Rapid, simple RNA-Seq library prep workflow with custom enrichment, combining cDNA synthesis and adapter tagging into a single step.
Assay time
Hands-on time
Input quantity
Illumina Rapid RNA Prep with Enrichment delivers a streamlined, tagmentation-based workflow for targeted RNA-Seq. It supports low-input and formalin-fixed, paraffin-embedded (FFPE) samples while enabling high-quality data for gene expression, fusion detection, small variant detection, and splicing isoform analysis.
Prepare sequencing-ready RNA libraries in ~6.5 hours with less than 1.5 hours of hands-on time. The streamlined workflow reduces manual intervention, helping labs increase throughput and efficiency.
Generate high-quality RNA-Seq data from a broad range of input amounts, supporting flexible study designs and varied sample types without compromising data integrity.
Achieve reliable performance from 20 ng to 1000 ng total RNA, including challenging FFPE samples. The assay delivers strong sensitivity and reproducibility for confident downstream analysis.
| Assay time | 6.5 hr |
|---|---|
| Automation capability | Liquid handling robot(s) |
| Description | A fast, targeted RNA-Seq workflow that integrates library preparation and enrichment, reducing steps and assay time compared to standard RNA Prep with Enrichment while supporting low-input and FFPE samples. |
| Hands-on time | < 1.5 hr |
| Input quantity | 1-1000 ng total RNA, minimum of 20ng for FFPE samples |
| Instruments | 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 System, MiSeq i100 Plus System |
| Mechanism of action | Bead-linked transposome tagmentation, hybrid-capture enrichment |
| Method | 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 | Any species, Human, Virus |
| Strand specificity | Non-stranded |
| Technology | Sequencing |
| Variant class | Single nucleotide polymorphisms (SNPs), Gene fusions, Transcript variants, Single nucleotide variants (SNVs), Insertions-deletions (indels) |
Illumina Rapid RNA Prep with Enrichment enables preparation of sequencing-ready targeted RNA-Seq libraries for gene expression and variant analysis in as little as 6.5 hours with less than 1.5 hours hands-on time.
Illumina Rapid RNA Prep with Enrichment
| Instrument | Recommended number of samples | Read length |
|---|---|---|
| NextSeq 2000 System, NovaSeq X System, MiSeq i100 System, NovaSeq 6000 System | A 100 gene panel targeting 500× coverage of the mRNA transcripts averaging 2000 bp per gene, with a target of 5000 reads per gene, would require 500,000 reads per sample. For FFPE samples, at least 20 ng input of RNA is recommended. |
2 × 100 bp (minimum for variant detection) |
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.
Detect cancer gene expression and transcriptome changes and identify novel cancer transcripts with RNA next-generation sequencing (RNA-Seq).
| Illumina Rapid RNA Prep with Enrichment | Illumina RNA Prep with Enrichment | |
|---|---|---|
| Assay time | 6.5 hr | < 9 hr |
| Automation capability | Liquid handling robot(s) | Liquid handling robot(s) |
| Description | A fast, targeted RNA-Seq workflow that integrates library preparation and enrichment, reducing steps and assay time compared to standard RNA Prep with Enrichment while supporting low-input and FFPE samples. | 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 |
| Hands-on time | < 1.5 hr | < 2 hr |
| Input quantity | 1-1000 ng total RNA, minimum of 20ng for FFPE samples | 10 ng RNA, 20 ng FFPE RNA, up to 1000 ng high-quality RNA |
| Instruments | 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 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 System, MiSeq i100 Plus System |
| Mechanism of action | Bead-linked transposome tagmentation, hybrid-capture enrichment | Bead-linked transposome |
| Method | mRNA sequencing, Targeted RNA sequencing, Target enrichment | mRNA sequencing, Targeted RNA sequencing, Target enrichment |
| Multiplexing | Up to 384 Unique Dual Indexes (UDIs) | Up to 384 Unique Dual Indexes (UDIs) |
| Nucleic acid type | RNA | RNA |
| Specialized sample types | Low-input samples, FFPE tissue | Low-input samples, FFPE tissue |
| Species category | Any species, Human, Virus | Any species, Human, Virus |
| Strand specificity | Non-stranded | Non-stranded |
| Technology | Sequencing | Sequencing |
| Variant class | Single nucleotide polymorphisms (SNPs), Gene fusions, Transcript variants, Single nucleotide variants (SNVs), Insertions-deletions (indels) | Single nucleotide polymorphisms (SNPs), Gene fusions, Transcript variants, Single nucleotide variants (SNVs), Insertions-deletions (indels) |
DesignStudio Custom Assay Design Tool
DesignStudio is a web-based assay design tool to help researchers design and order custom genotyping microarray probes or custom sequencing assays.
