An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

Zhang, W.; Ding, W.; Li, K.; Chang, L.; Klein, A.; Baez-Becerra, C. T.; Rink, J. A.; Bartlett, A.; Chen, H.; Schenker, N.; Johansen, N.; Mollenkopf, T.; Fu, Y.; Yang, X.; Liu, S.; Seng, C.; Miao, B.; Liu, T.; Zhu, Q.; Hodge, R. D.; Bakken, T. E.; Lein, E. S.; Hawrylycz, M.; Xu, X.; Behrens, M. M.; Ren, B.; Ecker, J. R.; Wang, T.; Li, D.

doi:10.64898/2026.01.29.702575

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bioRxiv · 10.64898/2026.01.29.702575

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

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Abstract

The basal ganglia regulate motor, cognitive, and affective behaviors, and their dysfunction underlies diverse neurological and psychiatric disorders. Comprehensive, accessible multi-omics resources are needed to understand the regulatory mechanisms governing basal ganglia cell types. Here we present an open, interactive web-based platform for exploring single-cell multi-omics datasets from basal ganglia, generated using 10X Multiome, snm3C-seq, and Paired-Tag technologies from the BICAN (NIH BRAIN Initiative Cell Atlas Network) consortium. The platform is available at https://basalganglia.epigenomes.net/ and enables integrated visualization of gene expression, chromatin accessibility, DNA methylation, histone modifications, and chromatin conformation across cell types and human, macaque, marmoset, and mouse species, with direct genome browser support and comparative epigenomic functionality. Representative analyses demonstrate cell-type-specific regulatory landscapes, conserved and species-specific regulatory elements, and links between epigenomic regulation and transcription. This resource provides a scalable, community-oriented foundation for advancing basal ganglia biology and interpreting regulatory mechanisms relevant to brain function and disease. HighlightsO_LIIntegrated single-cell epigenomic resource for basal ganglia C_LIO_LIInteractive genome browser enables multi-omics and cross-species exploration C_LIO_LIReveals cell-type-specific and species-specific regulatory landscapes C_LIO_LISupports community access to complex brain epigenomic datasets C_LI

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Zhang, W., Ding, W., Li, K., Chang, L., Klein, A., Baez-Becerra, C. T., Rink, J. A., Bartlett, A., Chen, H., Schenker, N., Johansen, N., Mollenkopf, T., Fu, Y., Yang, X., Liu, S., Seng, C., Miao, B., Liu, T., Zhu, Q., Hodge, R. D., Bakken, T. E., Lein, E. S., Hawrylycz, M., Xu, X., Behrens, M. M., Ren, B., Ecker, J. R., Wang, T., Li, D.. 2026-01-30. An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia. https://doi.org/10.64898/2026.01.29.702575

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