Whole transcriptome data of zebrafish exposed to chronic dose of depleted uranium.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28831411", "kind": "science-record", "revision": 8, "content_hash": "sha256:4e97babd78600b13f0520ff09de9f88d9a0a370cd65797c1a82c48650bd448c6", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T22:43:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Whole transcriptome data of zebrafish exposed to chronic dose of depleted uranium.", "doi": "10.1016/j.dib.2017.07.071", "pmid": "28831411", "authors": ["Olivier Armant", "Kewin Gombeau", "Christelle Adam Guillermin"], "journal": "Data in brief", "year": 2017, "abstract": "The concentration of depleted uranium (DU) in the environment is expected to increase due to anthropogenic activities, posing potential risks on ecosystems. The effects of chronic exposure to DU at concentration close to the environmental standards (0.3-30 µg DU/L) are scarcely characterised. Genomic alterations caused by low doses of pollutants can potentially propagate over generations, but how these effects may affect the health of the progeny remain uncertain for the vast majority of toxicants. The present dataset describes the transcriptomic effects of a chronic exposure to 20 µg DU/L during 10 days on adult zebrafish (Danio rerio) organs, the brain, the testis and the ovaries. The potential multigenerational effects of DU were assessed on the progeny of the adult exposed fish at the two-cells stage and after four days of development. We describe in this article the summary statistics of the differential gene expression analysis and focus on key molecular pathways affected by an exposure to a low concentration of DU. The data presented in this study supports the observation made in Armant et al. (2017) [1] (https://doi.org/10.1016/j.dib.2016.05.007) that DU can induce a molecular stress in both adult zebrafish and their progeny. The raw dataset has been deposited at the Gene Expression Omnibus (GEO) repository under the accession number GEO:GSE96603.", "claims": [{"id": "claim-method", "statement": "Quantification and normalization of the mapped reads at the level of gene model were performed with DESeq. 2 [4]. Adjusted p-values (False Discovery Rate, FDR)<0.01 and fold-change>=±2 were used to detect significant differential gene expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28831411", "locator": "sections[10] \"Data analysis\" paragraph 2", "quote": "Quantification and normalization of the mapped reads at the level of gene model were performed with DESeq. 2 [4]. Adjusted p-values (False Discovery Rate, FDR)<0.01 and fold-change>=±2 were used to detect significant differential gene expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available with this article, and via NCBI′s GEO accession number GEO:GSE96603http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96603", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28831411", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data are available with this article, and via NCBI′s GEO accession number GEO:GSE96603http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96603"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study supports the observation that DU can induce a molecular stress in both adult zebrafish and their progeny; differential expression was detected with DESeq.2 using an adjusted false discovery rate below 0.01 and fold change of at least ±2, and the source data are available through GEO accession GEO:GSE96603.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28831411", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data presented in this study supports the observation made in Armant et al. (2017) [1] (https://doi.org/10.1016/j.dib.2016.05.007) that DU can induce a molecular stress in both adult zebrafish and their progeny."}, {"asset": "source:pmid:28831411", "locator": "sections[10] \"Data analysis\" paragraph 2", "quote": "Quantification and normalization of the mapped reads at the level of gene model were performed with DESeq. 2 [4]. Adjusted p-values (False Discovery Rate, FDR)<0.01 and fold-change>=±2 were used to detect significant differential gene expression."}, {"asset": "source:pmid:28831411", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw dataset has been deposited at the Gene Expression Omnibus (GEO) repository under the accession number GEO:GSE96603."