Theory:  The RNA-Seq course is designed to introduce participants to wet-lab and dry-lab (bioinformatic) procedures associated with global gene expression profiling using a low-cost version of RNA-seq (Meyer et al, 2011), which became known as tag-based RNA-seq.  We will focus on the theory of next-generation sequencing (NGS), the diversity of RNA-seq methods, and the specifics of our low-cost RNA-seq approach.  
 
Wet lab: We will be isolating RNA using an RNAeasy kit (Qiagen) and quantifying RNA yields using Nanodrop 2000 (Thermo-Fisher).  After fragmentation, we will proceed with cDNA synthesis and amplification, addition of barcodes, and quantification of the final samples.
 
Dry lab: This course will include an introduction to UNIX, working on a large computer cluster (Lonestar, part of TACC), read quality filtering, mapping to the reference transcriptome, processing counts data using DESeq package, generating heat maps, and analysis of gene expression correlations.  We will also briefly cover transcriptome assembly using Trinity.  
 
Project: Corals are capable of receiving up to 100% of their nutritional requirements from their photosynthetic dinoflagellate endosymbionts (zooxanthellae).  In unfavorable conditions, such as bleaching episodes in which corals lose their symbionts, corals may engage in heterotrophic feeding to meet their nutritional needs.  We are interested in identifying gene expression biomarkers that would indicate which strategy a coral is using to meet its nutritional requirements: translocation from autotrophic symbionts, heterotrophic assimilation, or both.  
 
Instructor: Mikhail V. Matz , Teaching Assistants:  Groves Dixon and Marie Strader
cost: US $2000
 
 
Global gene expression profiling with
tag-based RNA-seq
 
July 7-14