W336 RNA-Seq Applications on the Ion Torrent PGM

Date: Tuesday, January 17, 2012
Time: 5:20 PM
Room: Pacific Salon 3
Kelli Bramlett , Life Technologies, Austin, TX
Jeff Schageman , Life Technologies, Austin, TX
Luming Qu , Life Technologies, Austin, TX
Jose Cienfuegos , Life Technologies, Austin, TX
Bob Setterquist , Life Technologies, Austin, TX
RNA-Seq technology has become widely utilized as a tool to understand the transcriptome of a given experimental system. This method utilizes next generation sequencing platforms to sequence a cDNA library in order to gain information about the RNA content and transcriptional status of an experimental system. Profiling the transcriptome of a system in this way has become an invaluable tool in many genomic studies. The Ion Torrent Personal Genome Machine (PGM™) utilizes revolutionary technology, simplifying next generation sequencing instrumentation to make this technique available to a wider group of individuals beyond the basic researcher. The PGM™ instrument combines semiconductor technology with simplified chemistry including natural nucleotides and no enzymatic cascades to create a simple and scalable sequencing platform devoid of the need for expensive and complicated optics and imaging capabilities. We will present transcriptome analysis from both RNA-Seq small RNA and mRNA libraries analyzed on the Ion Torrent PGM™ instrument. The mRNA transcriptome profiles of two well studied RNAs utilized in the historic Microarray Quality Consortium (MAQC) were analyzed by PGM™ sequencing and compared to publically available MAQC transcriptome profiles from microarray and TaqMan® platforms. In addition, small RNA analysis from PGM™ sequencing will be presented. The miRNA content of multiple RNA types was profiled using PGM™ data compared to Affymetrix miRNA microarrays and TaqMan Low Density Arrays. These studies demonstrating comparable mRNA and miRNA profiles from diverse analysis platforms solidifies the Ion Torrent PGM™ sequencing system as a viable platform for RNA-Seq and differential expression studies of the transcriptome.