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

Jialin Chen¹, Hao Yu¹, Chunjing Bian²

¹Jinfeng Laboratory, Chongqing 401329, China.

Computational and Structural Biotechnology Journal

|December 3, 2025

Summary

BMDB is a new database integrating single-cell data to map the bone marrow microenvironment. It provides reference atlases and tools for exploring hematopoiesis and disease.

Keywords:

Bone marrow niche Reference atlas Single-cell RNA sequencing Web server

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Area of Science:

Hematology
Genomics
Bioinformatics

Background:

The bone marrow microenvironment is crucial for blood formation (hematopoiesis) and disease, but its complexity is not fully understood.
Existing single-cell RNA sequencing (scRNA-seq) data is fragmented, hindering comprehensive analysis of the bone marrow niche.
A unified resource is needed to integrate diverse scRNA-seq datasets for studying the bone marrow microenvironment across different conditions.

Purpose of the Study:

To create an integrated database and web platform, BMDB, for comprehensive analysis of the bone marrow microenvironment.
To establish species- and stage-specific reference atlases from a large collection of scRNA-seq data.
To provide interactive tools for exploring cellular heterogeneity, gene function, and disease associations within the bone marrow.

Main Methods:

Aggregated 435,682 single cells from 142 healthy and 82 pathological human and mouse samples.
Developed an integrated database (BMDB) and web platform with modules for data exploration and analysis.
Implemented reference-guided analysis for user-uploaded scRNA-seq datasets, enabling cell type annotation.

Main Results:

Established high-quality, harmonized reference atlases for human and mouse bone marrow microenvironments.
Facilitated improved cross-study comparability and translational analyses of bone marrow data.
Enabled functional exploration, dynamic comparisons, and knowledge discovery through interactive tools and knowledge graphs.

Conclusions:

BMDB serves as a valuable, integrated resource for the scientific community to investigate bone marrow heterogeneity and hematopoietic regulation.
The platform enhances the systematic exploration of the bone marrow microenvironment in both health and disease.
BMDB supports advanced analyses, including mapping user data onto reference atlases for cell annotation and downstream research.