Jane Shingles, Robert Johnsen, Qianru Li, Ian A Hope, Jennifer Rosenberg, John Reece-Hoyes, Alain Carnec, David Lee, Rebecca Newbury, Denis Dupuy, Wiliam A Mohler, Rock Pulak, Marc Vidal, David Baillie, Nicolas Bertin, Ryan Viveiros, Don Moerman, Domena Tu
[
International Worm Meeting,
2005]
The field of systems biology attempts to provide a systems level understanding of biological processes by building descriptive and mechanistic models of biological phenomena. An important aspect of the complexity of metazoan organisms lies within the differential expression of the genes that drives cell diferentiation. The long-term goal of the C. elegans localizome is to generate a gene expression and protein localization map, for most genes, across development. We present solutions for the major challenges of a C. elegans proteome-wide localizome map. We generated a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing GFP. Version 1 of the worm promoterome is a resource of ~6,500 C. elegans promoters that can be transferred rapidly into various Multisite Gateway Destination vectors to drive expression of GFP, or other markers, either directly from promoters or in fusion with a protein-encoding ORFs. We will describe a new method that uses a nematode profiler/sorter system. This system allows the high-throughput mapping of gene expression patterns along the anterior-posterior axis of each animal. As thousands of animals from a mixed population of worms are analyzed, fluorescence traces can be arranged by size into Post-embryonic Developmental Expression Chronograms (PDECs). A PDEC provides a reconstituted "time-lapse" image of gene expression throughout larval to adult development across the length of the worms body. Although the spatial resolution of the PDEC is lower than that of traditional microscopic analyses, this data format allows automated comparison and clustering of expression patterns, while also giving access to a clear temporal context of gene expression. We acquired PDECs for over 1,500 GFP-strains generated mainly by the C. elegans Gene Expression Consortium and the Hope lab. We will discuss how these data can be used in combination with interactome, transcriptome and phenome datasets, and also how they compare to manual annotations performed through microscopic observation.