20044763, Illumina RNA Prep with Enrichment – Customer Site

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.

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
Illumina RNA Prep with Enrichment
NextSeq 500/550 System
NextSeq 1000/2000 System
NovaSeq 6000 System
DRAGEN RNA Pipeline
RNA-Seq Differential Expression
RNA-Seq Alignment App
DRAGEN Microbial Enrichment Plus

Project recommendations
Instrument: Recommended number of samples
NextSeq 550 System: Illumina RNA Prep with Enrichment + Exome Panel Mid output: 5 High output: 16 (based on 25M reads per sample)
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)
P2: 16
P3: 48
NovaSeq 6000 System: Illumina RNA Prep with Enrichment + Exome Panel SP: 32 S1: 64 S2: 164 S4: 384 (based on 25M reads per sample)
SP: 32
S1: 64
S2: 164
S4: 384
MiSeq System: Illumina RNA Prep with Enrichment + Viral Surveillance Panel or Pan-Coronavirus Panel Up to 25 samples (based on 1M reads per sample)
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)
Up to 384 samples (based on 1M reads per sample)

Related applications and methods
Microbial genomics
Use NGS to discover novel microbes, monitor outbreaks, analyze food sources, and more.
Cancer RNA sequencing
Detect cancer gene expression and transcriptome changes and identify novel cancer transcripts with RNA-Seq.

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
BCR-ABL 1 (K-562): 7.4
TPM3-NTRK1 (colorectal cancer): 2.5

Advancements in translational biomarker identification from cell-free RNA
Optimized workflows for custom targeted enrichment, from oligo probe design to NGS data analysis
Comprehensive solution, from probe design to data analysis, for multiple targeted sequencing applications. Our custom-designed panels ensure high uniformity and coverage, with enhanced coverage of GC-rich and difficult to sequence areas.
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. View less
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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. View less
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. View less
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. View less
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. View less
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. View less
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. View less
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. View less
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. View less
Pan-Coronavirus Panel, RUO 96 Rxns
20088155
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. View less
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. View less
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. View less
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What plexity is associated with the 16 and 96 reaction kits?
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