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bioRxiv · 10.1101/2025.09.30.679413

Exploring the correspondence between gene expressionand thalamic nuclei using the THALMANAC resource

Turner, M. A.·Chartrand, T.·Summers, M. T.·Hooper, M.·van Velthoven, C.·Waters, J.·de Vries, S.·Zeng, H.·Tasic, B.·Svoboda, K.·Long, B.
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Abstract

The thalamus connects the sensory organs and major subcortical brain regions with the neocortex. The thalamus has long been divided into multiple discrete nuclei, based on cytoarchitecture, histochemical stains, and mesoscale connectivity. However, thalamic nuclei do not completely describe thalamic organization. For example, some boundaries between thalamic nuclei are disputed, whereas other nuclei are known to contain subdomains with distinct connectivity and function. Moreover, the correspondence between cellular gene expression and other properties of thalamic projection neurons remains to be established. Spatial analysis of single cell gene expression provides a basis for reevaluating thalamic organization. We present the THALMANAC, (THALamusMERFISH ANalysis and ACcess) a Findable, Accessible, Interoperable, Reusable and Reproducible (FAIRR) resource for exploring and analyzing single-cell transcriptomic variation in the thalamus. The THALMANAC provides streamlined access to thalamic gene expression data registered to the common coordinate framework and tools for quantitative analysis and visualization of these data, all encapsulated in a reproducible, cloud computing platform. Using this resource, we find that gene expression generally supports the parcellation of thalamus into distinct nuclei. Some nuclei, such as the anteromedial nucleus, are additionally composed of discrete subdomains, while other nuclei share patterns of gene expression or are arrayed on a spatial gradient of gene expression. The THALMANAC establishes spatial transcriptomic data as a foundation for delineating thalamic organization. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/679413v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d517fcorg.highwire.dtl.DTLVardef@119dccdorg.highwire.dtl.DTLVardef@ef2cd6org.highwire.dtl.DTLVardef@68adac_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Turner, M. A., Chartrand, T., Summers, M. T., Hooper, M., van Velthoven, C., Waters, J., de Vries, S., Zeng, H., Tasic, B., Svoboda, K., Long, B.. 2025-10-02. Exploring the correspondence between gene expressionand thalamic nuclei using the THALMANAC resource. https://doi.org/10.1101/2025.09.30.679413

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