PLG0036 Field-omics - analysis of ‘-omics’ data in field trials and controlled environments (3 ECTS) 15th – 19th of October 2012 at SLU Alnarp
The last years’ rapid technological advancements have enabled genome-scale capturing of biological processes. Gene expression analysis by microarrays as well as protein and metabolite identification by mass spectrometry are today common techniques used in many laboratories. However, combining different types of data and making biological sense out of large datasets remains challenging. The generation of such large datasets - often referred to as ’-omics’ data - demands partly new considerations for experimental set-ups, sampling, data analysis and visualization.
This course will focus on theoretical and practical aspects when designing experiments for the generation of ’-omics’ data and how to go from sampling to interpreting the results and finding biologically relevant conclusions. Strategies both in field trials and in controlled environments will be covered. Suitable statistical methods to deal with the variation in this type of data will be presented.
Dan Jacobson (Stellenbosch University), Jan-Eric Englund (SLU), Kim Esbensen (Aalborg University), Antonio Ferrera (UCP-ESB), Magnus Fontes (Lund University), Ann-Mari Fransson (SLU),Kåre Lehmann Nielsen (Aalborg University), Fredrik Levander (Lund University), Erland Liljeroth (SLU), Kerstin Nagel (Jülich) Rodomiro Ortiz (SLU), Wolfram Weckwerth (University of Vienna)
Experimental design for field trials and in controlled environments. Methods to record climate data and soil properties. Phenotyping and scoring plant material. Sampling of plant material. Pooling strategies. Survey of available ’-omics’ techniques and their suitability for different types of data. Interpretation and visualization of data by e.g. pathway and gene set enrichment analysis. Biomarker discovery. Using sequence information and inferring cross-species information for functional annotation. The use of ’-omics’ data for plant breeding.
The overall goal is to point out the possibilities in using ’-omics’ techniques, but also to highlight possible pitfalls. The potential in using ’-omics’ data in future plant breeding efforts will also be discussed.
For questions, please contact course leaders Dan Jacobson and Erik Alexandersson.
Course venue: 15-19 October 2012 at SLU Alnarp
Course syllabus: http://tiny.cc/09e0aw