Discover and Profile Expression of Small RNAs


Cutting-edge Ambion® RNA technology, combined with accessible semiconductor sequencing, enables any lab to harness the power of hypothesis-free small RNA analysis.

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Application Note

Read the application note describing the high quality data generated on the Ion PGM™ System

Intro to Small RNA Sequencing

Read more about the basics of small RNA sequencing and solutions for the Ion PGM™ System

Informatics Solutions

Learn about small RNA sequencing informatics solutions for the fastest way to get to your biological results.

Small RNA Sequencing Workflow for the Ion PGM™ System

1 Purify

Use the mirVana™ miRNA Isolation Kit to isolate small RNA from tissues and cells.

2 Construct
Construct library for RNA-Seq

Use the Ion Total RNA-Seq Kit v2 and optional Ion Xpress™ RNA-Seq Barcode 1-16 Kit to make small RNA libraries that preserve strand information.

3 Prepare
Prepare Template for RNA-Seq

The Ion OneTouch™ 2 System is fully automated and requires just minutes of hands-on time.

4 Run
Run Sequence for RNA Sequencing

Use one of three Ion PGM™ chips to discover and profile small RNA on the Ion PGM™ Sequencer. Barcodes allow you to tailor the number of reads for your experiment.

5 Analyze
Analyze data for RNA Sequencing

Torrent Suite™ Software automatically provides sequence reads in exportable FASTQ format, which can be uploaded to third-party software.

Small RNA Sequencing Informatics Solutions

Ion Torrent™ semiconductor sequencing combines a simple, integrated wet-lab workflow with Torrent Suite™ Software and third-party solutions for fast identification, characterization, and reporting of small RNA expression.

Torrent Suite™ Software automatically provides the sequence reads in exportable FASTQ format, which can be uploaded to third-party analysis software. Post-run sequencing data are available for download with a simple right-click. Reports are also easily browsed, with expandable analysis plots and straightforward tables summarizing key results to help ensure that sequencing runs are of high quality.

Third-party software, such as Partek® Flow® software packages, performs read alignment, microRNA level abundance measurements, and multi-sample differential microRNA expression analysis. Additionally, it provides quality control metrics and interactive data visualization.

Introduction to Small RNA Sequencing

Since the discovery of microRNA in the early 1990s, the study of RNA transcription and regulation of gene expression has grown tremendously through the use of hypothesis-driven microarrays. With the advent of next-generation sequencing (NGS) in the last decade, researchers have harnessed the power of deep sequencing to further reveal the complexity of these small RNA species, which include many types of RNA such as microRNA (miRNA), short interfering RNA (siRNA), and piwi-interacting RNA (piRNA), among others.

The Ion Personal Genome Machine® (PGM™) System further elevates the rate of discovery by using hypothesis-free small RNA sequencing, making NGS accessible to any lab with any budget.

Ambion® RNA kits are the best way to isolate and purify your samples to achieve high-quality capture of small RNA species. Leveraging the knowledge leadership of Ambion and integrating kits that isolate and purify small RNA species creates a complete solution that is optimized for small RNA analysis on the Ion PGM™ System. The scalability of the Ion PGM™ System allows you to include a few or many samples per run, giving you the flexibility to repeat experimental designs. Although other NGS platforms can also analyze small RNA, their ultrahigh throughput requires batching hundreds of samples per run, creating a less economical and less flexible solution that can actually delay time-to-results.

The Ion PGM™ Sequencer offers better sensitivity, generating data superior to that obtained using microarrays—for a comparable price. Ion small RNA sequencing surpasses microarrays as a tool for expression analysis, with these advantages:

  • Superior sensitivity to detect more transcripts and subtle changes in gene expression
  • Discrimination between transcripts from closely related genes or those generated by alternate splicing or processing
  • Sequence information that enables the detection of novel and fusion transcripts
  • Digital output enabling results to be compared over time and between studies and labs
  • Close correlation with TaqMan® assay results

Solutions for Small RNA Sequencing

Start your analysis today with the following products:

The Ion PGM™ System, combined with Ambion® RNA kits, delivers fast, flexible, and high-quality sequencing of small RNA, at an affordable price.