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study supports the observation that DU can induce a molecular stress in both adult zebrafish and their progeny; differential expression was detected with DESeq.2 using an adjusted false discovery rate below 0.01 and fold change of at least ±2, and the source data are available through GEO accession GEO:GSE96603.", "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:28831411"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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Biological replicates are indicated as well as the number of reads, the quality score (Phred score, Q) and the read's length. PF: reads passing the Illumina's chastity filter.", "structure": {"pmcid": "PMC5554979", "section_index": 5, "section_title": "Data", "row_count": 36, "column_count": 9}, "table": {"label": "Table 1", "caption": "Description of the zebrafish samples collected in the study. Biological replicates are indicated as well as the number of reads, the quality score (Phred score, Q) and the read's length. PF: reads passing the Illumina's chastity filter.", "rows": [["Sample name", "Tissu/Stage", "Organism", "Genotype", "Treatment", "Description", "Reads", "Q (PF)", "Length"], ["C2cells_r1", "2 cells embryos", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "Two cells embryos obtained from non exposed adult", "136,445,062", "38.57", "51"], ["C2cells_r2", "2 cells embryos", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "Two cells embryos obtained from non exposed adult", "84,864,394", "38.62", "51"], ["C2cells_r4", "2 cells embryos", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "Two cells embryos obtained from non exposed adult", "64,705,960", "38.62", "51"], ["C96hpf_l1", "96 hpf larvae", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "96hpf larvae obtaiend from non exposed adult", "74,497,510", "35.93", "70"], ["C96hpf_l2", "96 hpf larvae", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "96hpf larvae obtaiend from non exposed adult", "101,797,850", "35.87", "70"], ["C96hpf_l3", "96 hpf larvae", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "96hpf larvae obtaiend from non exposed adult", "71,463,198", "35.88", "70"], ["CbrainF_b2", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from non exposed adult females", "99,758,552", "35.71", "70"], ["CbrainF_b3", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from non exposed adult females", "69,241,514", "35.71", "70"], ["CbrainF_b5", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from non exposed adult females", "102,185,518", "35.7", "70"], ["CbrainM_b1", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from non exposed adult males", "42,244,184", "35.71", "70"], ["CbrainM_b4", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from non exposed adult males", "91,270,976", "35.73", "70"], ["CbrainM_b5", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from non exposed adult males", "119,455,624", "35.71", "70"], ["CovaryF_g1", "Adult ovary", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Ovaries dissected from non exposed adult females", "80,198,724", "35.72", "70"], ["CovaryF_g2", "Adult ovary", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Ovaries dissected from non exposed adult females", "107,238,778", "35.66", "70"], ["CovaryF_g5", "Adult ovary", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Ovaries dissected from non exposed adult females", "55,595,382", "35.62", "70"], ["CtestesM_g1", "Adult testis", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Testies dissected from non exposed adult males", "117,865,394", "35.68", "70"], ["CtestesM_g3", "Adult testis", "Danio rerio", "Wild type AB", "20 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exposed adult", "70,360,064", "35.89", "70"], ["U96hpf_l2", "96 hpf larvae", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "96hpf larvae obtaiend from depleted uranium exposed adult", "79,320,508", "35.86", "70"], ["U96hpf_l3", "96 hpf larvae", "Danio rerio", "Wild type AB", "Progeny of adult exposed fish", "96hpf larvae obtaiend from depleted uranium exposed adult", "71,471,552", "35.88", "70"], ["UbrainF_b2", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from depleted uranium exposed adult