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Targeted RNA Sequencing for Gene Expression and Transcriptome Analysis
Fast and simple targeted RNA sequencing with Ion AmpliSeq technology
Comprised of targets selected from over 20,000 well annotated RefSeq genes, Ion AmpliSeq RNA and transcriptome panels help to empower fusion detection and high-throughput gene expression analysis with high sensitivity and specificity. These panels are straightforward to implement as they take advantage of the simple and fast sequencing workflow of the Ion GeneStudio S5 and Ion Chef Systems, offering a simpler and cost-effective alternative to whole transcriptome sequencing.
Featured articles
Learn how researchers use the Ion AmpliSeq Transcriptome Gene Expression assay in biomarker discovery
Using the mouse model in your research? Learn how to measure expression levels of over 20,000 mouse RefSeq genes.
See how gene-level transcript profiling using a targeted transcriptome panel compares to whole transcriptome results
Targeted next-generation sequencing (NGS) provides a wider quantitative dynamic range and improved transcript detection compared to conventional microarray analysis. Ion AmpliSeq RNA and transcriptome panels are based on Ion AmpliSeq technology, which allows you to amplify thousands of targets in a single tube simultaneously, delivering outstanding data quality with low input RNA requirements (as little as 500 pg of unfixed RNA), FFPE compatibility (as little as 5 ng), and superior throughput flexibility. Furthermore, targeted RNA sequencing can be used to detect fusion transcripts from chromosomal rearrangements, which are critical initiating steps of tumorigenesis.
Ready-to-use panels
Ion AmpliSeq Transcriptome Human and Mouse Gene Expression Kits
The Ion AmpliSeq Transcriptome Human Gene Expression Kit and Ion AmpliSeq Transcriptome Mouse Gene Expression Kit are comprehensive tools for gene-level expression analysis. Targeting >20,000 human or mouse RefSeq transcripts in a single reaction with an FFPE-compatible workflow, the complete Ion AmpliSeq Transcriptome solution is compatible with existing downstream microarray or next-generation sequencing (NGS) analysis pipelines for fast and straightforward data interpretation.
Learn more about Targeted Transcriptome Sequencing for Human and Mouse ›
Application note: Simple, scalable transcriptome-level gene expression analysis with next-generation sequencing
Ion AmpliSeq RNA Fusion Lung Cancer Research Panel
Developed with input from the OncoNetwork Consortium, the Ion AmpliSeq RNA Fusion Lung Cancer Research Panel was designed to detect expression imbalance in fusion driver genes using only 10 ng of FFPE RNA. The panel is a single pool of primers targeting fusion transcripts included in the ALK, RET, ROS1, and NTRK genes.
Design your own Ion AmpliSeq RNA custom panel
Creating and ordering custom panels is easy with Ion AmpliSeq Designer—a free, online assay design tool that connects you directly to our assay design pipeline. Create and order custom RNA panels by simply selecting your targets of interest or entering your specific genomic content online, and we will design and create a customized Ion AmpliSeq panel just for you. Leveraging more than a decade of expertise powering the Applied Biosystems TaqMan Custom Assay design pipeline, the Ion AmpliSeq Designer tool produces optimized primer designs in as little as a few minutes. You now have the flexibility to analyze panels of genes of your choosing, such as those implicated in a particular disease state or representing specific biological pathways with anywhere from 12 to 1,200 human amplicons in a single reaction. Each design accounts for GC content, is filtered for repeats and SNPs, and selects target exons that represent the maximum number of transcripts for genes having multiple transcript isoforms documented in standard databases such as RefSeq.
Pre-designed customizable panels
Pre-designed Ion AmpliSeq panels have amplicon designs that have been evaluated through Ion AmpliSeq Transcriptome Human Gene Expression Panel. Their content includes gene lists curated from KOL publications and databases. They are customizable, so you can add or remove genes to update the amplicon list.
Panel content for our pre-designed panels is available on AmpliSeq.com to customize and order.
Learn more about pre-designed and fully customizable Ion AmpliSeq RNA panels ›
Pre-designed Ion AmpliSeq panels:
- Ion AmpliSeq RNA MAPK Pathway Research Panel
- Ion AmpliSeq RNA WNT Pathway Research Panel
- Ion AmpliSeq RNA Human Oncology Pathway Research Panel
- Ion AmpliSeq RNA Research Panels
Targeted RNA sequencing workflow for the Ion GeneStudio S5 or Ion PGM systems
Select from our ready-to-use gene panels or design your own panel.
Target amplification in a single reaction.
Isothermal amplification with Ion Chef System.
Learn more about Ion Chef System ›
Sequencing using Ion S5 System or Ion PGM System.
Learn more about Ion PGM & Ion S5 System ›
Data analysis with Torrent Suite Software and third party software (for more extensive analysis).
Select from our ready-to-use gene panels or design your own panel.
Target amplification in a single reaction.
Isothermal amplification with Ion Chef System.
Learn more about Ion Chef System ›
Sequencing using Ion S5 System or Ion PGM System.
Learn more about Ion PGM & Ion S5 System ›
Data analysis with Torrent Suite Software and third party software (for more extensive analysis).
Targeted RNA sequencing informatics solutions
Torrent Suite Software coordinates all the experiment planning and data processing steps necessary to complete your targeted sequencing workflow. New product templates enable users to plan targeted runs simply and quickly. In just a few hours, raw data are captured on the Ion PGM or Ion GeneStudio S5 sequencer and transferred to the Torrent Server for base calling. Digital counting is then completed using the AmpliSeqRNA plug-in, which reports normalized transcript counts in spreadsheet file formats, enabling users to import data into other software packages for differential expression analysis.
Excellent correlation with TaqMan Assays
Universal human reference (UHR) RNA and human brain reference (HBR) RNA control samples were used to compare fold change for each of the 50 genes included in the Ion AmpliSeq RNA Cancer Research Panel against the fold change calculations of the same genes with TaqMan Gene Expression Assays. A resulting correlation of 0.989 was observed. These results show the accuracy of the gene expression data obtained with the Ion AmpliSeq RNA workflow.
* Based on recommendations of multiplexing 4-6 libraries generated using the Ion AmpliSeq™ RNA Apoptosis Panel on one 318™ chip.
**The content provided herein may relate to products that have not been officially released and is subject to change without notice.