, Novel transcripts, Transcript variants |
Library Prep & Array Kit Selector
Find the right sequencing library preparation kit or microarray for your needs. Filter by method, species, and more. Compare, share, and order kits.
On-bead tagmentation and a single, 90-min hybridization step combine to deliver a faster workflow with fewer steps compared to TruSeq RNA Exome.
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).
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.
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.
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%) |
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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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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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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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.
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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Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
Library prep and enrichment kit that delivers highly sensitive, comprehensive respiratory pathogen identification and antimicrobial resistance insights.
A high-performance, fast, and reliable human whole-exome sequencing solution that includes a comprehensive, up-to-date exome enrichment panel.
Whole-genome sequencing and characterization of 66 viruses including SARS-CoV-2, influenza, and polio with target enrichment.
Reagents for the NextSeq 1000/2000 System feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
Unique dual (UD) indexes enable preparation of high-quality libraries that can be multiplexed for increased throughput and cost-saving benefits.
Offers a 90-min workflow to prepare DNA libraries for small genomes, PCR amplicons, plasmids, and cDNA sequencing, with a low DNA input requirement.
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