RNA Library Preparation

Simple, Customized RNA-Seq Workflows

RNA library preparation with highly accurate results

Advances in RNA-Seq library prep are revolutionizing the study of the transcriptome.

Whole Transcriptome

Measure gene and transcript abundance; detect known and novel features in coding and noncoding RNA. Targeted hybridization removes abundant rRNA to focus on high-value portions of the transcriptome.


Quantify gene expression, identify known and novel isoforms in the coding transcriptome, detect gene fusions, and measure allele-specific expression.

RNA Enrichment

Analyze gene expression in a focused set of genes of interest. Provides quantitative expression information as well as the detection of small variants and gene fusions.

RNA Amplicon

Use ultra-deep sequencing of polymerase chain reaction (PCR) amplicons for analysis of RNA sequences of interest, differential expression analysis, allele-specific expression measurement, and gene fusion verification.

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Time to Compare Custom Enrichment Workflows

Our time-lapse video shows how the entire RNA or DNA workflow can complete before your shift is done, with only 2 hours hands-on time. (DNA workflow shown.)

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Introducing Enhanced RNA-Seq Library Prep Portfolio

These solutions for studying RNA for infectious disease, oncology, and genetic disease research offer rapid turn-around time, broad study flexibility and sequencing scalability.

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Choosing an RNA Kit for Your Experiment

Application Product Benefits
Total RNA Sequencing Illumina Stranded Total RNA Prep
  • Integrated enzymatic RNA depletion removes both rRNA and globin mRNA in a single, rapid step
  • One tube to deplete abundant transcripts from multiple species provides flexibility for mixed samples
  • Use with human, mouse, rat, bacteria and epidemiology samples
  • Broad RNA input range, rapid protocol, cost-effective sequencing with up to 384 UDIs
  • Ligation method results in high coverage uniformity and reliability even from degraded samples
  • Measure fold changes in FFPE and low-quality samples
mRNA Sequencing Illumina Stranded mRNA Prep
  • Cost-effective, scalable RNA sequencing of coding transcriptome with precise measurement of strand orientation
  • Broad RNA input range, rapid protocol, cost-effective sequencing with up to 384 UDIs
  • Wide dynamic range for more accurate measurement of gene expression
  • Poly(A) capture, ligation-based addition of adapters and indexes
Targeted RNA Sequencing Illumina RNA Prep with Enrichment
  • Exceptionally fast tagmentation-based library prep enables deep insights into many transcripts of interest, including the RNA exome
  • Single hybridization step
  • No mechanical shearing needed
  • Benefit of panel modularity
  • Compatible with low quality / degraded / FFPE tissue
  • Respiratory virus detection with oligo panel

Overall the high performance, flexibility and streamlined single-day workflow make these kits an ideal solution for RNA prep.

Dr. Christopher Noune, Australian Genome Research Facility

RNA Library Prep At-a-Glance

Application Whole transcriptome mRNA RNA enrichment
Hands-on time < 3 hrs < 3 hrs < 2 hrs
Turnaround time ~7 hrs 6.5 hrs < 9 hrs
Input 1 to 1000 ng standard quality RNA; 10 ng for optimal performance and FFPE samples 25 to 1000 ng standard quality RNA 10 ng standard quality RNA; 20 ng RNA for low quality / degraded / FFPE
Automation capability Liquid handling robots Liquid handling robots Liquid handling robots
PCR protocol No No Yes
Library Quant needed? Yes Yes Yes
Fragmentation included? Yes Yes Not required
Product Illumina Stranded Total RNA Prep Illumina Stranded mRNA Prep Illumina RNA Prep with Enrichment

All three kits allow you to decrease sequencing costs by loading up to 384 samples on a single NovaSeq S4 Flow Cell using 384 unique dual indexes for higher throughput sequencing.

The Benefits of Tagmentation

Bead-linked transposome tagmentation is an innovative technology used in our library preparation portfolio. On-bead tagmentation lets you get to sequence-ready libraries faster than before by simultaneously fragmenting the gDNA and adding the Illumina sequencing primers. Normalize your library without ancillary reagents or equipment. Reduce turnaround time and complexity.

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Understanding Adapter Ligation

The other key technology used in our NGS library prep is adapter ligation, long known for consistent, high-quality data. Libraries are prepared by fragmenting a gDNA or cDNA sample and ligating specialized adapters to both fragment ends. These adapters contain the full complement of sequencing primer hybridization sites. This eliminates the need for additional PCR steps, making the process fully automatable.

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Frequently Purchased Together

Ask an expert how you can get the most with Illumina Library Prep

We'll walk through your needs and make recommendations.

RNA-Seq Library Prep Methods and Use Cases

Tale of Two Kits

A critical comparison between two popular RNA Library Prep Kits reveals new information of interest to researchers conducting RNA sequencing studies.

RNA Methods Poster

A comprehensive set of NGS methods for analyzing:

  • RNA transcription
  • RNA–protein interactions
  • Low levels of RNA
  • RNA modifications
  • RNA structure
RNA Methods Review

This article collection describes various NGS methods for RNA sequencing, compiled from the scientific literature including pros and cons, publication summaries, and references.

Product Selection Tools

Library Prep Kit Selector

Find the right sequencing library preparation kit or microarray for your needs. Filter kits by method, species, and more. Compare, share, and order kits.

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Sequencing Method Explorer

Explore library preparation methods for RNA transcription, RNA low-level detection, RNA modifications, RNA structure, and RNA-protein interactions.

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Related Solutions


Increase the number of samples sequenced per run and optimize high-throughput sequencing using unique dual index adapters.


Unique molecular identifiers (UMIs) provide error correction and accuracy and can reduce false-positive variant calls while increasing variant detection sensitivity.


Our partners have developed both high- and low-throughput walk-away automation methods that span our library prep portfolio.

RNA Sequencing

Detect both known and novel features in a single assay, including transcript isoforms, gene fusions, and single nucleotide variants, all without prior knowledge.