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scBrainScope: cross-species multidimensional brain atlas
Siying Qin1, Yuexi Yang1, Haoyu Wang1
1State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China.
Nucleic Acids Research
|November 17, 2025
Summary
scBrainScope is a new interactive brain atlas integrating single-cell and spatial transcriptomic data across species and conditions. This resource aids exploration of brain cell identity, gene programs, and organization for neuroscience research.
Area of Science:
- Neuroscience
- Genomics
- Bioinformatics
Background:
- The brain's complexity necessitates integrated data resources.
- Existing brain atlases lack comprehensive gene expression and analysis tools.
- Understanding brain evolution, development, and disease requires multi-dimensional data integration.
Purpose of the Study:
- To develop scBrainScope, an interactive transcriptomic atlas of the brain.
- To integrate diverse brain datasets, including single-cell, bulk RNA, and spatial sequencing data.
- To provide analytical tools for exploring brain features across species, regions, developmental stages, and diseases.
Main Methods:
- Compiled single-cell sequencing data from 135 species (433 brain regions, 198 developmental stages, 100 diseases).
- Integrated 737 bulk RNA sequencing datasets and 1154 spatial datasets.
- Developed six atlas modules (AtlasScope, RegionScope, TissueScope, SpaceScope, PathoScope, AgeScope) and three analytical modules (sPandora, ePandora, cPandora).
Main Results:
- Created a comprehensive, interactive transcriptomic atlas of the brain.
- Enabled multi-scale and multi-dimensional investigation of cell identity, gene programs, and spatial organization.
- Facilitated comparative analysis across diverse species, developmental stages, and neurological conditions.
Conclusions:
- scBrainScope offers a valuable, data-rich resource for neuroscience, evolutionary biology, and translational medicine.
- The platform supports in-depth exploration of brain transcriptomics.
- Provides a foundation for future discoveries in brain research and disease understanding.
