Abstract

A major challenge in understanding vertebrate embryogenesis is the lack of
topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 hours of development. We obtained 152,977 spots at a resolution of 10 × 10 × 15 μm1 with spatial coordinates. Meanwhile, we identified spatial modules and co-expressed genes for specific tissue organizations. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development. The vast sequencing data from these spatial-temporal experiments were generated by the DNBSEQ-T7 sequencer with high accuracy, low cost, and fast turnaround time.

Introduction

Embryogenesis in vertebrates is an intricate and dynamic process. The zebrafish model is commonly used to study vertebrate embryogenesis. A significant challenge in deciphering embryogenesis is the lack of topographical information that can enable the correlation of cellular differentiation with environmental cues. Recent progress in sequencing technology has made it possible to assemble a single-cell atlas during the development of model organisms, thereby enabling the multi-modal information analysis of the whole genome, including the epigenetic state, RNA levels, and protein levels of a single cell.^2,3 However, spatial and temporal relationships with the transcriptome states in developing zebrafish remain unknown. At present, in situ hybridization enables the exploration of expression patterns of specific genes during development but not global changes in the …

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