Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA138129 | ENA |
REPOSITORIES: ENA
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Project description:We analyzed if genomic responses of adult zebrafish tissues can reproduce the mammalian known inflammatory process induced by acute endotoxin stress. Although the strength of the inflammatory process was influenced by tissue nature, gene regulation was well conserved across evolution and zebrafish genomic responses highly correlated with mammals’ inflammatory reactions after lipopolysaccharide stimulation.
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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.
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