Transcriptome analysis of primary bovine extra-embryonic cultured cells.

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In mammals, extra-embryonic tissues are essential to support not only embryo patterning but also embryo survival, especially in late implanting species. These tissues are composed of three cell types: trophoblast (bTCs), endoderm (bXECs) and mesoderm (bXMCs). Until now, it is unclear how these cells interact. In this study, we have established primary cell cultures of extra-embryonic tissues from bovine embryos collected at day-18 after artificial insemination. We used our homemade bovine 10K array (GPL7417) to analyze the gene expression profiles of these primary extra-embryonic cultured cells compared to the corresponding cells from in vivo micro-dissected embryos. Here, we described the experimental design, the isolation of bovine extra-embryonic cell types as well as the microarray expression analysis. The dataset has been deposited in Gene Expression Omnibus (GEO) (accession number GSE52967). Finally, these primary cell cultures were a powerful tool to start studying their cellular properties, and will further allow in vitro studies on cellular interactions among extra-embryonic tissues, and potentially between extra-embryonic vs embryonic tissues.", "claims": [{"id": "claim-data-access", "statement": "The dataset has been deposited in Gene Expression Omnibus (GEO) (accession number GSE52967).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697347", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The dataset has been deposited in Gene Expression Omnibus (GEO) (accession number GSE52967)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used log-transformed and mean-centered microarray data and deposited the dataset in Gene Expression Omnibus under accession GSE52967, with a direct link to the source data provided.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26697347"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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