Illumina Rapid RNA Prep with Enrichment observed padded read enrichment performance
Four RNA enrichment panels containing 20 to 109 genes were evaluated. Seraseq Fusion RNA Mix v2 and Seraseq FFPE Tumor Fusion RNA Reference Material v2 were sequenced on a NextSeq 2000 System using 2 × 151 bp paired end reads. For these samples, enrichment hybridization time was 12 hr overnight.
Illumina Rapid RNA Prep with Enrichment observed median fragment length
Four RNA enrichment panels containing 20 to 109 genes were evaluated. Seraseq Fusion RNA Mix v2 and Seraseq FFPE Tumor Fusion RNA Reference Material v2 were sequenced on a NextSeq 2000 System using 2 × 151 bp paired end reads. For these samples, enrichment hybridization time was 12 hr overnight.
Illumina Rapid RNA Prep with Enrichment observed duplicate read enrichment performance
Four RNA enrichment panels containing 20 to 109 genes were evaluated. Seraseq Fusion RNA Mix v2 and Seraseq FFPE Tumor Fusion RNA Reference Material v2 were sequenced on a NextSeq 2000 System using 2 × 151 bp paired end reads. For these samples, enrichment hybridization time was 12 hr overnight.
Illumina Rapid RNA Prep with Enrichment custom panel coverage depth
Over 70% of the panel targets are covered with a mean ≥ 100× coverage and over 80% with mean ≥ 50× coverage in formalin-fixed paraffin-embedded (FFPE) samples. In universal human reference (UHR) samples, > 80% of targets reach mean coverage > 100× and > 88% of targets reach mean coverage > 50×. Five RNA enrichment panels containing 10 to 109 genes were evaluated.
Reads mapping to gene transcript regions
Reads mapping to exons in the observed transcripts were 75–85% for 10 genes, but 85–90% for larger panels of 20–109 genes. Five RNA enrichment panels containing 10 to 109 genes were evaluated. Seraseq Fusion RNA Mix v2, Seraseq FFPE Tumor Fusion RNA Reference Material v2, and universal human reference (UHR) RNA samples were sequenced on a NovaSeq 6000 system using 2 × 101 bp bp paired end reads. For these samples, overnight enrichment hybridization time was 12 hr.
Learn more about the benefits of on-bead tagmentation.
Illumina Rapid RNA Prep, (S) Tagmentation (96 samples)
20158824
Includes reagents for preparing 96 samples of Rapid RNA libraries with Illumina Purification Beads. UD Indexes sold separately. Compatible with mRNA Capture kit for complete mRNA library prep workflow or RiboZero Plus kits for complete Total RNA library prep workflow or RNA Fast Hyb Enrichment kits for complete RNA Enrichment workflow, each sold separately.
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Illumina Rapid RNA Prep, (S) Tagmentation (16 samples)
20158823
Includes reagents for preparing 16 samples of Rapid RNA libraries with Illumina Purification Beads. UD Indexes sold separately. Compatible with mRNA Capture kit for Rapid mRNA library prep workflow or RiboZero Plus kits for Rapid Total RNA library prep workflow or Fast Hyb Enrichment kits for Rapid RNA Enrichment library prep workflow, each sold separately.
