Abstract
The EmbryoGENE Network (2008–2013) has assembled data from more than 764 DNA arrays covering the entire transcriptome of bovine oocytes, embryos, and somatic cells, such as granulosa and cumulus cells. The data were obtained using the same extraction-amplification-hybridization-analysis protocols enabling normalization and statistical analysis across time, tissues, and experiments. To provide the scientific community with this information in an organised and functional matter, we have created a web application (http:// http://emb-bioinfo.fsaa.ulaval.ca/granulosaIMAGE/) where the information on 40,000 genes products from 4 tissues are currently available: oocytes (mainly at the germinal vesicle stage), blastocysts in different culture conditions (namely in vitro, in vivo, different concentrations of lipids, free radicals and glucose, as well as blastocysts from cloning, vitrification, and different breeds). Also represented is the complete panel of late folliculogenesis from 3 mm upward including growing, plateau, and atretic phase oocytes, as well as their response to LH and several types of ovarian stimulation. In addition, a postpartum panel of dominant follicles (PGF2α synchronized at Day 30, 60, 90, 12) with high or low BHB (beta-hydroxybutyrate) or vitamin treated (B-6 and B-9) is represented. In each of the panels, a red background indicates differential expression for any given gene or isoform (40,000 on the EmbryoGENE array). To complete the information, a RNAseq experiment was performed on each stage from the germinal vesicle oocyte to the blastocyst (including early and late 8 cell) and presented as an absolute expression level, which is a measure of the total number of RNA molecules for the selected family of transcripts. The web application also provides relative expression values, which measure the proportion of the total transcripts represented by the selected family of transcripts. This information is provided as a graphical representation from the germinal vesicle to the blastocyst stage. This source of information may be cited either by referring to the website or by citing each individual analysis (>20 published papers from >20 principal investigators from Canada and abroad, all publicly available) used to assemble the profiles. We anticipate that this site will be useful to all scientists in bovine reproduction. The EmbryoGENE network was supported by NSERC Canada and Semex Canada for the bovine side.
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