A targeted method for both small RNA profiling and discovery applications

Sequence the complete range of small RNA and miRNA species

Small RNA Sequencing

Small noncoding RNAs act in gene silencing and post-transcriptional regulation of gene expression. Small RNA sequencing (RNA-Seq) is a technique to isolate and sequence small RNA species, such as microRNAs (miRNAs). Small RNA-Seq can query thousands of small RNA and miRNA sequences with unprecedented sensitivity and dynamic range.

With small RNA-Seq you can discover novel miRNAs and other small noncoding RNAs, and examine the differential expression of all small RNAs in any sample. You can characterize variations such as isomiRs with single-base resolution, as well as analyze any small RNA or miRNA without prior sequence or secondary structure information.

Generate miRNA sequencing libraries directly from total RNA to understand the role of noncoding RNA.

  • Understand how post-transcriptional regulation contributes to phenotype
  • Identify novel biomarkers
  • Capture the complete range of small RNA and miRNA species

Epigenetic Analysis and Small RNA-Seq

Illumina offers a broad portfolio of epigenetic analysis tools for investigators interested in studying epigenetic modifications and small RNA gene regulation.

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Find out how researchers used Illumina sequencing technology to study a honeysuckle-encoded microRNA that targets influenza A viruses.

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Honeysuckle, miRNA, and the flu

Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of sequencing data worldwide.*

In addition to our industry-leading data quality, Illumina offers a simple workflow for small RNA and miRNA sequencing that simplifies the entire process, from library preparation to data analysis and biological interpretation.

Click on the below to view products for each workflow step.

TruSeq Small RNA Library Prep Kit

Simple, cost-effective solution for generating small RNA libraries directly from total RNA. Supports customizable size selection to investigate any small RNA between 17 to 35 nucleotides.

Library Prep Kit Selector Library Prep Kit Selector

Determine the best kit for your needs based on project type, starting material, and method or application.

MiniSeq System

Targeted Power. Access proven Illumina quality with this small, robust NGS system. From 1-12 small RNA samples per run.

MiSeq Series

Focused power. Speed and simplicity for targeted and small genome sequencing. From 1-12 small RNA samples per run.

NextSeq Series

Flexible power. Speed and simplicity for everyday genomics. Up to 48 small RNA samples per run.

HiSeq Series

Production power. Max throughput and lowest cost for production-scale genomics. Up to 96 small RNA samples per run.

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and buffers tailored to each Illumina sequencing system.

BaseSpace Small RNA App

Aligns reads against four reference databases, and outputs hits to mature miRNAs, isomiRs, and piRNAs.

miRNAs Analysis App

Allows detection of differentially expressed miRNAs between 2 conditions. Performs adapter trimming, read counting, and more.

The Broad’s IGV

A genome browser developed by the Broad Institute of MIT and Harvard that displays NGS data for complex variant analysis.

Genomatix Pathway System (GePS)

Associates single gene or list of genes with annotation data for pathways, diseases, tissues, and small molecules.

iPathway Guide

Differential gene expression, drug interaction, and disease analysis.

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.

Access Illumina Quality NGS with the MiniSeq Benchtop Sequencer

Perform small RNA-Seq with a sequencing solution that fits your benchtop, your budget, and your workflow. Discover novel miRNAs and analyze any small noncoding RNA without prior sequence or secondary structure information.

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MiniSeq Desktop Sequencer
Cancer Research: Variant Detection
Cancer Research: Variant Detection

Small RNA sequencing enables the discovery profiling of miRNAs and other small noncoding RNAs present in the cancer transcriptome at extremely high coverage. Learn more about cancer transcriptome studies.

Complex Disease: RNA Editing
Complex Disease: RNA Editing

NGS-based profiling enables rapid, high-throughput analysis of the miRNA transcriptome, and can provide insights into complex disease-related RNA editing processes and mutational events. Learn more about complex disease research.

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Small RNA-Seq Best Practices Webinar
Small RNA-Seq Best Practices Webinar

Considerations for small RNA library prep, sequencing, and basic data analysis.

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Push-Button Informatics
Push-Button Informatics

Access user-friendly tools that enable researchers to easily analyze, store, and share NGS data.

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TruSeq Small RNA Library Prep Kit FAQs
TruSeq Small RNA Library Prep Kit FAQs

Get answers to the most frequently asked questions regarding small RNA-Seq.

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RNA-Seq on the NextSeq 500 System<
RNA-Seq on the NextSeq Series

A flexible, cost-effective solution for RNA sequencing provides a deeper understanding of biology.

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*Data calculations on file. Illumina, Inc., 2015