BICAN_BG_Paired-Tag

The basal ganglia (BG) are central subcortical hubs that coordinate movement, cognition, and affect, and are strongly implicated in numerous neurological and psychiatric disorders. However, the regulatory mechanisms that establish and maintain basal ganglia cell-type identity remain incompletely understood, limiting interpretation of non-coding genetic variation associated with brain disease. This project provides processed data and analysis resources supporting a comprehensive single-cell multi-omic Paired-Tag atlas of the adult human basal ganglia. In this study, histone modification profiles (H3K27ac, H3K27me3, and H3K9me3) were jointly measured with transcriptomes at single-nucleus resolution across multiple anatomically defined BG subregions. Integrated analyses of chromatin states and gene expression delineate cell-type–resolved regulatory programs, including active and repressive regulatory elements, transcription factor networks, and spatially organized epigenomic features. Cross-species comparisons between human and mouse further identify conserved core neuronal regulatory circuits alongside divergent, inducible regulatory programs. This Zenodo repository hosts processed, analysis-ready datasets and summary tables, including: Due to file size constraints, raw sequencing data are not stored here. Raw Paired-Tag and RNA sequencing data are available through the NeMO Archive: https://assets.nemoarchive.org/dat-rrstbt3 Interactive visualization and exploration portals are available at: https://basalganglia.epigenomes.net/ https://wangcluster.wustl.edu/~wzhang/projects/MSN_epigenome/ Together, these resources provide a reference atlas of basal ganglia regulatory landscapes and a foundation for linking cell-type–specific regulatory elements to neuropsychiatric disease risk and variant interpretation.