Spatially resolved molecular and cellular atlas of the mouse brain

Lei Han; Zhen Liu; Zehua Jing; Yuxuan Liu; Huizhong Chang; Junjie Lei; Yujie Peng; Kexin Wang; Yuanfang Xu; Wei Liu; Zihan Wu; Qian Li; Xiaoxue Shi; Mingyuan Zheng; He Wang; Juan Deng; Yanqing Zhong; Hailin Pan; Jun-Kai Lin; Ruiyi Zhang; Yu Chen; Jinhua Wu; Mingrui Xu; Biyu Ren; Mengnan Cheng; Qian Yu; Xinxiang Song; Yanbing Lu; Yuanchun Tang; Nini Yuan

doi:10.1101/2023.12.03.569501

NeurosciencebioRxivDec 3, 2023

Preprint

Spatially resolved molecular and cellular atlas of the mouse brain

Lei Han iD, Zhen Liu iD, Zehua Jing iD, Yuxuan Liu, Huizhong Chang iD, Junjie Lei, Yujie Peng iD, Kexin Wang iD, Yuanfang Xu, Wei Liu iD, Zihan Wu iD, Qian Li iD, Xiaoxue Shi, Mingyuan Zheng iD, He Wang iD, Juan Deng iD, Yanqing Zhong, Hailin Pan iD, Jun-Kai Lin, Ruiyi Zhang iD, Yu Chen, Jinhua Wu iD, Mingrui Xu iD, Biyu Ren iD, Mengnan Cheng, , Sha Liao iD

Abstract

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding function of the brain. Here, using snRNA-seq and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters with single-cell resolution involving over 6 million cells as well as for 29,655 genes. We have identified new astrocyte clusters, and demonstrated that distinct cell clusters exhibit preference for cortical subregions. In addition, we identified 155 genes exhibiting regional specificity in the brainstem, and 513 long non-coding RNA exhibited regional specificity in the adult brain. Parcellation of brain regions based on spatial transcriptomic information showed large overlap with that by traditional method. Furthermore, we have uncovered 411 transcription factor regulons with spatiotemporal specificity during development. Thus, our study has discovered genes and regulon with spatiotemporal specificity, and provided a high-resolution spatial transcriptomic atlas of the mouse brain.

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