What is transcriptome sequencing?

Transcriptome sequencing, or RNA sequencing (RNA-Seq), provides fundamental insights into how genomes are organized and regulated—giving us valuable information about the internal state of cells and how the altered expression of genetic variants contributes to complex diseases research. RNA sequencing relies on next-generation sequencing (NGS) methodology and techniques.

We offer two great options for transcriptome analysis:

  • Whole transcriptome sequencing, or RNA-Seq, for both discovery and gene expression analysis. Use the Ion Proton™ System combined with Ambion® RNA purification and Ion Torrent™ library construction kits for identification and quantitation of both known and novel transcripts, including gene fusions and splice variants.
  • Ion AmpliSeq™ Transcriptome solution for gene-level expression analysis. Ideal for traditional gene expression analysis, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit targets >20,000 RefSeq transcripts using as little as 10 ng RNA input with a fast and FFPE-compatible workflow.

    Learn more about the Ion AmpliSeq™ Transcriptome Solution ›

Ion Torrent™ Transcriptome Certified Service Provider Program

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Read more about the basics of transcriptome sequencing and solutions for the Ion Proton™ System

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Learn about transcriptome analysis solutions for the fastest way to get to your biological results

Advantages of RNA-Seq over microarray techniques:

  • Increase sensitivity—increase your dynamic range to detect more RNA species as well as fusion transcripts and low-abundance isoforms
  • Quantify changing expression levels—NGS provides a representation of absolute expression, allowing you to identify and characterize low-abundance transcripts during development and under different conditions
  • Discover biomarkers—the depth of NGS sequencing coverage enables transcriptome-wide biomarker discovery, linking specific disorders to regions of the human genome in your research.

Transcriptome sequencing workflow overview

We offer a complete RNA sequencing solution for gene expression research. From sample prep to analysis, we enable you to discover more when you perform RNA sequencing. We also support verification of your findings with our suite of qPCR systems and reagents.

Our whole-transcriptome RNA sequencing workflow provides you with:

  • Rapid results
  • Lowest cost per sample on a benchtop sequencer
  • Flexible throughput 
  • Streamlined data analysis
1 Enrich RNA
Enrich RNA Library

The RiboMinus™ Eukaryote Kit v2 provides more than 90% rRNA depletion, increasing the sequencing power of the Ion Proton™ System
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2 Construct
Construct library for RNA-Seq

The Ion Total RNA-Seq Kit v2 provides a fast, simple workflow with as little as 100 ng of total RNA input, while maintaining strand orientation and minimizing bias and error. The RiboMinus™
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3 Prepare
Prepare Template for RNA-Seq

The Ion Chef™ System* will provide high-throughput automated template preparation and chip loading for users of all expertise. Lower-throughput users can choose the Ion OneTouch™ 2 System
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4 Run
Run Sequence for RNA Sequencing

The Ion Proton™ System is ideal for sequencing of transcriptomes and exomes. The sequencing run time is only 4 hours, enabling the entire workflow from library to primary data
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5 Analyze data & validate
Analyze data for RNA Sequencing

Torrent Suite™ Software automatically provides the sequence reads in exportable FASTQ format which can be uploaded to third-party software, such as Partek® Flow® software packages
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For targeted RNA sequencing, our Ion AmpliSeq™ RNA technology streamlines the library preparation process by allowing for the rapid preparation of RNA amplicon libraries targeted to specific genes of interest. Design assays targeted to genes relevant to your research, or use our ready-made panels. Evaluate gene expression changes in key genes important to your study without the need for larger whole-transcriptome studies.



Hear scientists describe how they have sequenced RNA using the Ion Proton™ System.

Transcriptome Analysis Informatics Solutions

Ion Torrent™ semiconductor sequencing combines the simple, integrated wet lab workflow with Torrent Suite™ Software and third party solutions for fast identification, characterization and reporting of the most biologically interesting transcripts.

Torrent Suite™ Software provides you the tools that take you from raw sequence data to informative results, including optimized signal processing, base calling, transcriptome analysis, sequence alignment, and variant analysis. 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.

Transcriptome specific workflows in third party software such as Partek® Flow® software package then performs read alignment, transcript level abundance measurements and multi-sample differential gene expression analysis. Additionally, providing quality control metrics and interactive data visualization.

Partek® Flow® software for Ion Proton™ System
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