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

Development of gene expression signatures after knocking down of miR-132 in zebrafish

Project description:To further development of the gene expression, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that are regulated in miR-132 knockdown zebrafish. Zebrafish larvae were injected with Control MO or miR-132 MO at one-cell stage. Then the upregulated genes are combined to the miRNA prediction alagorithm. 21 genes were picked up and verifed by luciferase assay. The total RNA was extracted from 3 dpf zebrafish injected with 8 ng control or miR-132 MO MO. The RNA was applied for the microarray gene proliling

2016-08-09 | E-GEOD-85291 | biostudies-arrayexpress

Danio rerio

Project description:Raf/MEK signatures in zebrafish liver cells

| PRJNA142819 | ENA

Danio rerio

Project description:Raw sequence reads of miR-462/miR-731 knockdwon zebrafish embryos

| PRJNA401346 | ENA

Danio rerio

Project description:[E-MTAB-308] Zebrafish gene 3 prime end pull down for genome annotation

| PRJNA134397 | ENA

Danio rerio

Project description:Changes of gene expression signatures in Tg(RE:HSE:EGFP) zebrafish embryos