Gene expression profiling by high throughput sequencing to determine signatures for the bovine receptive uterus at early gestation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484233", "kind": "science-record", "revision": 8, "content_hash": "sha256:298d13e232367960bbc6d2aafc74e7bba15b6ff9c6926b09a76f6633bd73becf", "created_at": "2026-11-01T15:40:12Z", "updated_at": "2026-11-01T22:42:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling by high throughput sequencing to determine signatures for the bovine receptive uterus at early gestation.", "doi": "10.1016/j.gdata.2015.05.030", "pmid": "26484233", "authors": ["Veerle Van Hoeck", "Saara C Scolari", "Guilherme Pugliesi", "Angela M Gonella-Diaza", "Sónia C S Andrade", "Gustavo R Gasparin", "Luiz L Coutinho", "Mario Binelli"], "journal": "Genomics data", "year": 2015, "abstract": "The uterus plays a central role among the reproductive tissues in the context of early embryo-maternal communication and a successful pregnancy depends on a complex series of endometrial molecular and cellular events. The factors responsible for the initial interaction between maternal and embryonic tissues, leading to the establishment of pregnancy, remain poorly understood. In this context, Illumina's next-generation sequencing technology has been used to discover the uterine transcriptome signature that is favourable for ongoing pregnancy. More specifically, the present report documents on a retrospective in vivo study in which data on pregnancy outcome were linked to uterine gene expression signatures on day 6 (bovine model). Using the RNA-Seq method, 14.654 reference genes were effectively analysed for differential expression between pregnant and non-pregnant uterine tissue. Transcriptome data revealed that 216 genes were differently expressed when comparing uterine tissue from pregnant and non-pregnant cows. All read sequences were deposited in the Sequence Read Archive (SRA) of the NCBI (http://www.ncbi.nlm.nih.gov/sra). 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 GSE65117. This allows the research community to enhance reproducibility and allows for new discoveries by comparing datasets of signatures linked to receptivity and/or pregnancy success. The resulting information can serve as tool to identify valuable and urgently needed biomarkers for scoring maternal receptivity and even for accurate detection of early pregnancy, which is a matter of cross-species interest. Beyond gene expression analysis as a marker tool, the RNA-Seq information on pregnant uterine tissue can be used to gain novel mechanistic insights, such as by identifying alternative splicing events, allele-specific expression, and rare and novel transcripts that might be involved in the onset of maternal receptivity. This concept is unique and provides a new approach towards strategies that are highly needed to improve efficiency of fertility treatments.", "claims": [{"id": "claim-data-access", "statement": "All read sequences were deposited in the Sequence Read Archive (SRA) of the NCBI (http://www.ncbi.nlm.nih.gov/sra). 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 GSE65117.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484233", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All read sequences were deposited in the Sequence Read Archive (SRA) of the NCBI (http://www.ncbi.nlm.nih.gov/sra). 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 GSE65117."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using DESeq2 with Benjamini–Hochberg false-discovery-rate correction, the study identified 216 genes differentially expressed between pregnant and non-pregnant bovine uterine tissue; the source reads are deposited in NCBI’s Sequence Read Archive, with an overview of the gene-expression data available through GEO Series accession GSE65117.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "After normalization, the log2 fold change was obtained through a general linear model approach, the significance test was followed by the FDR-Benjamini-Hochberg [6] correction for multiple tests."}, "evidence": [{"asset": "source:pmid:26484233", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Transcriptome data revealed that 216 genes were differently expressed when comparing uterine tissue from pregnant and non-pregnant cows."}, {"asset": "source:pmid:26484233", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All read sequences were deposited in the Sequence Read Archive (SRA) of the NCBI (http://www.ncbi.nlm.nih.gov/sra)."}, {"asset": "source:pmid:26484233", "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 GSE65117."}, {"asset": "source:pmid:26484233", "locator": "sections[7] \"RNA-Seq and analysis\" paragraph 2", "quote": "After normalization, the log2 fold change was obtained through a general linear model approach, the significance test was followed by the FDR-Benjamini-Hochberg [6] correction for multiple tests."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using DESeq2 with Benjamini–Hochberg false-discovery-rate correction, the study identified 216 genes differentially expressed between pregnant and non-pregnant bovine uterine tissue; the source reads are deposited in NCBI’s Sequence Read Archive, with an overview of the gene-expression data available through GEO Series accession GSE65117.", "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:26484233"], "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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