Single-cell spatial transcriptomic atlas of the whole mouse brain

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

doi:10.1016/j.neuron.2025.02.015

Single-cell spatial transcriptomic atlas of the whole mouse brain

Lei Han
, Zhen Liu
, Zehua Jing
, Yuxuan Liu
, Yujie Peng
, Huizhong Chang
, Junjie Lei
, Kexin Wang
, Yuanfang Xu
, Wei Liu
, Zihan Wu
, Qian Li
, Xiaoxue Shi
, Mingyuan Zheng
, He Wang
, Juan Deng
, Yanqing Zhong
, Hailin Pan
, Junkai Lin
, Ruiyi Zhang

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

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.

Original language	English
Pages (from-to)	2141-2160.e9
Journal	Neuron
Volume	113
Issue number	13
DOIs	https://doi.org/10.1016/j.neuron.2025.02.015
State	Published - 9 Jul 2025
Externally published	Yes

Keywords

Stereo-seq
development
mouse brain
non-coding gene
parcellation
transcriptome

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10.1016/j.neuron.2025.02.015

Cite this

@article{bba465f0ba2b4a8298594b0fd23e6258,

title = "Single-cell spatial transcriptomic atlas of the whole mouse brain",

abstract = "A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.",

keywords = "Stereo-seq, development, mouse brain, non-coding gene, parcellation, transcriptome",

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

note = "Publisher Copyright: {\textcopyright} 2025 Elsevier Inc.",

year = "2025",

month = jul,

day = "9",

doi = "10.1016/j.neuron.2025.02.015",

language = "英语",

volume = "113",

pages = "2141--2160.e9",

journal = "Neuron",

issn = "0896-6273",

publisher = "Cell Press",

number = "13",

}

Han, L, Liu, Z, Jing, Z, Liu, Y, Peng, Y, Chang, H, Lei, J, Wang, K, Xu, Y, Liu, W, Wu, Z, Li, Q, Shi, X, Zheng, M, Wang, H, Deng, J, Zhong, Y, Pan, H, Lin, J, Zhang, R, Chen, Y, Wu, J, Xu, M, Ren, B, Cheng, M, Yu, Q, Song, X, Lu, Y, Tang, Y, Yuan, N, Sun, S, An, Y, Ding, W, Sun, X, Wei, Y, Zhang, S, Dou, Y, Zhao, Y, Han, L, Zhu, Q, Xu, J, Wang, S, Wang, D, Bai, Y, Liang, Y, Liu, Y, Chen, M, Xie, C, Bo, B, Li, M, Zhang, X, Ting, W, Chen, Z, Fang, J, Li, S, Jiang, Y, Tan, X, Zuo, G, Xie, Y, Li, H, Tao, Q, Li, Y, Liu, J, Liu, Y, Hao, M, Wang, J, Wen, H, Liu, J, Yan, Y, Zhang, H, Sheng, Y, Yu, S, Liao, X, Jiang, X, Wang, G, Liu, H, Wang, C, Feng, N, Liu, X, Ma, K, Xu, X, Han, T, Cao, H, Zheng, H, Chen, Y, Lu, H, Yu, Z, Zhang, J, Wang, B, Wang, Z, Xie, Q, Pan, S, Liu, C, Xu, C, Cui, L, Li, Y, Liu, S, Liao, S, Chen, A, Wu, QF, Wang, J, Liu, Z, Sun, Y, Mulder, J, Yang, H, Wang, X, Li, C, Yao, J, Xu, X, Liu, L, Shen, Z, Wei, W & Sun, YG 2025, 'Single-cell spatial transcriptomic atlas of the whole mouse brain', Neuron, vol. 113, no. 13, pp. 2141-2160.e9. https://doi.org/10.1016/j.neuron.2025.02.015