females", "67,726,036", "35.69", "70"], ["UbrainF_b4", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from depleted uranium exposed adult females", "82,049,972", "35.67", "70"], ["UbrainF_b5", "Adult brain", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Brain dissected from depleted uranium exposed adult females", "66,539,292", "35.62", "70"], ["UbrainM_b2", "Adult brain", "Danio 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uranium exposed adult males", "67,017,732", "35.88", "70"], ["UtestesM_g3", "Adult testis", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Testies dissected from depleted uranium exposed adult males", "65,968,150", "35.92", "70"], ["UtestesM_g5", "Adult testis", "Danio rerio", "Wild type AB", "20 µg/L depleted uranium", "Testies dissected from depleted uranium exposed adult males", "79,436,904", "35.83", "70"]], "row_count": 36, "column_count": 9, "numeric_cells": 152, "header_rows": 1, "locator": "section[5]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:28831411:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c0185b1f155158176eacdd1edf7cdc68677211a04a2f658294bd132bbaad5ab0", "bytes": 1587, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#t0010", "version": null, "note": "List of the 22 samples with the lowest biological variabilities.", "structure": {"pmcid": "PMC5554979", "section_index": 5, "section_title": "Data", "row_count": 23, "column_count": 3}, "table": {"label": "Table 2", "caption": "List of the 22 samples with the lowest biological variabilities.", "rows": [["Sample name", "Tissu/stage", "Treatment"], ["C2cells_r1", "2 cells embryos", "Progeny of adult exposed fish"], ["C2cells_r2", "2 cells embryos", "Progeny of adult exposed fish"], ["C2cells_r4", "2 cells embryos", "Progeny of adult exposed fish"], ["C96hpf_l2", "96 hpf larvae", "Progeny of adult exposed fish"], ["C96hpf_l3", "96 hpf larvae", "Progeny of adult exposed fish"], ["CbrainF_b2", "Adult brain", "20 µg/L depleted uranium"], ["CbrainF_b5", "Adult brain", "20 µg/L depleted uranium"], ["CovaryF_g1", "Adult ovary", "20 µg/L depleted uranium"], ["CovaryF_g2", "Adult ovary", "20 µg/L depleted uranium"], ["CtestesM_g3", "Adult testis", "20 µg/L depleted uranium"], ["CtestesM_g5", "Adult testis", "20 µg/L depleted uranium"], ["U2cells_r1", "2 cells embryos", "Progeny of adult exposed fish"], ["U2cells_r3", "2 cells embryos", "Progeny of adult exposed fish"], ["U2cells_r5", "2 cells embryos", "Progeny of adult exposed fish"], ["U96hpf_l2", "96 hpf larvae", "Progeny of adult exposed fish"], ["U96hpf_l3", "96 hpf larvae", "Progeny of adult exposed fish"], ["UbrainF_b2", "Adult brain", "20 µg/L depleted uranium"], ["UbrainF_b5", "Adult brain", "20 µg/L depleted uranium"], ["UovaryF_g1", "Adult ovary", "20 µg/L depleted uranium"], ["UovaryF_g4", "Adult ovary", "20 µg/L depleted uranium"], ["UtestesM_g3", "Adult testis", "20 µg/L depleted uranium"], ["UtestesM_g5", "Adult testis", "20 µg/L depleted uranium"]], "row_count": 23, "column_count": 3, "numeric_cells": 26, "header_rows": 1, "locator": "section[5]/table-wrap[2]#t0010"}}, {"id": "asset:table:pmid:28831411:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7a6cbd04b70970919c2f6c1e2492a090fb6504b0320e382dfc538cae0a827d53", "bytes": 504, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[3]#t0015", "version": null, "note": "Summary statistics of the differentially expressed genes (threshold FDR<0.01 and fold change>=±2). The number of genes is indicated for each category.", "structure": {"pmcid": "PMC5554979", "section_index": 5, "section_title": "Data", "row_count": 6, "column_count": 4}, "table": {"label": "Table 3", "caption": "Summary statistics of the differentially expressed genes (threshold FDR<0.01 and fold change>=±2). The number of genes is indicated for each category.", "rows": [["DU/Ctrl", "Up-regulated", "Down-regulated", "Total"], ["Two-cells", "2482", "4106", "6588"], ["96 hpf", "573", "62", "635"], ["Brain", "46", "1026", "1072"], ["Testis", "132", "295", "427"], ["Ovaries", "302", "169", "471"]], "row_count": 6, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[5]/table-wrap[3]#t0015"}}, {"id": "asset:table:pmid:28831411:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:907bb7fb61421165a0a33fe18bbec88c850a80b14bcb5089356244d9a911cf0a", "bytes": 3023, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[4]#t0020", "version": null, "note": "Gene