足细胞是维持肾滤过屏障完整性的关键细胞。最近的几项研究以深分辨率分析了足细胞中的基因组和转录组。这种“足细胞”研究的途径是通过各种技术实现的,包括1)单细胞转录组学,2)有和没有基因编码标记的FACS,和3)深层蛋白质组学。然而,各种组学技术和研究的数据目前还没有很好地相互整合。这里,我们的目标是建立一个共同的,通过整合大量RNA测序,简化了小鼠足细胞基因组的知识库,FACS分选足细胞的大量蛋白质组学,和单细胞转录组学。对来自不同实验室的每种组学技术的三个公开可用数据集进行了生物信息整合和可视化。我们的方法不仅揭示了足细胞的保守过程,而且还揭示了所用技术的优点和局限性。我们发现高表达的聚糖糖基磷脂酰肌醇锚合成和周转,以及视黄醇代谢,足细胞的特征研究相对不足。此外,肌动蛋白结合分子以足细胞特异性方式组织,与其他肾小球细胞相比,足细胞中的差异表达证明了这一点。我们编译了一个基于Web的“PodIent”应用程序,该应用程序说明了集成数据集的功能。通过在绝对和相对定量中查询感兴趣的基因的足细胞身份,同时还使用关键字链接到功能注释,从而实现用户驱动的探索性分析。基因本体论术语,和基因集富集。该共识草案是迈向肾脏细胞共同分子组学知识的第一步。新的和注意足细胞是肾小球滤过的关键组成部分,在各种肾脏疾病中受到影响。这里,我们提出了一个综合的,整个蛋白质组学的分子同一性的强大定义,单细胞转录组学,以及对天然小鼠足细胞的大量转录组学研究。我们创建了“PodIdent”应用程序,一个新的知识库,促进获取足细胞的特定蛋白质的存在和表达。
The podocyte is a key cell in maintaining renal filtration barrier integrity. Several recent studies have analyzed the genome and transcriptome in the podocyte at deep resolution. This avenue of \"podocyte-ome\" research was enabled by a variety of techniques, including 1) single-cell transcriptomics, 2) FACS with and without genetically encoded markers, and 3) deep proteomics. However, data across various omics techniques and studies are currently not well integrated with each other. Here, we aimed to establish a common, simplified knowledge base for the mouse podocyte-ome by integrating bulk RNA sequencing, bulk proteomics of FACS-sorted podocytes, and single-cell transcriptomics. Three publicly available datasets of each omics technique from different laboratories were bioinformatically integrated and visualized. Our approach not only revealed conserved processes of podocytes but also sheds light on the benefits and limitations of the used technologies. We identified that high expression of glycan glycosylphosphatidylinositol anchor synthesis and turnover, as well as retinol metabolism, were relatively understudied features of podocytes. In addition, actin-binding molecules were organized in a podocyte-specific manner, as evidenced by differential expression in podocytes compared with other glomerular cells. We compiled a Web-based \"PodIent\" application that illustrates the features of the integrated dataset. This enables user-driven exploratory analysis by querying genes of interest for podocyte identity in absolute and relative quantification while also linking to functional annotation using keywords, Gene Ontology terms, and gene set enrichments. This
consensus draft is a first step toward common molecular omics knowledge of kidney cells.NEW & NOTEWORTHY Podocytes are key components of glomerular filtration and are affected in various kidney diseases. Here, we present an integrated, robust definition of molecular identity across proteomic, single-cell transcriptomics, and bulk transcriptomic studies on native mouse podocytes. We created the \"PodIdent\" app, a novel knowledge base promoting access to the presence and expression of specific proteins for podocytes.