Transcriptome Sequencing by Ion Torrent Next-Generation Sequencing
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Read more about the basics of transcriptome sequencing and solutions for the Ion Proton™ System
Learn about transcriptome analysis solutions for the fastest way to get to your biological results
Transcriptome workflow for 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.
Introduction to Transcriptome Sequencing
Understanding the structure, function, and organization of information within genomes is central to basic and translational research. Transcriptome sequencing, often referred to as RNA-Seq or RNA sequencing, provides the most complete method of analyzing the transcriptional content of cells. With the advent of deep-sequencing technologies, it has become increasingly evident that transcription in human cells is an intricate and dynamic process comprising a variety of RNA species including short RNAs, polyadenylated RNA, and non-adenylated transcripts.
Interrogate Transcriptional Content
Transcriptome sequencing or RNA-Seq offers a hypothesis-neutral approach to interrogating the transcriptional content of a genome. Compared with conventional methods such as microarray analyses that only allow the characterization of transcripts present on the microarray, transcriptome sequencing is a powerful and cost-efficient method for identifying and quantifying RNA. Differential gene expression can be quantified, enabling correlation with phenotypic information. Sequencing the transcriptome facilitates the identification of alternative splicing and transcript isoforms as well as aiding gene discovery.
Detect Fusion Transcripts
Further, allele-specific gene expression can be ascertained when corresponding whole genome sequencing (WGS) or exome sequencing data are available. Importantly, this approach can detect fusion transcripts from chromosomal rearrangements that are critical initiating steps of tumorigenesis. Transcriptome sequencing can be used to validate single nucleotide polymorphisms (SNPs) from WGS or exome sequencing experiments and used to discover SNPs in organisms with inadequate (or no) genome sequence information.
Solutions for Transcriptome Sequencing
Transcriptome analysis provides fundamental insights into how genomes are organized and regulated and how transcription is altered during development and disease. Consider the following solutions to begin whole transcriptome sequencing in your lab:
- The Ion Proton™ System will produce 1 to 4 transcriptomes per run with the Ion PI™ Chip, and up to 16 transcriptomes with the Ion PII™ Chip*
- The Ion Total RNA-Seq Kit v2 enables construction of strand-specific libraries in approximately 5 hours
- The Ambion® RiboMinus™ Eukaryote Kit v2 is designed to remove the highly expressed and uninformative rRNA species
- The Ambion® ERCC RNA Spike-In Mix comprises a set of unlabeled, polyadenylated transcripts designed to be added to an RNA analysis experiment after sample isolation in order to measure dynamic range, the lower limit of detection, and fold-change response
*The content provided herein may relate to products that have not been officially released and is subject to change without notice.
For Research Use Only. Not for use in diagnostic procedures.
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™ Eukaryote Kit v2 provides more than 90% rRNA depletion increasing the sequencing power of the Ion Proton™ System. The Ambion® ERCC RNA Spike-In Mix comprises a set of unlabeled, polyadenylated transcripts designed to be added to an RNA analysis experiment after sample isolation in order to measure dynamic range, the lower limit of detection, and fold-change response
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, available now, for fully automated template preparation.
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 analysis results in under 24 hours. Torrent Suite™ Software offers simple run setup using predesigned workflows and run monitoring in real time.
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. This software then performs read alignment, transcript level abundance measurements and multi-sample differential gene expression analysis. Additionally, it provides quality control metrics and interactive data visualization.