A novel dataset for identifying sex-biased genes in Drosophila.

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To accurately identify genes differentially expressed between males and females in Drosophila, we sequenced the testis and ovary transcriptomes of D. yakuba, D. pseudoobscura, and D. ananassae and used them to identify sex-biased genes in the latter two species. We highlight the increased sensitivity and improved power of sex-biased gene detection methods when using our testis/ovary data versus male and female whole body transcriptome data. We thus provide a resource specifically designed to accurately identify and characterize sex-biased genes across Drosophila. This dataset is available through NCBI GEO accession GSE52058.", "claims": [{"id": "claim-method", "statement": "We identified sex-biased genes in WB, reproductive tract, or testis/ovary samples using Cuffdiff v2.1.0 with default options, which include pooled sample dispersion estimates and geometric normalization of gene-level counts 6, and edgeR v3.4.0 7.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25031657", "locator": "sections[2] \"METHODS\" paragraph 4", "quote": "We identified sex-biased genes in WB, reproductive tract, or testis/ovary samples using Cuffdiff v2.1.0 with default options, which include pooled sample dispersion estimates and geometric normalization of gene-level counts 6, and edgeR v3.4.0 7."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This dataset is available through NCBI GEO accession GSE52058.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25031657", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This dataset is available through NCBI GEO accession GSE52058."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Applying Cuffdiff and edgeR to testis/ovary RNA-seq data deposited in NCBI GEO under accession GSE52058, the paper found that edgeR was more sensitive, whereas Cuffdiff produced greater overlap between sex-biased genes identified in whole-body and testis/ovary analyses.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25031657", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We highlight the increased sensitivity and improved power of sex-biased gene detection methods when using our testis/ovary data versus male and female whole body transcriptome data."}, {"asset": "source:pmid:25031657", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This dataset is available through NCBI GEO accession GSE52058."}, {"asset": "source:pmid:25031657", "locator": "sections[3] \"RESULTS\" paragraph 2", "quote": "In general, Cuffdiff resulted in greater overlap than edgeR of the sex-biased genes found in both WB and testis/ovary analyses (Pearson's χ2, p < 1e-04), while edgeR was more sensitive."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Applying Cuffdiff and edgeR to testis/ovary RNA-seq data deposited in NCBI GEO under accession GSE52058, the paper found that edgeR was more sensitive, whereas Cuffdiff produced greater overlap between sex-biased genes identified in whole-body and testis/ovary analyses.", "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:25031657"], "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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