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

Danio rerio

Project description:Transcriptome response to genistein in zebrafish embryos

| PRJNA150451 | ENA

Danio rerio

Project description:Zebrafish larvae response to AgNPs and AgNO3

| PRJNA260469 | ENA

Danio rerio

Project description:Transcriptome analysis of the zebrafish embryonic host response to Edwardsiella tarda infection [experiment B]

| PRJNA143271 | ENA

Danio rerio

Project description:Zebrafish response to Mycobacterium marinum infection (Affymetrix series)