Spatially resolved molecular and cellular atlas of the mouse brain

Author:

Han Lei,Liu Zhen,Jing Zehua,Liu Yuxuan,Chang Huizhong,Lei Junjie,Peng Yujie,Wang Kexin,Xu Yuanfang,Liu Wei,Wu Zihan,Li Qian,Shi Xiaoxue,Zheng Mingyuan,Wang He,Deng Juan,Zhong Yanqing,Pan Hailin,Lin Junkai,Zhang Ruiyi,Chen Yu,Wu Jinhua,Xu Mingrui,Ren Biyu,Cheng Mengnan,Yu Qian,Song Xinxiang,Lu Yanbing,Tang Yuanchun,Yuan Nini,Sun Suhong,An Yingjie,Ding Wenqun,Sun Xing,Wei Yanrong,Zhang Shuzhen,Dou Yannong,Zhao Yun,Han Luyao,Zhu Qianhua,Xu Junfeng,Wang Shiwen,Chen Hanbo,Wang Dan,Bai Yinqi,Liang Yikai,Liu Yuan,Chen Mengni,Xie Chun,Bo Binshi,Li Mei,Zhang Xinyan,Ting Wang,Chen Zhenhua,Fang Jiao,Li Shuting,Jiang Yujia,Tan Xing,Zuo Guolong,Xie Yue,Li Huanhuan,Tao Quyuan,Li Yan,Liu Jianfeng,Liu Yuyang,Hao Mingkun,Wang Jingjing,Wen Huiying,Liu Jiabing,Yan Yizhen,Zhang Hui,Sheng Yifan,Han Min,Yu Shui,Liao Xiaoyan,Jiang Xuyin,Wang Guangling,Liu Huanlin,Wang Congcong,Feng Ning,Liu Xin,Ma Kailong,Xu Xiangjie,Han Tianyue,Cao Huateng,Zheng Huiwen,Chen Yadong,Lu Haorong,Yu Zixian,Zhang Jinsong,Wang Bo,Wang Zhifeng,Xie Qing,Pan Shanshan,Liu Chuanyu,Xu Chan,Cui Luman,Li Yuxiang,Liu Shiping,Liao Sha,Chen Ao,Wu Qing-Feng,Wang Jian,Liu Zhiyong,Sun Yidi,Mulder Jan,Yang Huanming,Wang Xiaofei,Li Chao,Yao Jianhua,Xu Xun,Liu Longqi,Shen Zhiming,Wei Wu,Sun Yan-GangORCID

Abstract

AbstractA 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.

Publisher

Cold Spring Harbor Laboratory

Reference96 articles.

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