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

We employed Stereo-seq, a high-definition spatially resolved transcriptomic technology, to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryo. We profiled 91 embryo sections covering six critical time points (3.3, 5.25, 10, 12, 18, 24hpfs) during the first 24 hours of development, obtaining a total of 139,391 spots at cellular size (~100 µm2) with spatial coordinates.We also performed single-cell RNA-seq at the correspondent timepoints. Raw data of Stereo-seq were deposited in https://db.cngb.org/stomics/project/STT0000007. Raw data of scRNA-seq were deposited in https://db.cngb.org/search/project/CNP0002220/.