Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

Computational solutions for spatial transcriptomics

“…The HDST and Seq-Scope studies demonstrated that the high-resolution arrays can locate even rare cell types and resolve the gene expression differences at subcellular resolution, which makes for example the nuclear-to-cytoplasmic type of RNA-velocity of analysis feasible for spatial barcode ST methods [9] , [25] . The preprints showcase the capabilities and limitations of Stereo-Seq with tumor leading-edge samples [65] and high-resolution spatial transcriptome atlases produced from regenerating axolotl brains and the developmental stages of the mouse, zebrafish, and fruit fly embryos [7] , [66] , [67] , [68] . Already these detailed transcriptome atlases, after being released into the public domain, could provide a rich resource of transcriptomic data to analyze the developmental process and brain regeneration of multicellular organisms.…”

How to make spatial maps of gene activity — down to the cellular level

“…Even so, the team has used the method to construct 3D atlases that chart the spatial shifts in gene expression "One can get to a much higher-level understanding of the physiology or pathology in a tissue." that accompany embryonic development in mice 7 , flies 9 and zebrafish 10 .…”

Time-Aligned Hourglass Gastrulation Models in Rabbit and Mouse

“…This approach can also be instrumental to elucidate the intrinsic and extrinsic function of genes in embryonic cell specification 25 . Together with technologies for mapping cell lineage trees (Reviewed in 26 ), and spatial transcriptomics [27][28][29] , this can be even further refined to obtain a true holistic view of embryonic development.…”

“…However, we observed noticeable changes in specification timing of some lineages, and divergence of primordial germ cells programs, which in the rabbit do not activate mesoderm genes. Comparative analysis of temporal differentiation models provides a new basis for studying the evolution of gastrulation dynamics across mammals.with technologies for mapping cell lineage trees (Reviewed in 26 ), and spatial transcriptomics [27][28][29] , this can be even further refined to obtain a true holistic view of embryonic development.Importantly, embryonic atlases were recently described from precious and limited primate 30,31 and human 20,32 samples, but the temporal resolution in these systems is limited. Here, we adapt the rabbit as a second high resolution single cell model for mammalian gastrulation.…”