Quake Stephen R
Department of Bioengineering, Stanford University; Stanford, CA, USA.
bioRxiv. 2025 Aug 27:2024.12.03.626516. doi: 10.1101/2024.12.03.626516.
The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from nine new donors, doubles the number of cells in Tabula Sapiens, and adds four new tissues. This new data includes four donors with multiple organs contributed, thus providing a unique data set in which genetic background, age, and epigenetic effects are controlled for. We analyzed the combined Tabula Sapiens data for expression of transcription factors, thereby providing putative cell type specificity for nearly every human transcription factor and as well as new insights into their regulatory roles. We analyzed the molecular phenotypes of senescent cells across the entire data set, providing new insight into both the universal attributes of senescence as well as those aspects of human senescence that are specific to particular organs and cell-types. Similarly, we analyzed sex-specific gene expression across all of the identified cell types and discovered which cell types and genes have the most distinct sex based gene expression profiles. Finally, to enable accessible analysis of the voluminous medical records of Tabula Sapiens donors, we created a web application powered by a large language model that allows users to ask general questions about the health history of the donors.
《智人细胞图谱》是一份参考人类细胞图谱，包含来自二十多个器官和组织的单细胞转录组数据。在此，我们报告《智人细胞图谱》2.0版，其中包括来自九名新捐赠者的数据，使《智人细胞图谱》中的细胞数量增加了一倍，并新增了四个组织。这些新数据包括四名捐赠了多个器官的捐赠者的数据，从而提供了一个独特的数据集，其中基因背景、年龄和表观遗传效应均得到了控制。我们分析了《智人细胞图谱》的综合数据中转录因子的表达情况，从而为几乎每一种人类转录因子提供了假定的细胞类型特异性，并对其调控作用有了新的认识。我们分析了整个数据集中衰老细胞的分子表型，为衰老的普遍特征以及人类衰老中特定于特定器官和细胞类型的那些方面提供了新的见解。同样，我们分析了所有已识别细胞类型中的性别特异性基因表达，发现了哪些细胞类型和基因具有最明显的基于性别的基因表达谱。最后，为了便于对《智人细胞图谱》捐赠者的大量医疗记录进行分析，我们创建了一个由大语言模型驱动的网络应用程序，用户可以询问有关捐赠者健康史的一般问题。
