RNA-seq dataset of the chorioallantoic membrane of male and female chicken embryos, after 11 and 15 days of incubation.

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Developing from day 6 of incubation, the CAM progressively differentiates into three functional layers (the chorionic epithelium in contact with the inner eggshell, the highly vascularized mesoderm, and the allantoic epithelium), between 11 and 15 days of incubation. This article describes the RNASeq dataset and the analyses performed on total CAMs collected from male and female embryos after 11 and 15 days of incubation. The datasets are available at the NCBI Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo) using GSE199780 as the accession number. The statistical analysis of the data allowed identifying genes differentially expressed depending on the sex of the embryo at two time points of CAM differentiation. Knowing that the CAM is widely used as a model to study tumour growth, metastasis or wound healing, the resulting analysis highlights the necessity to include this sex variable in experimental assays to avoid any bias of interpretation. Indeed, the functional annotation of genes that are differentially expressed between male and female CAMs revealed an enrichment of activities and functions related to lipid metabolism, bone formation, and morphogenesis suggesting that the response of the CAM to external and experimental stimuli might be different depending on the sex of the embryo.", "claims": [{"id": "claim-method", "statement": "For each gene, a negative binomial generalized linear model (GLM) [13] was fitted with a group factor combining the factors “day of incubation” (EID11, EID15) and “sex”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39263233", "locator": "sections[9] \"Differential analysis\" paragraph 2", "quote": "For each gene, a negative binomial generalized linear model (GLM) [13] was fitted with a group factor combining the factors “day of incubation” (EID11, EID15) and “sex”."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the results and the discussion are available at the Gene Expression Omnibus (GEO) repository at http://www.ncbi.nlm.nih.gov/geo/ using the accession number GSE199780. The script R and the results for the differential analysis and the functional enrichment tests (supplementary files Tables S1-S3) were stored in the repository Hennequet-Antier, Christelle, 2024, “CAM_RNA-Seq”, https://doi.org/10.57745/6YDAQD, Recherche Data Gouv.\nTranscriptome of the chicken chorioallantoic membrane from male and female embryos, after 11 and 15 days of incubation (Original data) (Gene Expression Omnibus (GEO)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39263233", "locator": "sections[24] \"Data Availability Statement\" paragraphs 1-3", "quote": "The datasets supporting the results and the discussion are available at the Gene Expression Omnibus (GEO) repository at http://www.ncbi.nlm.nih.gov/geo/ using the accession number GSE199780. The script R and the results for the differential analysis and the functional enrichment tests (supplementary files Tables S1-S3) were stored in the repository Hennequet-Antier, Christelle, 2024, “CAM_RNA-Seq”, https://doi.org/10.57745/6YDAQD, Recherche Data Gouv.\nTranscriptome of the chicken chorioallantoic membrane from male and female embryos, after 11 and 15 days of incubation (Original data) (Gene Expression Omnibus (GEO))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:39263233"], "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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