A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus
Zebrafish (Danio rerio) are a good model for cancer research including studies on chemotherapy treatments. We treated wild-type and miR-34a deletion mutant zebrafish embryos at 24 h post-fertilization with 1 µM of the topoisomerase I inhibitor, camptothecin (CPT), for 4 h to catalogue gene expressio...
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Elsevier
2024-12-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340924010035 |
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| author | Sergey V. Prykhozhij Kevin Ban Zane L. Brown Kim Kobar Gabriel Wajnberg Charlotte Fuller Simi Chacko Jacynthe Lacroix Nicolas Crapoulet Craig Midgen Adam Shlien David Malkin Jason N. Berman |
| author_facet | Sergey V. Prykhozhij Kevin Ban Zane L. Brown Kim Kobar Gabriel Wajnberg Charlotte Fuller Simi Chacko Jacynthe Lacroix Nicolas Crapoulet Craig Midgen Adam Shlien David Malkin Jason N. Berman |
| author_sort | Sergey V. Prykhozhij |
| collection | DOAJ |
| description | Zebrafish (Danio rerio) are a good model for cancer research including studies on chemotherapy treatments. We treated wild-type and miR-34a deletion mutant zebrafish embryos at 24 h post-fertilization with 1 µM of the topoisomerase I inhibitor, camptothecin (CPT), for 4 h to catalogue gene expression changes induced by this DNA damage treatment and to understand if these changes are influenced by loss of miR-34a. The 4 sample groups of 3 independent biological samples consisting of 30 embryos each were analyzed by RNA-sequencing using the recently updated zebrafish transcriptome annotation based on GRCz11, which enabled a more complete and sensitive read mapping and gene assignment than standard annotations. Using this gene expression estimates dataset as the primary resource, we performed a differentially expressed gene (DEG) analysis based on treatment as loss of miR-34a had minimal effects on CPT-induced expression changes. The DEGs were analyzed for Gene Ontology and KEGG pathway terms. Enriched terms and pathways among up-regulated genes were mostly related to stress, cell death, cell cycle regulation, transcriptional regulation, cell signalling, developmental processes and synthesis of retinol and steroid hormones. By contrast, down-regulated genes were most strongly associated with genes involved in key developmental processes, adhesion molecules, as well as some transport and metabolic pathways, together suggesting a “developmental shutdown”. We also identified interferon-regulated genes and p53 target genes activated or inhibited by DNA damage due to topoisomerase I inhibition, suggesting that they are important components of the response to this type of DNA damage in zebrafish embryos. |
| format | Article |
| id | doaj-art-2cf8347037df4b95a919db3322c6fd21 |
| institution | OA Journals |
| issn | 2352-3409 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj-art-2cf8347037df4b95a919db3322c6fd212025-08-20T02:18:48ZengElsevierData in Brief2352-34092024-12-015711104110.1016/j.dib.2024.111041A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression OmnibusSergey V. Prykhozhij0Kevin Ban1Zane L. Brown2Kim Kobar3Gabriel Wajnberg4Charlotte Fuller5Simi Chacko6Jacynthe Lacroix7Nicolas Crapoulet8Craig Midgen9Adam Shlien10David Malkin11Jason N. Berman12Children's Hospital of Eastern Ontario (CHEO) Research Institute and University of Ottawa, Ottawa, ON, Canada; Corresponding author.Children's Hospital of Eastern Ontario (CHEO) Research Institute and University of Ottawa, Ottawa, ON, CanadaDalhousie University Medical School, Halifax, NS, CanadaChildren's Hospital of Eastern Ontario (CHEO) Research Institute and University of Ottawa, Ottawa, ON, CanadaAtlantic Cancer Research Institute, Pavillon Hôtel-Dieu, Moncton, NB, CanadaHHS McMaster University Medical Centre, Division of Medical Microbiology, Hamilton, ON, CanadaAtlantic Cancer Research Institute, Pavillon Hôtel-Dieu, Moncton, NB, CanadaAtlantic Cancer Research Institute, Pavillon Hôtel-Dieu, Moncton, NB, CanadaAtlantic Cancer Research Institute, Pavillon Hôtel-Dieu, Moncton, NB, CanadaDepartment of Pathology, Dalhousie University, Halifax, NS, Canada; IWK Health Centre, Halifax, NS, CanadaGenetics and Genome Biology Program, Division of Hematology/Oncology, The Hospital for Sick Children, PGCRL, Toronto, ON, CanadaGenetics and Genome Biology Program, Division of Hematology/Oncology, The Hospital for Sick Children, PGCRL, Toronto, ON, Canada; Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, CanadaChildren's Hospital of Eastern Ontario (CHEO) Research Institute and University of Ottawa, Ottawa, ON, CanadaZebrafish (Danio rerio) are a good model for cancer research including studies on chemotherapy treatments. We treated wild-type and miR-34a deletion mutant zebrafish embryos at 24 h post-fertilization with 1 µM of the topoisomerase I inhibitor, camptothecin (CPT), for 4 h to catalogue gene expression changes induced by this DNA damage treatment and to understand if these changes are influenced by loss of miR-34a. The 4 sample groups of 3 independent biological samples consisting of 30 embryos each were analyzed by RNA-sequencing using the recently updated zebrafish transcriptome annotation based on GRCz11, which enabled a more complete and sensitive read mapping and gene assignment than standard annotations. Using this gene expression estimates dataset as the primary resource, we performed a differentially expressed gene (DEG) analysis based on treatment as loss of miR-34a had minimal effects on CPT-induced expression changes. The DEGs were analyzed for Gene Ontology and KEGG pathway terms. Enriched terms and pathways among up-regulated genes were mostly related to stress, cell death, cell cycle regulation, transcriptional regulation, cell signalling, developmental processes and synthesis of retinol and steroid hormones. By contrast, down-regulated genes were most strongly associated with genes involved in key developmental processes, adhesion molecules, as well as some transport and metabolic pathways, together suggesting a “developmental shutdown”. We also identified interferon-regulated genes and p53 target genes activated or inhibited by DNA damage due to topoisomerase I inhibition, suggesting that they are important components of the response to this type of DNA damage in zebrafish embryos.http://www.sciencedirect.com/science/article/pii/S2352340924010035Zebrafish (Danio rerio)CamptothecinTopoisomerase I inhibitorp53Interferon-stimulated geneChemotherapy |
| spellingShingle | Sergey V. Prykhozhij Kevin Ban Zane L. Brown Kim Kobar Gabriel Wajnberg Charlotte Fuller Simi Chacko Jacynthe Lacroix Nicolas Crapoulet Craig Midgen Adam Shlien David Malkin Jason N. Berman A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus Data in Brief Zebrafish (Danio rerio) Camptothecin Topoisomerase I inhibitor p53 Interferon-stimulated gene Chemotherapy |
| title | A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus |
| title_full | A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus |
| title_fullStr | A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus |
| title_full_unstemmed | A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus |
| title_short | A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosGene Expression Omnibus |
| title_sort | dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryosgene expression omnibus |
| topic | Zebrafish (Danio rerio) Camptothecin Topoisomerase I inhibitor p53 Interferon-stimulated gene Chemotherapy |
| url | http://www.sciencedirect.com/science/article/pii/S2352340924010035 |
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