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Ion AmpliSeq™ Transcriptome Human Gene Expression Kit

Fast and easy gene-level expression analysis starting with as little as 10 ng RNA.

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Transform your research by targeting >20,000 RefSeq transcripts, starting with as little as 10 ng of RNA input and a fast, FFPE-compatible workflow using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit and the Ion S5™ series sequencing systems.

  • Achieve cost-effective transcriptome sequencing without waiting weeks to batch samples
  • Perform gene-level expression surveys with as little as 1 hour of hands-on time for library preparation, and go from RNA to gene expression levels in less than 2 days
  • Software tools included for fast and easy analysis of sequencing reads; use your existing downstream microarray or next-generation sequencing (NGS) pipelines for gene-level differential expression data analysis
  • Survey precious FFPE samples with as little as 10 ng of input RNA using proven Ion AmpliSeq™ technology

  View an application note to see how gene expression results compare to microarray and qPCR data.

Looking for a gene expression signature in triple-negative breast cancer research samples using the Ion AmpliSeq Transcriptome Human Gene Expression kit

Is there only one way to do RNA-Seq library prep? Hear Milan Radovich, PhD, of Indiana University discuss his research on triple-negative breast cancer expression-based gene signatures.

Quantitative and differential gene expression analysis is fundamental to many biological research applications including gene regulation analysis, correlating gene expression with phenotypic information, and cellular pathway analysis. Conventional gene expression profiling methods include hybridization-based (microarray) and amplification-based (qRT-PCR) technologies. However, methods present certain limitations:

  • Despite requiring significant amounts of RNA, microarrays remain limited in their sensitivity and specificity
  • Although accepted as the gold standard for gene expression analysis, qRT-PCR is generally low-throughput, and substantial amounts of RNA are required if large numbers of genes are to be tested

As such, both technologies present workflow challenges when analyzing samples that are limited in quantity or quality, such as degraded RNA from FFPE tissues. Targeted sequencing using NGS and the Ion AmpliSeq Transcriptome Human Gene Expression Kit not only provides a representation of absolute expression, but also can identify and quantify low-abundance transcripts quickly and easily for both intact and degraded samples.

ampliSeqTranscriptome-figure-3

 


Improved gene-level transcript detection using the Ion AmpliSeq Transcriptome Human Gene Expression Kit and the Ion Proton System.   A Venn diagram demonstrating the concordance of genes identified by MAQC microarray data and the Ion AmpliSeq Transcriptome Human Gene Expression Kit.

Review gene expression data from FFPE-derived RNA samples sequenced using the Ion AmpliSeq Transcriptome Human Gene Expression Kit.

How do Ion Torrent NGS transcriptome profiling solutions compare to microarray analysis?

In contrast to microarray analyses that have limited sensitivity and complex workflows when analyzing degraded samples, transcriptome sequencing provides workflows with a greater quantitative linear dynamic range and improved detection at the extremes of the quantitation range.  The Ion AmpliSeq Transcriptome Human Gene Expression Kit is ideal for traditional gene expression analysis of known transcripts from the RefSeq database, while whole transcriptome sequencing expands your capabilities to enable discovery of novel transcripts including alternative splicing isoforms, gene fusions, and biomarkers. 

Learn more about Ion Torrent RNA sequencing solutions ›
  View the poster to see how Ion AmpliSeq Transcriptome, RNA-Seq and real-time PCR data compare ›

Gene expression analysis comparison

Gene expression comparison
Workflow for the Ion AmpliSeq Transcriptome Human Gene Expression Kit
1 Construct library
Ion Torrent library kits

• Perform reverse transcription and amplify >20,000 targets in a single reaction
• Digest primer sequences and ligate Ion Torrent specific adapter sequences

Hands-on time: ~ 1 hour

Products:
• Ion AmpliSeq Transcriptome Human Gene Expression Kit

2 Prepare template
Ion Chef™ System

• Load prepared library, prepackaged reagents, and up to 2 Ion 540 chips onto Ion Chef™ instrument
• Start run for automated template preparation and chip loading

Hands-on time:
15 minutes

Products:
• Ion 540 Kit-Chef

Learn more about
Ion Chef System ›

3 Run sequence
S5 system

• Initialize Ion S5 instrument
• Load sequencing-ready chip from Ion Chef System and start sequencing run

Hands-on time:
15 minutes

Products:
• Ion 540 Chip Kit

Learn more about
Ion S5 System ›

4 Analyze data
Ion Reporter™ Software

• Run AmpliSeqRNA plug-in to generate simple, easy-to-use read count data files
• Perform simple statistical analysis or import files into existing microarray analysis pipelines

Products: Torrent Suite™ Software

Learn more about
Torrent Suite Software ›

Ion S5 Series

Adopting NGS in your lab is now simpler than ever before. The Ion S5™ and Ion S5™ XL next-generation sequencing systems enable the simplest targeted sequencing workflow for your lab with superior speed and affordability. Focus your research efforts on applications that have the potential to be impactful. The Ion S5 and Ion S5 XL Systems have a modular build, so your lab has the flexibility to do multiple targeted sequencing applications on a single system.

Learn more about the Ion S5 Series ›

Straightforward, fast data analysis

Whole transcriptome sequencing is great for discovery, but not necessarily ideal for traditional gene expression analysis. Take advantage of the speed and increased sensitivity of NGS, while keeping sample preparation and data analysis simple with the Ion AmpliSeq Transcriptome Human Gene Expression Kit. Use the AmpliSeqRNA plug-in to generate easy-to-use read count data files and perform simple statistical analysis or import files into existing microarray or NGS analysis pipelines.

Data analysis software packages tested with output from the AmpliSeqRNA plug-in:

Bioconductor
  • DESeq
  • Limma
Partek Software
  • Partek™ Flow™ (starting with aligned BAM files generated in Torrent Suite Software)
  • Partek Genomics Suite™ Software