EAGER: Computed Tomography (CT) as a Novel Platform for Presenting Four-Dimensional (4D) 'omics' Expression Data: Tomato Fruit Development as Test Case

Cornell University, Ithaca NY

Investigators

Abstract

PI: Jocelyn K. Rose (Cornell University) CoPI: Zhangjun Fei (Cornell University) The application of 'omics' (next generation nucleic acid sequencing, proteomics etc.) approaches in the study of multicellular organisms have generated an enormous amount of data that is difficult to comprehend visually. This proposal outlines a strategy to create a novel, high resolution graphical interface to display 'omics' data in a scalable format that will allow easy visualization and interrogation in four dimensions (three dimensions through time). In this project tomato fruit development will be studied as a model system to generate tools to project data sets onto a digitized computed tomography (CT) composite image of the fruit and, thereby, create a 4D platform to spatially and temporally examine the regulatory and structural pathways underlying fruit development and metabolism. An important utility of this platform is that it is readily adaptable to any complex multicellular organisms (plants, animals etc.) whose structure is amenable to CT scans. The specific aims are to (1) generate a digitized CT based profile of tomato fruit development and ripening at the micron and/or submicron level of resolution, (2) develop laser capture microdissection RNA-Seq profiles of the five principal cell/tissue types in tomato fruit pericarp across the same developmental gradient and, (3) create a bioinformatics/analytical pipeline to integrate the data sets derived from aims 1 and 2. The project will train two postdoctoral research associates in modern biological and bioinformatics approaches. If successful, the imaging and RNA-Seq data will be combined with existing proteomic and metabolomic data and made publicly available as a Tomato Expression Atlas, which will be accessible through the Sol Genomics Network website (http://solgenomics.net). Opportunities for training in the use of the bioinformatics tools developed by the project will be made available at the annual Workshop in Plant Genomics and Systems Biology held at Cornell University.