Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA187332 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA-seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references, we implemented Palette to infer spatial gene expression from bulk RNA-seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates, establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps (DreAM). Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell-cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior (AP) axis, and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally, we difined a hox score, and comprehensively demonstrated the spatial collinearity of Hox genes at single-cell resolution during development.
2024-04-08 | GSE262578 | GEO
Project description:Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio
| PRJNA274362 | ENA
Project description:Methyl tert-butyl ether (MTBE) has been shown to target developing vasculature in piscine and mammalian model systems. In the zebrafish, MTBE induces vascular lesions throughout development. These lesions result from exposure to MTBE at an early stage in development (6-somites to Prim-5 stages). During this time period, transcript levels of vegfa, vegfc, and vegfr1 were significantly decreased in embryos exposed to 5 mM MTBE. We performed global gene analysis as an unbiased approach to discover possible modes of action of MTBE vascular toxicity. Embryos were exposed at 3 hours post fertilization (hpf) in triplicate to one of three concentrations of MTBE: 5mM (induces vascular lesions and significantly decreases vegfa), 0.625mM (NOAEL; no observed adverse effect level), and 0.00625mM (100-fold below NOAEL), or to embryo media (control). Samples were collected at 6-somites (~15hpf), 21-somites (~24 hpf), and Prim-5 (~30 hpf) stages of development. Embryos were meticulously staged at exposure and at the time of collection to maintain a homogeneous population. Our experimental design sought to explore the effect of three concentrations MTBE on three different stages of zebrafish embryonic development during the critical period established for the chemical. This time period also corresponds to an important time in the cardiovascular system develop of our model vertebrate.
2013-09-01 | E-GEOD-46371 | biostudies-arrayexpress
Project description:Global gene expression induced by CP1020 (Cyanopeptolin) in zebrafish eleuthero-embryo (Danio rerio)
| PRJNA216143 | ENA
Project description:Humans and animals have problems producing eggs with high embryo developmental competence, but the causes of poor egg quality are usually unknown. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading model for vertebrate development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were used to create pooled or replicated sample sets subjected to different levels of fractionation before LC-MS/MS. Obtained spectra were searched against a custom zebrafish proteome database and detected proteins were annotated, categorized and quantified based on their normalized spectral counts. Manual and automated enrichment analyses were highly confirmative, showing that good and poor quality eggs have disparate proteomes. Proteins involved in protein synthesis, energy metabolism, and lipid metabolism, and certain vitellogenin products were strikingly underrepresented in poor quality eggs. Poor quality eggs also had significantly higher representation of proteins related to immune system and endosome/lysosome functioning, oncogenes, and apoptosis, as well as lectins and egg envelope proteins. Quantitative comparisons of highly abundant proteins revealed 9 candidate egg quality markers warranting further study. In conclusion, the zebrafish egg proteome appears to be linked to embryo developmental potential, a phenomenon that begs further investigation.
2017-11-27 | PXD005129 | Pride
Project description:Humans and animals have problems producing eggs with high embryo developmental competence, but the causes of poor egg quality are usually unknown. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading model for vertebrate development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were used to create pooled or replicated sample sets subjected to different levels of fractionation before LC-MS/MS. Obtained spectra were searched against a custom zebrafish proteome database and detected proteins were annotated, categorized and quantified based on their normalized spectral counts. Manual and automated enrichment analyses were highly confirmative, showing that good and poor quality eggs have disparate proteomes. Proteins involved in protein synthesis, energy metabolism, and lipid metabolism, and certain vitellogenin products were strikingly underrepresented in poor quality eggs. Poor quality eggs also had significantly higher representation of proteins related to immune system and endosome/lysosome functioning, oncogenes, and apoptosis, as well as lectins and egg envelope proteins. Quantitative comparisons of highly abundant proteins revealed 9 candidate egg quality markers warranting further study. In conclusion, the zebrafish egg proteome appears to be linked to embryo developmental potential, a phenomenon that begs further investigation.
2017-11-27 | PXD005137 | Pride
Project description:Zebrafish embryo: Control vs. Nrf2a overexpression
| PRJNA340452 | ENA
Project description:Salmonella typhimurium infection of zebrafish embryo
| PRJNA112491 | ENA