BMDB: a comprehensive database and web server for integrated single-cell bone marrow microenvironment transcriptomic data

Background The bone marrow (BM) niche is a specialized microenvironment housing the hematopoietic stem and progenitor cells (HSPC) and orchestrating hierarchical hematopoiesis pathways. However, understanding its molecular and cellular intricacies remains incomplete. Single-cell RNA sequencing (scRNA-seq) technology has developed into a powerful tool for investigation of BM niche heterogeneity and functional diversity. Methods Here, we present BMDB, the first dedicated web-based data resource of BM niche transcriptome and tools for interactive data analysis; available at http://bmdb.jflab.ac.cn:18083/app/bmdb. Results BMDB features two sections: (ⅰ) a well-managed database compiling 123,915 single cells derived from 45 healthy and 20 diseased samples and (ⅱ) versatile data analysis tools that allows users to perform customized analysis on built-in datasets and users’ data. BMDB also provides access to the aforementioned high-quality mouse and human single-cell reference atlases of the BM niche. The core objectives of the analysis module are to identify distinct cell types, delineate their developmental trajectories, and elucidate their potential roles in hematopoiesis, including molecular mechanisms. Conclusion BMDB will serve as a significant resource for the study of the BM niche by virtue of its extensive functionality and analytical capabilities.