Abstract
The Genomics Research Group (GRG) presentation is intended to describe the current activities of the group in applying the latest tools and technologies for transcriptome analysis to determine the advantages and disadvantages of each of the platforms. We will present three ongoing projects. In the first project, we specifically evaluated microarrays, QPCR and Next Generation Sequencing (NGS) platforms for examining the sensitivity and specificity of microRNA detection using synthetic miRNA standards. In a second study, we used total RNA from Atlantic oyster samples to analyze the transcriptome and study the effect of oil spill and hypoxia as secondary stressor using next generation sequencing. Furthermore, we are now in the process of assembling the Atlantic oyster genome in collaboration with the Genomics Bioinformatics Research Group (GBIRG). We will also present our new project, which will involve the comparison of gene expression profiles of individual SUM149PT cells treated with the histone deacetylase inhibitor TSA vs. untreated controls. The goals of this project are to demonstrate RNA sequencing (RNA-seq) methods for profiling the ultra-low amounts of RNA present in individual cells, and to demonstrate the use of the Fluidigm system for cell capture and RNA amplification in C1 Single-Cell Auto Prep Integrated Fluidic Circuits (IFCs). In this session, we will discuss the technical challenges and the results obtained and expected from each of these projects.