The EmbryoGENE Platforms: Integration of Bovine Embryonic Genome-Wide DNA Methylome and Transcriptome

Over the past five years, the EmbryoGENE Network has developed a comprehensive set of tools to study the transcriptome and the DNA methylome of bovine embryos. These set of tools, which we call the EmbryoGENE platforms, contain an RNA expression microarray, EMBV3; a methyl-sensitive restriction based epigenetic microarray, EDMA; a Laboratory Information Management System (LIMS) for the management and storage of both types of datasets, ELMA; software for the analysis of two-color microarrays, FlexArray; and a comprehensive analysis pipeline for integrating both types of datasets, EMAP. Comprehensive documentation and standard operating procedures are provided every step of the way, making it easy for any researcher to go from biological samples to lists of differentially expressed genes and differentially methylated regions in bovine genome. So far, 764 transcriptomics microarrays and 86 DNA methylomics  microarrays have been hybridized, representing 22 experiments performed over 8 bovine tissue types. The EMAP and EDMA contain numerous features to integrate results across experiments and across the platforms, and generate numerous descriptive and comprehensive figures to help in the interpretation of the data. Planned developments include integrative meta-analysis of all of the previously accumulated data and the development of a bovine "Embryome" database which could be used as a reference when studying the bovine embryo and its associated tissues.