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:Expression data from Zebrafish larvae at 4dpf

| PRJNA393791 | ENA

Danio rerio

Project description:Temporal expression data from zebrafish pineal gland

| PRJNA177960 | ENA

Danio rerio

Project description:Expression data from young and old zebrafish brain.

| PRJNA231978 | ENA

Danio rerio

Project description:Gene expression analysis of zebrafish embryos depleted of arrb1 and/or arrb2 at 12 hpf