Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
Small Methods. 2023 Sep;7(9):e2201421. doi: 10.1002/smtd.202201421. Epub 2023 May 31.
The liver is critical for the digestive and immune systems. Although the physiology and pathology of liver have been well studied and many scRNA-seq data are generated, a database and landscape for characterizing cell types and gene expression in different liver diseases or developmental stages at single-cell resolution are lacking. Hence, scLiverDB is developed, a specialized database for human and mouse liver transcriptomes to unravel the landscape of liver cell types, cell heterogeneity and gene expression at single-cell resolution across various liver diseases/cell types/developmental stages. To date, 62 datasets including 9,050 samples and 1,741,734 cells is curated. A uniform workflow is used, which included quality control, dimensional reduction, clustering, and cell-type annotation to analyze datasets on the same platform; integrated manual and automatic methods for accurate cell-type identification and provided a user-friendly web interface with multiscale functions. There are two case studies to show the usefulness of scLiverDB, which identified the LTB (lymphotoxin Beta) gene as a potential biomarker of lymphoid cells differentiation and showed the expression changes of Foxa3 (forkhead box A3) in liver chronic progressive diseases. This work provides a crucial resource to resolve molecular and cellular information in normal, diseased, and developing human and mouse livers.
肝脏对于消化系统和免疫系统至关重要。尽管肝脏的生理学和病理学已经得到了很好的研究，并且产生了许多 scRNA-seq 数据，但缺乏用于在单细胞分辨率下描述不同肝脏疾病或发育阶段的细胞类型和基因表达的数据库和全景图。因此，开发了 scLiverDB，这是一个专门用于人类和小鼠肝脏转录组的数据库，旨在揭示各种肝脏疾病/细胞类型/发育阶段中肝脏细胞类型、细胞异质性和单细胞分辨率下基因表达的全景图。迄今为止，已整理了 62 个数据集，包括 9050 个样本和 1741734 个细胞。使用了统一的工作流程，包括质量控制、降维、聚类和细胞类型注释，以分析同一平台上的数据集；结合手动和自动方法进行准确的细胞类型识别，并提供了具有多尺度功能的用户友好的 Web 界面。有两个案例研究说明了 scLiverDB 的有用性，它确定了 LTB（lymphotoxin Beta）基因作为淋巴细胞分化的潜在生物标志物，并显示了 Foxa3（forkhead box A3）在肝脏慢性进行性疾病中的表达变化。这项工作为解析正常、患病和发育中的人类和小鼠肝脏中的分子和细胞信息提供了至关重要的资源。
