EmbryoGENE’s bovine and porcine transcriptomics Platform are now available. After processing more than 2 million bovine and porcine reads to extract targets for species specific genes, embryo specific genes, 3’ UTR variants and indel splice variants, the EmbryoGENE Bovine and Porcine microarrays were designed. In addition, augmented versions of the bovine and porcine genomes, which include information retrieved from sequencing results, were produced. These versions of the genomes can be consulted through our newly developed genome browser, which enables the visualization of genomic data at the chromosome, gene and oligonucleotide probe level and more. All the information obtained by the EmbryoGENE Network is periodically uploaded on the genome browser to facilitate analyses.
The transcriptomics platform also includes all the bioinformatics tools necessary for the analysis of microarray data, including ELMA (EmbryoGENE LIMS and microarray analysis), a QC module and microarray analysis software. ELMA’s goals are to store microarray data in a MIAME compliant fashion and facilitate future meta-analyses. Upon completion of a microarray experiment, users are asked to provide all the information about their experiment through ELMA and to upload their microarray intensity files. Protocols and Standard Operating Procedures (SOPs) are also available in ELMA and are used for all microarray related experiments. ELMA also produces the output file to be used by the analysis software. The QC module evaluates ELMA files to determine whether they can be used for further analyses. Distribution of signals for both channels is analyzed, as well as negative and spiked in controls to determine hybridization quality. Datasets that meet all quality criterions can be uploaded into the FlexArray microarray analysis platform. FlexArray is a Bioconductor R based software for the analysis of microarray data in a user friendly environment. These tools greatly facilitate gene expression analyses within the EmbryoGENE Network.