Source Data for Wang et al. 2021: Budding Epithelial Morphogenesis Driven by Cell-Matrix vs. Cell-Cell Adhesion

This dataset can be used to reproduce all plots in Wang et al., 2021 titled: "Budding Epithelial Morphogenesis Driven by Cell-Matrix vs. Cell-Cell Adhesion" in combination with the Jupyter notebook scripts available from this Github repository: https://github.com/snownontrace/public-scripts-Wang2020-branching-morphogenesis.git<br><br>1. Download and decompress the dataset zip file.<br>2. Place the "data" folder and the "scripts" folder (from GitHub) in the same folder.<br> Note: This folder organization is necessary because relative path is used to read in data in all scripts (e.g., '../data/specific_data_folder/data_table').<br>3. Run scripts to reproduce plots of interest. Refer to the table in the README file of the Github repository to find out which scripts were used to generate which figures.<br>Abstract:Many embryonic organs undergo epithelial morphogenesis to form tree-like hierarchical structures. However, it remains unclear what drives the budding and branching of stratified epithelia, such as in embryonic salivary gland and pancreas. Here, we performed live-organ imaging of mouse embryonic salivary glands at single-cell resolution to reveal that budding morphogenesis is driven by expansion and folding of a distinct epithelial surface cell sheet characterized by strong cell-matrix adhesions and weak cell-cell adhesions. Profiling of single-cell transcriptomes of this epithelium revealed spatial patterns of transcription underlying these cell adhesion differences. We then synthetically reconstituted budding morphogenesis by experimentally suppressing E-cadherin expression and inducing basement membrane formation in 3D spheroid cultures of engineered cells, which required β1 integrin-mediated cell-matrix adhesion for successful budding. Thus, stratified epithelial budding, the key first step of branching morphogenesis, is driven by an overall combination of strong cell-matrix adhesion and weak cell-cell adhesion by peripheral epithelial cells.<br>

本数据集可结合本GitHub仓库（https://github.com/snownontrace/public-scripts-Wang2020-branching-morphogenesis.git）提供的Jupyter 笔记本（Jupyter Notebook）脚本，复现Wang等人2021年题为《由细胞-基质黏附与细胞-细胞黏附驱动的出芽上皮形态发生》（Budding Epithelial Morphogenesis Driven by Cell-Matrix vs. Cell-Cell Adhesion）的论文中的全部图表。

1. 下载并解压数据集压缩包。
2. 将“data”文件夹与（从GitHub获取的）“scripts”文件夹置于同一目录下。注意：由于所有脚本均采用相对路径读取数据（例如`../data/specific_data_folder/data_table`），因此该文件夹组织结构为必需项。
3. 运行脚本以复现所需图表。可参考GitHub仓库README文件中的表格，查询生成对应图表所使用的脚本。

摘要：许多胚胎器官通过上皮形态发生过程形成树状分层结构。目前尚不清楚是什么驱动了复层上皮的出芽与分支，例如胚胎唾液腺与胰腺中的相关过程。本研究以单细胞分辨率对小鼠胚胎唾液腺进行活器官成像，揭示出芽形态发生由一类独特的上皮表面细胞层的扩增与折叠驱动：该细胞层具有强细胞-基质黏附与弱细胞-细胞黏附特性。对该上皮组织的单细胞转录组分析揭示了与这些细胞黏附差异相关的转录空间模式。随后，研究人员通过实验性抑制工程化细胞3D球体培养中的E-钙黏蛋白（E-cadherin）表达并诱导基底膜形成，人工重构了出芽形态发生过程；该过程成功出芽需要依赖β1整合素（β1 integrin）介导的细胞-基质黏附。综上，作为分支形态发生关键第一步的复层上皮出芽，是由外周上皮细胞的强细胞-基质黏附与弱细胞-细胞黏附共同驱动的。