Discover and profile expression of small RNAs


Cutting-edge Ambion® RNA technology, combined with accessible Ion Torrent™ next-generation sequencing, enables any lab to see and discover more with small RNA sequencing.

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Intro to small RNA sequencing

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

Informatics Solutions

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

Small RNA sequencing workflow

Learn about small RNA sequencing solutions

Solutions for small RNA sequencing

Ion PGM™ System with Ion 314™, Ion 316™, and Ion 318™ Chips

Ion Total RNA-Seq Kit v2 to purify small RNA and construct strand-specific libraries

PureLink® miRNA Isolation Kit fast, flexible, and high-quality sequencing of small RNA

Small RNA sequencing workflow for Ion Torrent™ next-generation sequencing systems

1 Purify

Use the PureLink® 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 Chef™ System offers automated high-throughput template preparation and chip loading for users of all expertise levels. Lower-throughput users can choose the Ion OneTouch™ 2 System.

4 Run
Run Sequence for RNA Sequencing

Discover and profile small RNA on the Ion PGM™ or Ion Proton™ systems. Barcodes allow you to tailor the number of reads to 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 BAM files, 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 high-quality sequencing runs.

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, 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.

Ambion® RNA kits are a great way to isolate and purify your samples to help 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 only a few or many samples per run, giving you the flexibility to quickly repeat experiments. Although other NGS platforms can also analyze small RNA, their ultrahigh-throughput format requires batching hundreds of samples per run, creating a less economical and less flexible solution when you only need to analyze a few samples, and delaying your time-to-results.

Ion Torrent™ next-generation sequencing systems offer better sensitivity, generating data superior to that obtained using microarrays at a comparable price. Choose the Ion PGM™ System for fast and accurate results for small RNA and targeted RNA studies. The Ion Proton™ System offers higher throughput, enabling you to scale from small RNA to whole-transcriptome analysis. Both systems surpass microarrays as a tool for expression analysis, with these advantages:

  • Superior sensitivity, with a greater dynamic range, to detect more transcripts and subtle changes in gene expression
  • Discrimination between transcripts from closely related genes or splice variants
  • 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