ontology analysis. The list provides the top 5 biological pathways impacted by DU in each dataset based on smallest p-values.", "structure": {"pmcid": "PMC5554979", "section_index": 5, "section_title": "Data", "row_count": 60, "column_count": 3}, "table": {"label": "Table 4", "caption": "Gene ontology analysis. The list provides the top 5 biological pathways impacted by DU in each dataset based on smallest p-values.", "rows": [["Set of genes", "Gene ontology term", "p-value"], ["Down in DU exposed brain", "Visual perception", "2.7E−08"], ["", "Sensory perception of light stimulus", "2.7E−08"], ["", "Cell adhesion", "6.3E−07"], ["", "Biological adhesion", "6.3E−07"], ["", "Response to light stimulus", "5.1E−06"], ["", "", ""], ["Up in DU exposed brain", "Response to lipid", "2.4E−03"], ["", "Response to lipopolysaccharide", "2.7E−03"], ["", "Ovulation", "3.1E−03"], ["", "Response to molecule of bacterial origin", "3.1E−03"], ["", "Response to organic substance", "3.5E−03"], ["", "", ""], ["Down in DU exposed testis", "Cell adhesion", "1.0E−04"], ["", "Biological adhesion", "1.0E−04"], ["", "Fin regeneration", "3.4E−04"], ["", "cGMP biosynthetic process", "4.9E−04"], ["", "cGMP metabolic process", "4.9E−04"], ["", "", ""], ["Up in DU exposed testis", "Centromere complex assembly", "8.2E−04"], ["", "Regulation of synapse structure or activation", "3.4E−03"], ["", "Peptidoglycan biosynthetic process", "4.4E−03"], ["", "Peptidoglycan-based cell wall biogenesis", "4.4E−03"], ["", "Protein side chain deglutamylation", "4.4E−03"], ["", "", ""], ["Down in DU exposed ovaries", "Aspartate family amino acid metabolic pr.", "4.1E−04"], ["", "Endomembrane system organization", "4.7E−03"], ["", "Androgen biosynthetic process", "5.9E−03"], ["", "Mitochondrial protein catabolic process", "5.9E−03"], ["", "Mitophagy by induced vacuole formation", "5.9E−03"], ["", "", ""], ["Up in DU exposed ovaries", "Neural tube development", "7.8E−07"], ["", "Embryonic appendage morphogenesis", "2.6E−06"], ["", "Pectoral fin development", "4.7E−06"], ["", "Fin morphogenesis", "5.2E−06"], ["", "Appendage morphogenesis", "8.2E−06"], ["", "", ""], ["Down in 2 cells stage", "ncRNA metabolic process", "1.6E−14"], ["", "Nucleic acid metabolic process", "3.6E−14"], ["", "Cellular macromolecule metabolic process", "3.7E−12"], ["", "Organelle organization", "2.6E−11"], ["", "Heterocycle metabolic process", "3.2E−11"], ["", "", ""], ["Up in 2 cells stage", "Cytoplasmic transport", "3.8E−06"], ["", "Organelle organization", "7.2E−06"], ["", "ER to Golgi vesicle-mediated transport", "1.1E−05"], ["", "Double-strand break repair", "1.3E−05"], ["", "mRNA processing", "1.5E−05"], ["", "", ""], ["Down in 96hpf larva", "Thyroid hormone generation", "2.1E−03"], ["", "Thyroid hormone metabolic process", "2.1E−03"], ["", "Hydrogen peroxide biosynthetic process", "2.1E−03"], ["", "Circadian rhythm", "3.0E−03"], ["", "Homophilic cell adhesion via plasma memb.", "3.4E−03"], ["", "", ""], ["Up in 96hpf larva", "Oxidation-reduction process", "6.6E−22"], ["", "Single-organism metabolic process", "1.4E−20"], ["", "Small molecule metabolic process", "1.4E−16"], ["", "Organic acid metabolic process", "9.9E−15"], ["", "Lipid metabolic process", "1.3E−14"]], "row_count": 60, "column_count": 3, "numeric_cells": 54, "header_rows": 1, "locator": "section[5]/table-wrap[4]#t0020"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Quantification and normalization of the mapped reads at the level of gene model were performed with DESeq. 2 [4]. Adjusted p-values (False Discovery Rate, FDR)<0.01 and fold-change>=±2 were used to detect significant differential gene expression."}}, {"id": "method-2", "family": "multi_omics_integration", "specific": "pathway_progeny", "label": "Multi-omics integration", "dsl_operations": ["multiomics_factor_analysis", "joint_pathway_score"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["aligned_multi_layer_matrices"], "evidence": {"score": 0.7, "band": "medium", "quote": "progeny"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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Adjusted p-values (False Discovery Rate, FDR)<0.01 and fold-change>=±2 were used to detect significant differential gene expression."], "order_basis": "analysis_only", "id": "assay:1"}]}