biostudies-literatureQin SSpecial Research Fund for Central Universities, Peking Union Medical CollegeGusu Innovation and Entrepreneurship Leading Talents ProgramNCTIB Fund for R&D Platform for Cell and Gene TherapyCAMS Innovation Fund for Medical SciencesNCTIB Fund for R&D Platform for Cell and Gene TherapySuzhou Municipal Key LaboratoryNational Natural Science Foundation of ChinaNatural Science Foundation of Jiangsu ProvinceScience and Technology Innovation 2030CAMS Innovation Fund for Medical Sciences (CIFMS)Non communicable Chronic Diseases-National Science and TechnologyBeijing Research Ward ExcellenceNational Key Research and Development Program of ChinaD958-D970https://www.ebi.ac.uk/biostudies/studies/S-EPMC12807650biostudies-literatureUnknown54(D1)As one of the most evolutionarily complex and functionally diverse organs, the brain is characterized by its intricate structure, developmental alterations, and cellular heterogeneity. Although extensive brain atlases exist, there remains an urgent need for an integration platform that brings together gene expression profiles and analysis tools to explore features across species, brain regions, developmental stages, and pathological conditions. Thus, we developed scBrainScope, a detailed and interactive transcriptomic atlas of the brain. Our platform brings together single cell sequencing data from 135 species, covering 433 brain regions, 198 developmental stages, and 100 neurological diseases. In addition, we compiled 737 bulk RNA sequencing datasets from 275 species, along with 1154 spatNucleic acids researchscBrainScope: cross-species multidimensional brain atlas.PMC12807650BK202202792021-I2M-1-0612021-I2M-1–07433320240892022-I2M-2-004BRWEP2024W114060100Central Research Institute Fund of Chinese Academy of Medical Sciences2022ZD02057002021-I2M-1-0742024YFC3607500323005602022-RC416-01ZXL2022475SZS2023005SZS20220052024ZD05196002022-I2M-2–004Xu LLi CMa YWang HHuang LLi MQin SChen DGuan YYang YQiu XHe YWang SChen YWang XPeng LDeng YfalsescBrainScope: cross-species multidimensional brain atlas.As one of the most evolutionarily complex and functionally diverse organs, the brain is characterized by its intricate structure, developmental alterations, and cellular heterogeneity. Although extensive brain atlases exist, there remains an urgent need for an integration platform that brings together gene expression profiles and analysis tools to explore features across species, brain regions, developmental stages, and pathological conditions. Thus, we developed scBrainScope, a detailed and interactive transcriptomic atlas of the brain. Our platform brings together single cell sequencing data from 135 species, covering 433 brain regions, 198 developmental stages, and 100 neurological diseases. In addition, we compiled 737 bulk RNA sequencing datasets from 275 species, along with 1154 spat2026-01-01T00:00:00Z2026 Jan2026-06-06T15:59:46.138Z2026-06-02T03:09:25.986ZS-EPMC128076504124395510.1093/nar/gkaf1092