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Danio rerio

ABSTRACT: Zebrafish Development

PROVIDER: PRJNA79973 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR099320.fastq.gz	Fastqsanger.gz
	SRR099321.fastq.gz	Fastqsanger.gz
	SRR099322.fastq.gz	Fastqsanger.gz
	SRR099323.fastq.gz	Fastqsanger.gz
	SRR099324.fastq.gz	Fastqsanger.gz

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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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