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Posted: December 18, 2008

New Reagents Reduce Time, Cost and Experimental Variability of Genomic Analysis Library Preparation

(Nanowerk News) Invitrogen, part of Life Technologies Corporation, a provider of innovative life science solutions, today announced the introduction of two reagent solutions to simplify genomic and transcriptome analysis on next-generation, high-throughput genomic analysis platforms. Both solutions provide basic and clinical researchers with an innovative workflow that greatly reduces the time, cost, and experimental variability associated with next-generation sequencing library preparation.
The RiboMinus™ kit and the E-Gel® SizeSelect™ 2% pre-cast agarose gels simplify the workflows and reduce the experimental time and cost of applications such as discovery and characterization of the entire transcriptome, validation of whole genome association results, targeted resequencing, chromatin immunoprecipitation (ChIP), rare and somatic mutation detection, and epigenetic studies. The solutions are compatible with next-generation high-throughput genome analysis platforms, including Life Technologies' Applied Biosystems SOLiD™ System, Illumina's Genome Analyzer and Roche's Genome Sequencer FLX System.
The RiboMinus for RNA-sequencing kits are available in two configurations: a universal kit for eukaryotes and a more specialized kit for plants. They are used for the enrichment of RNA for whole transcriptome analysis for ribonucleic acid sequencing or RNA-Sequencing applications. The kit enables the depletion of large ribosomal RNA, the most abundant RNA in the transcriptome, by using oligonucleotide probes containing locking nucleic acids and magnetic bead separation technology. The ability to deplete the ribosomal RNA is significant because the abundant RNAs often mask the messenger RNAs that play an influential role in gene expression, which may affect the detection of novel RNA transcripts within a cell. For example, scientists may use the RiboMinus kit to discover low abundance RNA sequences associated with human disease, as well as in agricultural systems that help determine the factors involved in drought and pest resistance.
The E-Gel SizeSelect 2% pre-cast agarose gels are designed to simplify the separation and recovery of nucleic acid fragments of less than 1000 base pairs for short read fragment library construction. For most next generation sequencing platforms, the nucleic acids strands need to be broken into smaller fragments of specific size ranges to efficiently sequence templates in applications, such as targeted and whole genome resequencing, transcriptome analysis, small RNA discovery, ChIP analysis, methylated DNA profiling and de novo assembly. E-Gel SizeSelect 2% system reduces the time needed to complete this step from hours to less than 15 minutes without any need for further purification. The E-Gel system has been used in fragment and mate-pair/paired end library construction on the Applied Biosystems SOLiD System and the Illumina Genome Analyzer.
Dr. Jim Knowles, Professor and Associate Chair for Research Psychiatry and Behavioral Sciences at the University of Southern California's Zilkha Neurogenetic Institute at the Keck School of Medicine is using the E-Gel SizeSelect 2% system for the discovery of genetic factors that predispose individuals to psychiatric illnesses. His research team is focusing on projects including panic disorder, obsessive-compulsive disorder, nicotine addiction, opiate addiction, major depression and pulmonary arterial hypertension.
"We have used the E-Gel SizeSelect 2% system to select different size fractions of DNA during library preparation for next-generation DNA sequencing," said Dr. Knowles. "In comparison with agarose gels, this has been accomplished quickly and efficiently, with a higher yield, while requiring minimal technical skills."
Life Technologies Corporation markets the life science industry's most comprehensive portfolio of solutions for genomic analysis through its Invitrogen and Applied Biosystems units.
"Simplifying sequencing workflows enables researchers to generate more useful data per experiment and allow them to focus on the biology," said Rob Bennett, Life Technologies' Research and Development Leader for Advanced Sequencing Applications. "Life Technologies is developing innovative solutions that will be compatible with all next-generation DNA sequencing platforms to accelerate research and meet the market demand for faster and cost-effective sequencing."
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Source: Invitrogen (press release)
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