ELMA: A Platform for Transcriptional and Epigenetic Microarray Studies of Livestock Embryos

The goal of the EmbryoGENE NSERC Strategic Research Network is to characterize gene expression and epigenetic patterns in developing porcine and bovine embryos. To this end EmbryoGENE has developed custom microarray platforms for both species. Here we describe a web-based application for the management and analysis of microarray data called ELMA (EmbryoGENE LIMS and Microarray Analysis). ELMA provides complete details about the available microarray platforms, including up-to-date probe and target annotation. EmbryoGENE has created a standardized and well-tested set of protocols for working with microarrays and embryo samples, all of which are available through ELMA. The LIMS component of ELMA stores information about a microarray experiment in a MIAME compliant fashion and can export experimental data in the convenient GEOarchive format. ELMA currently contains data from over 1700 array hybridizations. To assist in assessing data quality, ELMA creates a variety of informative QC plots, which are associated with every uploaded data set. In-depth data analysis is performed by ELMA using integrated R scripts and the results are stored in the underlying relational database. Gene card integration allows quick visualization of expression data for all probes that target a particular gene. Advanced search capabilities allow microarray results to be compared across several experiments, and data from multiple experiments can be pooled and reanalyzed. The EmbryoGENE Network recently developed a bovine epigenetic microarray platform and is currently creating one for swine. ELMA data input and analysis workflows have been updated to incorporate the epigenetic platform.