Technical Objectives

The technology platforms at the core of the research programme have been selected to provide quantitative information at all relevant levels of organisation: growth variables recorded at the level of whole plant, organ and cell; profiling of the genome, transcriptome, proteome and metabolome; protein-protein and protein-DNA interaction networks. They can be ranked in four classes:

1. Well-established methods, but only exceptionally applied at this scale to study a single biological system in an integrative framework, requiring standardisation of existing protocols and datasets; they include microarray transcript profiling, HTP real time RT-PCR, flow cytometry, large-scale recombinational cloning methods, GFP-fusion subcellular localisation, yeast two-hybrid, tandem affinity purification, mass spectrometry, chromatin immunoprecipitation;
2. More advanced profiling techniques; they include large-scale SNP genotyping, systematic enzyme profiling (>40 activities) of identical samples, ITRAQ for relative protein quantitation, FT-IR microspectroscopy, bimolecular fluorescence complementation;
3. Novel HTP techniques requiring extensive development and aimed at taking full advantage of Arabidopsis as a model species; they include automated leaf structure analysis at cell-level resolution, in planta two-hybrid based on antibiotic selection, Arabidopsis cell-based assays and high content screening to study systematically the results of genetic (genome scale) or chemical (library scale) perturbations;
4. Software tools enabling data integration and biological system modelling.