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Dr. Andy Felton, Senior Director of Product Management at Ion Torrent describes Ion Torrent’s RNA-Seq technology and advantages over microarrays.

An introduction to RNA-Seq on the Ion (PGM™) Sequencer that provides a fast, affordable, easy-to-use alternative to microarrays for transcript expression analysis.

Fast and simple RNA sequencing

The Ion PGM™ Sequencer puts RNA-Seq within reach of any lab, providing a fast, affordable, easy-to-use system for expression analysis of miRNA and mRNA. Offering better sensitivity, the Ion PGM™ Sequencer generates data superior to that obtained using microarrays—for a comparable price.

Ion RNA-Seq surpasses microarrays as a tool for expression analysis by offering:

  • Superior sensitivity to detect more transcripts and subtle changes in gene expression
  • Discrimination between transcripts from closely related genes or those that result from alternative 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 to TaqMan® assays


Ion semiconductor sequencing on the Ion PGM™ System offers:


• Easy library construction with automation-friendly magnetic bead cleanup
• No gel size selection needed for small RNA libraries
• Intuitive data analysis solutions familiar to microarray users


• 3 Ion Chips allow changing the number of reads by changing the chip
• 16 barcodes for sample multiplexing
• 35- to 200-base read length for sequencing microRNA or mRNA


• Library construction in less than 6 hours
• Sequence in as little as 1 hour for small RNAs and 2.5 hours for mRNAs

Ion RNA-Seq Workflow

1 Purify

Use the mirVana™ miRNA Isolation Kit to isolate small RNA from tissues and cells or the “mRNA from total RNA” protocol for the Dynabeads® mRNA DIRECT™ Micro Kit to purify mRNA with minimal rRNA contamination.


2 Construct Library

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

3 Prepare Template

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


4 Run Sequence

Perform gene expression profiling by sequencing or small RNA analysis on the Ion PGM™ Sequencer. Three Ion Chip sizes and barcodes allow you to tailor the number of reads for your experiment.

5 Analyze Data

Torrent Suite software takes voltage to aligned sequence and outputs standard file formats that can be used by many software solutions for secondary analysis.

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. The content provided herein may relate to products that have not been officially released and is subject to change without notice.