Affiliation:
1. 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
2. College of Life Science and Technology Huazhong University of Science and Technology Wuhan 430074 China
3. Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering Hainan University Haikou Hainan 570228 China
Abstract
AbstractThe 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.
Funder
National Basic Research Program of China
Science, Technology and Innovation Commission of Shenzhen Municipality
Fundamental Research Funds for the Central Universities
Subject
General Materials Science,General Chemistry