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Illumina® RNA Fast Hyb Enrichment (96 Samples)
20040541
Includes fast hybridization enrichment reagents from the Illumina RNA Prep with Enrichment kit for 32, 3-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 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 Custom Enrichment Panel V2 (32 µl, 120 bp)
20073953
Illumina Custom Enrichment Panel V2 enables 120 bp double-stranded custom panel design from 100 up to 1,000,000 probes using DesignStudio or Concierge Services and provides 32 µl of material (sufficient for 8 enrichment reactions when paired with Illumina DNA Prep with Enrichment). Library prep, enrichment, and index adapter reagents need to be ordered separately.
Illumina Custom Enrichment Panel V2 (384 µl, 120 bp)
20073952
Illumina Custom Enrichment Panel V2 enables 120 bp double-stranded custom panel design from 100 up to 1,000,000 probes using DesignStudio or Concierge Services and provides 384 µl of material (sufficient for 96 enrichment reactions when paired with Illumina DNA Prep with Enrichment). Library prep, enrichment, and index adapter reagents need to be ordered separately.
Illumina Custom Enrichment Panel V2 (1536 µl, 120 bp)
20111339
Illumina Custom Enrichment Panel V2 enables 120 bp double-stranded custom panel design from 100 up to 1,000,000 probes using DesignStudio or Concierge Services and provides 1536 µl of material (sufficient for 384 enrichment reactions when paired with Illumina DNA Prep with Enrichment). Library prep, enrichment, and index adapter reagents need to be ordered separately.
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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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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Illumina Rapid RNA Prep with Enrichment uses a novel method for rapid library preparation consisting of the following steps:
Step 1: Combine first- and second-strand cDNA synthesis with on-bead tagmentation in a single-tube reaction
Step 2: Index PCR and cleanup to generate sequencing-ready libraries
Step 3: Perform target enrichment with a simplified 90-minute hybridization step
Step 4: Post-enrichment amplification and cleanup prior to sequencing
Illumina Rapid RNA Prep with Enrichment supports a wide range of RNA inputs from 1 ng to 1000 ng total RNA. It is compatible with high-quality RNA as well as challenging samples, including FFPE, enabling consistent performance across diverse study designs.
For FFPE samples, at least 20 ng input of RNA is recommended.
Illumina Custom Enrichment Panel v2 enables targeted RNA-Seq applications, including differential gene expression, transcript counting, gene fusion detection, isoform and alternative splicing analysis, SNV analysis, and pathway analysis. Custom panels can be designed to match specific research needs, supporting flexible and focused study designs.
Custom Illumina enrichment panels for human RNA applications can be designed using the Illumina DesignStudio portal, a free online design tool. Probes are placed in an exon‑informed manner that avoids spanning exon–exon junctions, enabling the same custom panel to be used for both gene expression analysis and the detection of known and novel gene fusions. Design support for non‑human content is available through the Illumina Concierge design team.
For Illumina RNA Enrichment with Custom panels, the target number of reads per sample depends upon the panel size and data analysis goals. For gene expression profiling we would recommend targeting about 1000–2000 clusters per gene target. For detection of low frequency fusion or small nucleotide variants in a somatic tumor sample we would recommend targeting about 500× coverage of the target mRNA transcript region, or about 5000 reads per gene, assuming an average mRNA transcript length of 2000 bp. This high depth of coverage allows for detection of low frequency variants and accounts for variation in gene expression across the gene panel targets in the sample.
Reagents for the MiSeq i100 Series feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
Reagents for the NextSeq 1000/2000 System feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
Reagent kits for the NovaSeq X Series include a reagent cartridge, buffer cartridge, flow cell, lyo insert, pre-load buffer, and library tube strip.
Offers a 90-min workflow to prepare DNA libraries for small genomes, PCR amplicons, plasmids, and cDNA sequencing, with a low DNA input requirement.
A fast, integrated workflow for producing enriched and indexed sequencing libraries from a broad range of sample types and RNA input quantities.
A high-performance, fast, and reliable human whole-exome sequencing solution that includes a comprehensive, up-to-date exome enrichment panel.
Comprehensive gene fusion detection covering 507 genes from FFPE and other cancer research samples.
Target 1385 cancer genes for gene expression, variant, and fusion detection studies in many RNA sample types, including blood, bone marrow, and FFPE tissue.
Reagents for the NextSeq 1000/2000 System feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
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