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Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
Developmental Cell ( IF 11.8 ) Pub Date : 2022-05-04 , DOI: 10.1016/j.devcel.2022.04.009
Chang Liu 1 , Rui Li 1 , Young Li 1 , Xiumei Lin 2 , Kaichen Zhao 3 , Qun Liu 4 , Shuowen Wang 5 , Xueqian Yang 3 , Xuyang Shi 2 , Yuting Ma 6 , Chenyu Pei 3 , Hui Wang 3 , Wendai Bao 3 , Junhou Hui 7 , Tao Yang 8 , Zhicheng Xu 8 , Tingting Lai 8 , Michael Arman Berberoglu 3 , Sunil Kumar Sahu 7 , Miguel A Esteban 9 , Kailong Ma 7 , Guangyi Fan 4 , Yuxiang Li 7 , Shiping Liu 1 , Ao Chen 10 , Xun Xu 11 , Zhiqiang Dong 5 , Longqi Liu 1
Affiliation  

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 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. 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.



中文翻译:

斑马鱼胚胎发生过程中基因表达景观和发育轨迹的时空映射

理解脊椎动物胚胎发生的一个主要挑战是缺乏地形转录组学信息,这些信息可以帮助在细胞命运决定的层次结构中关联微环境线索。在这里,我们使用 Stereo-seq 对 91 个斑马鱼胚胎切片进行了分析,覆盖了发育的前 24 小时内的六个关键时间点,在 10 × 10 × 15 μm 的分辨率下总共获得了 152,977 个点3(接近细胞大小)与空间坐标。同时,我们确定了特定组织组织的空间模块和共变基因。通过对每个时间点的 Stereo-seq 和 scRNA-seq 数据进行综合分析,我们重建了斑马鱼胚胎发生过程中细胞命运转变和分子变化的空间分辨发育轨迹。我们进一步研究了配体-受体对的空间分布,并确定了斑马鱼胚胎发育过程中潜在的重要相互作用。我们的研究为旨在了解脊椎动物发育的进一步研究提供了基本参考。

更新日期:2022-05-04
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