Transcriptomic dataset of zebrafish tissues following chronic alcohol exposure and withdrawal.

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Transcriptome profiling can provide insights into the dynamic changes in global gene expression profiles induced by chronic alcohol exposure and withdrawal. Male and female zebrafish were continually exposed to 0.5% ethanol for a period of 9 weeks. Upon completion of alcohol treatment, the fish were subjected to a withdrawal program for 9 weeks. Brain and liver tissues of control, alcohol exposed and withdrawal fish were isolated and the extracted RNA was sequenced on Illumina HiSeq 2000. The resultant paired end reads were mapped to the zebrafish reference genome (danRer10). The mapped transcripts were quantified for their expression and subjected to differential expression analysis across the three conditions. Gene ontology enrichment analysis of the differentially regulated genes was carried out to identify affected biological processes. The data for this project is available as a GEO dataset under Accession number GSE143416. The gene expression data discussed here accompanies the research article entitled 'Tissue-specific transcriptome recovery on withdrawal from chronic alcohol exposure in zebrafish'.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis amongst the three conditions viz, control, alcohol-exposed and withdrawal was performed based on an empirical Bayesian method using the tool, EBSeq [7].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33163595", "locator": "sections[7] \"Data analysis\" paragraph 2", "quote": "Differential expression analysis amongst the three conditions viz, control, alcohol-exposed and withdrawal was performed based on an empirical Bayesian method using the tool, EBSeq [7]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data for this project is available as a GEO dataset under Accession number GSE143416.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33163595", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data for this project is available as a GEO dataset under Accession number GSE143416."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33163595"], "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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The fish were subjected to continuous 0.5% ethanol exposure for 9 weeks followed by a 9-week withdrawal program without any ethanol in the water tank. RNA was extracted from brain and liver tissue. Samples were pooled according to their respective condition and genders and sequenced. RNAseq was performed on Illumina HiSeq 2000 to obtain paired end libraries of read length 100 bp with at least 25 million reads per sample."], ["Data source location", "Zebrafish (Danio Rerio) maintained at CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB) zebrafish facility located at Hyderabad, Telangana, India"], ["Data accessibility", "Repository name: NCBI Gene Expression OmnibusData identification number: GSE143416Direct URL to data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143416"], ["Related research article", "Sofia Banu, Surabhi Srivastava, Arif Mohammed, Gopal Kushawah, Divya Tej Sowpati, Rakesh K Mishra, Tissue-specific transcriptome recovery on withdrawal from chronic alcohol exposure in zebrafish, Alcohol. In Press. https://doi.org/10.1016/j.alcohol.2020.10.001"]], "row_count": 10, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}, {"id": "asset:table:pmid:33163595:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e5800b809085fe87191da499f9f4841bf065330051dec477a7db908d92770f65", "bytes": 2374, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Details of transcriptomic data submitted to the NCBI Sequence Read Archive (SRA).", "structure": {"pmcid": "PMC7607250", "section_index": 3, "section_title": "Data Description", "row_count": 27, "column_count": 8}, "table": {"label": "Table 1", "caption": "Details of transcriptomic data submitted to the NCBI Sequence Read Archive (SRA).", "rows": [["Sample", "Tissue", "Condition", "Sex", "Raw reads (In million)", "Uniquely mapped (In million)", "% Alignment", "SRA Accession"], ["CTMB1", "Brain", "Control", "Male", "75.26", "66.46", "88.31%", "SRX7538216"], ["CTMB2", "Brain", "Control", "Male", "56.37", "49.47", "87.77%", "SRX7538217"], ["CTFB1", "Brain", "Control", "Female", "36.34", "30.27", "83.31%", "SRX7538218"], ["CTFB2", "Brain", "Control", "Female", "42.33", "36.35", "85.88%", "SRX7538219"], ["CTFB3", "Brain", "Control", "Female", "35.59", "31.00", "87.12%", "SRX7538220"], ["ALMB1", "Brain", "Alcohol-exposed", "Male", "33.40", "29.58", "88.58%", "SRX7538221"], ["ALMB2", "Brain", "Alcohol-exposed", "Male", "28.86", "25.59", "88.68%", "SRX7538222"], ["ALFB1", "Brain", "Alcohol-exposed", "Female", "25.01", "22.18", "88.68%", "SRX7538223"], ["ALFB2", "Brain", "Alcohol-exposed", "Female", "28.61", "25.11", "87.78%", "SRX7538224"], ["WDMB1", "Brain", "Withdrawal", "Male", "50.33", "44.28", "87.98%", "SRX7538225"], ["WDMB2", "Brain", "Withdrawal", "Male", "39.55", "32.95", "88.32%", 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