TY - JOUR

T1 - Single-cell spatial transcriptomic atlas of the whole mouse brain

AU - Han, Lei

AU - Liu, Zhen

AU - Jing, Zehua

AU - Liu, Yuxuan

AU - Peng, Yujie

AU - Chang, Huizhong

AU - Lei, Junjie

AU - Wang, Kexin

AU - Xu, Yuanfang

AU - Liu, Wei

AU - Wu, Zihan

AU - Li, Qian

AU - Shi, Xiaoxue

AU - Zheng, Mingyuan

AU - Wang, He

AU - Deng, Juan

AU - Zhong, Yanqing

AU - Pan, Hailin

AU - Lin, Junkai

AU - Zhang, Ruiyi

AU - Chen, Yu

AU - Wu, Jinhua

AU - Xu, Mingrui

AU - Ren, Biyu

AU - Cheng, Mengnan

AU - Yu, Qian

AU - Song, Xinxiang

AU - Lu, Yanbing

AU - Tang, Yuanchun

AU - Yuan, Nini

AU - Sun, Suhong

AU - An, Yingjie

AU - Ding, Wenqun

AU - Sun, Xing

AU - Wei, Yanrong

AU - Zhang, Shuzhen

AU - Dou, Yannong

AU - Zhao, Yun

AU - Han, Luyao

AU - Zhu, Qianhua

AU - Xu, Junfeng

AU - Wang, Shiwen

AU - Wang, Dan

AU - Bai, Yinqi

AU - Liang, Yikai

AU - Liu, Yuan

AU - Chen, Mengni

AU - Xie, Chun

AU - Bo, Binshi

AU - Li, Mei

AU - Zhang, Xinyan

AU - Ting, Wang

AU - Chen, Zhenhua

AU - Fang, Jiao

AU - Li, Shuting

AU - Jiang, Yujia

AU - Tan, Xing

AU - Zuo, Guolong

AU - Xie, Yue

AU - Li, Huanhuan

AU - Tao, Quyuan

AU - Li, Yan

AU - Liu, Jianfeng

AU - Liu, Yuyang

AU - Hao, Mingkun

AU - Wang, Jingjing

AU - Wen, Huiying

AU - Liu, Jiabing

AU - Yan, Yizhen

AU - Zhang, Hui

AU - Sheng, Yifan

AU - Yu, Shui

AU - Liao, Xiaoyan

AU - Jiang, Xuyin

AU - Wang, Guangling

AU - Liu, Huanlin

AU - Wang, Congcong

AU - Feng, Ning

AU - Liu, Xin

AU - Ma, Kailong

AU - Xu, Xiangjie

AU - Han, Tianyue

AU - Cao, Huateng

AU - Zheng, Huiwen

AU - Chen, Yadong

AU - Lu, Haorong

AU - Yu, Zixian

AU - Zhang, Jinsong

AU - Wang, Bo

AU - Wang, Zhifeng

AU - Xie, Qing

AU - Pan, Shanshan

AU - Liu, Chuanyu

AU - Xu, Chan

AU - Cui, Luman

AU - Li, Yuxiang

AU - Liu, Shiping

AU - Liao, Sha

AU - Chen, Ao

AU - Wu, Qing Feng

AU - Wang, Jian

AU - Liu, Zhiyong

AU - Sun, Yidi

AU - Mulder, Jan

AU - Yang, Huanming

AU - Wang, Xiaofei

AU - Li, Chao

AU - Yao, Jianhua

AU - Xu, Xun

AU - Liu, Longqi

AU - Shen, Zhiming

AU - Wei, Wu

AU - Sun, Yan Gang

PY - 2025/7/9

Y1 - 2025/7/9

N2 - A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.

AB - A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.

KW - Stereo-seq

KW - development

KW - mouse brain

KW - non-coding gene

KW - parcellation

KW - transcriptome

UR - https://www.scopus.com/pages/publications/105000791001

U2 - 10.1016/j.neuron.2025.02.015

DO - 10.1016/j.neuron.2025.02.015

M3 - 文章

C2 - 40132589

AN - SCOPUS:105000791001

SN - 0896-6273

VL - 113

SP - 2141-2160.e9

JO - Neuron

JF - Neuron

IS - 13

ER -

Single-cell spatial transcriptomic atlas of the whole mouse brain

Abstract

Keywords

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