BMDB: An integrated database and web platform for single-cell transcriptomic profiling of bone marrow microenvironment

Comput Struct Biotechnol J. 2025 Nov 15;27:5159-5172. doi: 10.1016/j.csbj.2025.11.028. eCollection 2025.

ABSTRACT

The bone marrow microenvironment orchestrates hematopoiesis and disease processes, yet its profound cellular and molecular complexity remains incompletely resolved. While single-cell RNA sequencing offers unprecedented resolution, the lack of a unified resource integrating niche-specific data across health and disease states, and developmental stages hinders systematic exploration. Here, we present BMDB (https://bmdb.jflab.ac.cn:8084/), an integrated database and web platform aggregating 435,682 single cells from 142 healthy and 82 pathological human and mouse samples, establishing species- and stage-specific reference atlases that harmonize niche cell annotation, improve cross-study comparability, and enable translational analyses. Its interactive web platform provides modules for functional exploration, reference-guided analysis, dynamic comparison across states, and knowledge graphs linking genes, variants, pathways, and pathologies. Additionally, users can upload their own scRNA-seq datasets to map onto the reference atlas for cell type annotation and downstream analyses. Collectively, BMDB provides high-quality reference atlases and interactive tools, serving as a valuable resource for investigating bone marrow microenvironment heterogeneity and hematopoietic regulation.

PMID:41334179 | PMC:PMC12666060 | DOI:10.1016/j.csbj.2025.11.028