Oviductal transcriptional profiling of a bovine fertility model by next-generation sequencing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28664146", "kind": "science-record", "revision": 8, "content_hash": "sha256:af49ec0368008733db3b7ac036f5245d372f8a52e50a01927cc460dc90f868e6", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T22:43:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Oviductal transcriptional profiling of a bovine fertility model by next-generation sequencing.", "doi": "10.1016/j.gdata.2017.06.004", "pmid": "28664146", "authors": ["Angela Maria Gonella-Diaza", "Sónia Cristina da Silva Andrade", "Mariana Sponchiado", "Guilherme Pugliesi", "Fernando Silveira Mesquita", "Veerle Van Hoeck", "Ricardo de Francisco Strefezzi", "Gustavo R Gasparin", "Luiz L Coutinho", "Mario Binelli"], "journal": "Genomics data", "year": 2017, "abstract": "In cattle, the oviduct plays a fundamental role in the reproductive process. Oviductal functions are controlled by the ovarian sex steroids: estradiol and progesterone. Here, we tested the hypothesis that the exposure to contrasting sex steroid milieus differentially impacts the oviductal transcriptional profile. We manipulated growth of the pre-ovulatory follicle to obtain cows that ovulated a larger (LF group) or a smaller (SF group) follicle. The LF group presented greater proestrus/estrus concentrations of estradiol and metaestrus concentrations of progesterone (Gonella-Diaza et al. 2015 [1], Mesquita et al. 2014 [2]). Also, the LF group was associated with greater fertility in timed-artificial insemination programs (Pugliesi et al. 2016 [3]). Cows were slaughtered on day 4 of the estrous cycle and total RNA was extracted from ampulla and isthmus fragments and analyzed by RNAseq. The resulting reads were mapped to the bovine genome (Bos taurus UMD 3.1, NCBI). The differential expression analyses revealed that 325 and 367 genes in ampulla and 274 and 316 genes in the isthmus were up-regulated and down-regulated in LF samples, respectively. To validate the RNAseq results, transcript abundance of 23 genes was assessed by qPCR and expression patterns were consistent between the two techniques. A functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Processes enriched in the LF group included tissue morphology changes (extracellular matrix remodeling), cellular changes (proliferation), and secretion changes (growth factors, ions and metal transporters). An overview of the gene expression data was deposited in the NCBI's Gene Expression Omnibus (GEO) and is accessible through the accession number GSE65681. In conclusion, differences in the peri-ovulatory sex steroid milieu modify the oviductal gene expression profiles. Such differences may be associated with the greater fertility of the LF cows. This dataset is useful for further investigations of the oviductal biology and the impact of sex-steroid on the female reproductive tract.", "claims": [{"id": "claim-data-access", "statement": "All reads sequences are available in the Sequence Read Archive (SRA) of the NCBI and an overview of the gene expression results is also available in NCBI's Gene Expression Omnibus (GEO) under the accession number GSE65681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65681).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28664146", "locator": "sections[6] \"RNAseq and bioinformatics\" paragraph 2", "quote": "All reads sequences are available in the Sequence Read Archive (SRA) of the NCBI and an overview of the gene expression results is also available in NCBI's Gene Expression Omnibus (GEO) under the accession number GSE65681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65681)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The headline result was that contrasting peri-ovulatory sex-steroid milieus modify oviductal gene-expression profiles, potentially contributing to the greater fertility of cows that ovulated large follicles. Differential expression was analyzed with DESeq, and the paper identifies GEO accession GSE65681 as the route to the gene-expression overview, although the direct deposited-data link provided in the paper points to GSE65679.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28664146", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In conclusion, differences in the peri-ovulatory sex steroid milieu modify the oviductal gene expression profiles."}, {"asset": "source:pmid:28664146", "locator": "sections[6] \"RNAseq and bioinformatics\" paragraph 2", "quote": "All reads sequences are available in the Sequence Read Archive (SRA) of the NCBI and an overview of the gene expression results is also available in NCBI's Gene Expression Omnibus (GEO) under the accession number GSE65681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65681)."}, {"asset": "source:pmid:28664146", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65679"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The headline result was that contrasting peri-ovulatory sex-steroid milieus modify oviductal gene-expression profiles, potentially contributing to the greater fertility of cows that ovulated large follicles. Differential expression was analyzed with DESeq, and the paper identifies GEO accession GSE65681 as the route to the gene-expression overview, although the direct deposited-data link provided in the paper points to GSE65679.", "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:28664146"], "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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