Endometrial 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:26981354", "kind": "science-record", "revision": 8, "content_hash": "sha256:bca3b4a15e4396962c26fe7fbac54eed381d2ec786d461b2bdb734d156eb5ced", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T22:42:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Endometrial transcriptional profiling of a bovine fertility model by Next-Generation Sequencing.", "doi": "10.1016/j.gdata.2015.11.008", "pmid": "26981354", "authors": ["F S Mesquita", "R S Ramos", "G Pugliesi", "S C S Andrade", "V Van Hoeck", "A Langbeen", "M L Oliveira", "A M Gonella-Diaza", "G Gasparin", "H Fukumasu", "L H Pulz", "C M Membrive", "L L Coutinho", "M Binelli"], "journal": "Genomics data", "year": 2016, "abstract": "Studying the multitude of molecular networks and pathways that are potentially involved in a complex trait such as fertility requires an equally complex and broad strategy. Here, we used Next-Generation Sequencing for the characterization of the transcriptional signature of the bovine endometrial tissue. Periovulatory endocrine environments were manipulated to generate two distinctly different fertility phenotypes. Cycling, non-lactating, multiparous Nelore cows were manipulated to ovulate larger (> 13 mm; LF group; high fertility phenotype) or smaller (< 12 mm; SF group) follicles. As a result, greater proestrus estrogen concentrations, corpora lutea and early diestrus progesterone concentrations were also observed in LF group in comparison to SF group. Endometrial cell proliferation was estimated by the protein marker MKI67 on tissues collected 4 (D4) and 7 (D7) days after induction of ovulation. Total RNA extracts from D7 were sequenced and compared according to the transcriptional profile of each experimental group (LF versus SF). Functional enrichment analysis revealed that LF and SF endometria were asynchronous in regards to their phenotype manifestation. Major findings indicated an LF endometrium that was switching phenotypes earlier than the SF one. More specifically, a proliferating SF endometrium was observed on D7, whereas the LF tissue, which expressed a proliferative phenotype earlier at D4, seemed to have already shifted towards a biosynthetically and metabolically active endometrium on D7. Data on MKI67 support the transcriptomic results. RNA-Seq-derived transcriptional profile of the endometrial tissue indicated a temporal effect of the periovulatory endocrine environment, suggesting that the moment of the endometrial exposure to the ovarian steroids, E2 and P4, regulates the timing of phenotype manifestation. Gene expression profiling revealed molecules that may be targeted to elucidate ovarian steroid-dependent mechanisms that regulate endometrial tissue receptivity. Data was deposited in the SRA database from NCBI (SRA Experiment SRP051330) and are associated with the Bio-Project (PRJNA270391). An overview of the gene expression data has been deposited in NCBI's Gene Expression Omnibus (GEO) and is accessible through GEO Series accession number GSE65450. Further assessment of the data in combination with other data sets exploring the transcriptional profile of the endometrial tissue during early diestrus may potentially identify novel molecular mechanisms and/or markers of the uterine receptivity.", "claims": [{"id": "claim-data-access", "statement": "Data was deposited in the SRA database from NCBI (SRA Experiment SRP051330) and are associated with the Bio-Project (PRJNA270391). An overview of the gene expression data has been deposited in NCBI's Gene Expression Omnibus (GEO) and is accessible through GEO Series accession number GSE65450.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981354", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data was deposited in the SRA database from NCBI (SRA Experiment SRP051330) and are associated with the Bio-Project (PRJNA270391). An overview of the gene expression data has been deposited in NCBI's Gene Expression Omnibus (GEO) and is accessible through GEO Series accession number GSE65450."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using DESeq v1.12.1 with a 0.05 Benjamini–Hochberg false-discovery-rate threshold, the study found that “LF and SF endometria were asynchronous in regards to their phenotype manifestation,” with the LF endometrium shifting phenotypes earlier; the source data are accessible through SRA Experiment SRP051330, Bio-Project PRJNA270391, and GEO Series GSE65450.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR-Benjamini–Hochberg [9]."}, "evidence": [{"asset": "source:pmid:26981354", "locator": "sections[9] \"Bioinformatics\" paragraph 2", "quote": "The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR-Benjamini–Hochberg [9]."}, {"asset": "source:pmid:26981354", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Functional enrichment analysis revealed that LF and SF endometria were asynchronous in regards to their phenotype manifestation."}, {"asset": "source:pmid:26981354", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Major findings indicated an LF endometrium that was switching phenotypes earlier than the SF one."}, {"asset": "source:pmid:26981354", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data was deposited in the SRA database from NCBI (SRA Experiment SRP051330) and are associated with the Bio-Project (PRJNA270391)."}, {"asset": "source:pmid:26981354", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "An overview of the gene expression data has been deposited in NCBI's Gene Expression Omnibus (GEO) and is accessible through GEO Series accession number GSE65450."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using DESeq v1.12.1 with a 0.05 Benjamini–Hochberg false-discovery-rate threshold, the study found that “LF and SF endometria were asynchronous in regards to their phenotype manifestation,” with the LF endometrium shifting phenotypes earlier; the source data are accessible through SRA Experiment SRP051330, Bio-Project PRJNA270391, and GEO Series GSE65450.", "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:26981354"], "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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Larger follicle cows also presented greater estradiol concentrations in proestrus, larger corpora lutea and greater progesterone concentrations in early diestrus than small follicle cows. Cows were slaughtered and endometrial fragments collected on day 7 post-induction of ovulation. 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Here, we used Next-Generation Sequencing for the characterization of the transcriptio"], "order_basis": "paper_text_order:24", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on MKI67 support the transcriptomic results. RNA-Seq-derived transcriptional profile of the endom", "hree/group) were selected to be submitted to RNA-Seq. A multivariate analysis approach was taken", "endometrium on D7. Data on MKI67 support the transcriptomic results. 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