Redistribution of RNA localization in early embryos of zebrafish

This study investigates spatial transcriptomic dynamics during early embryogenesis in Danio rerio (zebrafish). Using TOMO-seq, we profiled RNA localization along the animal–vegetal axis at key embryonic stages for 1 hpf (~4-cell), 2 hpf (~64-cell), and 3 hpf (~1000-cell) embryos. Samples were collected in biological triplicates and sectioned into five defined regions (A–E) along the axis to assess spatial distribution. The data were used to analyze maternal RNA localization, transcript stability, and onset of zygotic transcription. Overall design: To investigate transcriptomic changes during early embryonic development, TOMO-seq was applied to a series of developmental stages: 1 hpf (~4-cell), 2 hpf (~64-cell), and 3 hpf (~1000-cell) stages. Biological triplicates were used for each condition. Samples were sectioned along the animal–vegetal axis into five distinct regions, labeled A through E, with region A representing the most animal and region E the most vegetal portion. This approach enabled the analysis of both temporal and spatial transcriptomic dynamics to uncover stage-specific transcriptomic changes occurring during the onset of embryogenesis.