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Danio rerio

ABSTRACT: Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio

PROVIDER: PRJNA274362 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1785160.fastq.gz	Fastqsanger.gz
	SRR1785161.fastq.gz	Fastqsanger.gz
	SRR1785162.fastq.gz	Fastqsanger.gz
	SRR1785163.fastq.gz	Fastqsanger.gz
	SRR1785164.fastq.gz	Fastqsanger.gz

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Construction of Danio rerio Asymmetrical Maps (DreAM)

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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Sequencing of Danio rerio skin for 3 age groups

Project description:Comparison of temporal gene expression profiles from Danio rerio skin. The RNA-seq data comprise 3 age groups at 5, 24 and 30 months. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

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Sequencing of Danio rerio skin for 2 age groups

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Sequencing of Danio rerio brain for 5 age groups

Project description:Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA-seq data comprise 5 age groups at 6, 12, 24, 36 and 42 months. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

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