AUG 21, 2013 11:00 AM PDT

Panel Discussion: Meeting the Demand of Increased NGS Capacity with Automated TruSeq Stranded mRNA Library Preparation

Speaker
  • Alisa Jackson, Moderator, Beckman Coulter, Inc. Zach Smith, MS, Project Scientist, The Center for Genomics and Bioinformatics, Indiana University Mary Blair, Senior Application Scientist,
    Biography
      Zach Smith serves as the next generation sequencing and laboratory automation specialist at the Center for Genomics and Bioinformatics at Indiana University, Bloomington. His duties include the construction of sequencing libraries for Illumina and Roche 454 sequencing platforms as well as the development of new automation protocols for NGS and genomics research. Mary Blair helps scientists address their automated sample preparation challenges. Mary is responsible for internal development of automated methods for popular Genomic sample preparation kits and protocols on Beckman Coulter's Biomek liquid handling platforms. These fully supported Biomek sample preparation methods are for popular applications such as NGS and qPCR. Fully implemented they yield consistent, quality samples at an increased throughput with decreased labor. Dave Delano manages products in Illumina's gene expression and regulation portfolio including RNA-seq, ChIP-Seq, and methylation applications.

    Abstract

    RNASeq has become the primary method for studying changes in gene expression in modern genomics research. By directly sequencing the various types of RNA molecules, including mRNA, ncRNA, and small RNA, researchers can build an accurate profile of gene expression under various conditions, allowing the elucidation of gene function and regulation. RNASeq has been further refined recently with the development of stranded RNASeq, which modifies the existing RNASeq library construction methodology to preserve information regarding which DNA strand the RNA transcript originated from. Among other advantages, stranded RNASeq allows for more accurate mapping of RNASeq transcripts to reference genomes, which in turn results in a more accurate view of the transcriptome. Increasingly, researchers are designing more complex experiments involving population level transcriptomic surveys and time course studies, both of which require high throughput RNASeq library construction methods that consistently generate high quality RNASeq libraries. In response, we developed an automated RNASeq library construction method using the Beckman Coulter Biomek FXP liquid handling system in conjunction with TruSeq Stranded mRNA library preparation chemistry from Illumina. By combining Illumina's proven chemistry with the highly efficient Biomek FXP liquid handling system, we have developed a flexible library construction protocol that allows for the creation of up to 96 individually indexed Illumina stranded mRNA libraries by a single technician over the course of approximately 8.5 hours of machine time.


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