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Allen mouse brain atlases reveal different neural connection and gene expression patterns in cerebellum gyri and sulci

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The recently released Allen Mouse Brain Connectivity Atlas provides a comprehensive mouse brain neuronal connectivity map from brain-wide injection sites via anterograde tracers coupled with serial two-photon tomography. In addition, the Allen Mouse Brain Atlas offers a genome-wide gene expression database built upon a series of in situ hybridization images, covering comprehensive expression energy of over 4,000 genes in coronal sections and over 20,000 genes in sagittal sections across the whole mouse brain. These concurrent and co-registered datasets provide an unparalleled opportunity for systematically analyzing and characterizing spatial neuronal connectivity and gene expression patterns. Inspired by our recent macroscale neuroimaging results showing that there are significantly different structural and functional connectivity patterns on the gyri and sulci of cerebral cortex in primate brains, the present work systematically examines the axonal connectivity and gene expression patterns on gyri and sulci of the cerebellum. Our results demonstrate that the cerebellum gyri and sulci of rodent brains are significantly different in both axonal connectivity and gene expression patterns. This discovery enriches and extends our prior findings in macroscale neuroimaging studies in primates. Additionally, this work offers novel insights on the molecular and structural architectures of the cerebellum in particular and the brain in general.

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We thank the Allen Institute for Brain Science for making the Allen Brain Atlas data available and Dr. Stephen Landowne for the editorial support. T. Liu was supported by NIH R01 DA-033393, NIH R01 AG-042599, NSF CAREER Award IIS-1149260, and NSF BME-1302089. S. Ji was supported by NSF DBI-1147134 and NSF DBI-1356621.

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Correspondence to Tianming Liu or Shuiwang Ji.

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Joint visualization of connectivity from an injection site (colored volume) and reconstructed cerebella cortex (white surface). Connectivity energy is rescaled by logarithm and the color bar is on the right. As highlighted by purple arrows, stronger connection to the gyri on cerebellum can be observed in comparison with sulci (magenta arrow). Connectivity from an injection site mapped to the reconstructed cerebellum cortex. The energy has been rescaled by logarithm and the color bar is on the right. The injection site is the same as supplemental figure 1. As highlighted by yellow arrows, more connections can be observed on gyri than sulci (red arrows). (PDF 196 kb)


Gyrus and sulcus abbreviations and the numbers of voxels in each gyrus and sulcus. The numbers of connected viral tracer injection sites are also given. (XLSX 10 kb)


Correspondence among structure abbreviations used in manuscript, structure full names used in the ARA, and the acronyms used in the ARA. (XLSX 10 kb)


Ordered injection sites to all gyri and sulci. The overall neuronal connectivity strength from 1019 injection sites to all gyri and sulci were ordered for each gyrus and sulcus, and the names of corresponding brain structures are given. (XLSX 138 kb)


Three lists of marker genes that identify gyri from sulci, gyri from negative, and sulci from negative. In each list, the top 200 genes are provided. (XLSX 16 kb)

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Zeng, T., Chen, H., Fakhry, A. et al. Allen mouse brain atlases reveal different neural connection and gene expression patterns in cerebellum gyri and sulci. Brain Struct Funct 220, 2691–2703 (2015).

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