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 altered expression of genetic variants contributes to complex disease research. Transcriptome sequencing relies on next-generation sequencing (NGS) methodology and techniques.

  Simple, Rapid and Reliable RNA Sequencing brochure

We offer two great options for transcriptome analysis:

  • Whole transcriptome sequencing, or RNA-Seq, for both discovery and gene expression analysis. Use the Ion GeneStudio S5 Systems combined with Invitrogen 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 AmpliSeq Transcriptome Human Gene Expression Kit application note

Gene expression research webinar

Exosome miRNA sequencing for biomarker profiling using Ion S5 System and Ion Total RNA-Seq Kit
Lesley Cheng, PhD, La Trobe University.

View webinar

Advantages of RNA-Seq over microarray techniques

  • Increased specificity and sensitivity—detect more RNA species, including fusion transcripts and closely related isoforms
  • Wider dynamic range—with sufficient read depth, the full breadth of biologically relevant expression changes can be detected using NGS approaches without the signal compression typical of microarray platforms
  • Digital output—NGS read count provides a representation of absolute expression, enabling you to identify and characterize low-abundance transcripts 
  • Detect both known and unknown transcripts and variants—the unbiased nature of NGS sequencing coverage enables true transcriptome-wide biomarker discovery that does not rely on prior knowledge of the genome

Whole 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 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 Invitrogen RiboMinus Eukaryote Kit v2 provides more than 90% rRNA depletion, which helps increase 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.
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3 Prepare
Prepare template for RNA-Seq

Use the Ion Chef System for walk-away template preparation and chip loading. Suitable for users of all experience levels.
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4 Run
Run sequence for RNA sequencing

The Ion GeneStudio S5 systems are ideal for sequencing of gene panels all the way to transcriptomes. The sequencing run time is as little as 2.5 hours, with only 15 minutes of setup time.
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5 Analyze data & validate
Analyze data for RNA sequencing

Torrent Suite Software automatically provides the sequence reads in exportable FASTQ or BAM formats, which can be uploaded to third-party software, such as Partek Flow software packages
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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. Sequencing run reports are 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 are available to perform read alignment, transcript level abundance measurements, and multi-sample differential gene expression analysis. Additionally, quality control metrics and interactive data visualization is provided.

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