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Cell transcriptomic atlas of the non-human primate Macaca fascicularis

Author

Listed:
  • Lei Han

    (BGI-Shenzhen
    BGI-Beijing
    Shenzhen Bay Laboratory)

  • Xiaoyu Wei

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Chuanyu Liu

    (BGI-Shenzhen
    BGI-Beijing
    Shenzhen Bay Laboratory)

  • Giacomo Volpe

    (IRCCS–Istituto Tumori ‘Giovanni Paolo II’)

  • Zhenkun Zhuang

    (BGI-Shenzhen
    South China University of Technology)

  • Xuanxuan Zou

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Zhifeng Wang

    (BGI-Shenzhen
    BGI-Beijing)

  • Taotao Pan

    (BGI-Shenzhen
    BGI-Beijing)

  • Yue Yuan

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Xiao Zhang

    (Jilin University)

  • Peng Fan

    (Jilin University)

  • Pengcheng Guo

    (Jilin University)

  • Yiwei Lai

    (Chinese Academy of Sciences)

  • Ying Lei

    (BGI-Shenzhen
    BGI-Beijing
    Shenzhen Bay Laboratory)

  • Xingyuan Liu

    (Jilin University)

  • Feng Yu

    (Chinese Academy of Sciences)

  • Shuncheng Shangguan

    (Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University)

  • Guangyao Lai

    (Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University)

  • Qiuting Deng

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Ya Liu

    (BGI-Shenzhen
    BGI-Beijing)

  • Liang Wu

    (BGI-Shenzhen
    BGI-Beijing
    University of Chinese Academy of Sciences)

  • Quan Shi

    (BGI-Shenzhen
    University of Copenhagen)

  • Hao Yu

    (BGI-Shenzhen)

  • Yunting Huang

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Mengnan Cheng

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Jiangshan Xu

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Yang Liu

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Mingyue Wang

    (BGI-Shenzhen)

  • Chunqing Wang

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Yuanhang Zhang

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Duo Xie

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Yunzhi Yang

    (Zhengzhou University)

  • Yeya Yu

    (Zhengzhou University)

  • Huiwen Zheng

    (Zhengzhou University)

  • Yanrong Wei

    (Zhengzhou University)

  • Fubaoqian Huang

    (BGI-Shenzhen
    South China University of Technology)

  • Junjie Lei

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Waidong Huang

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Zhiyong Zhu

    (BGI-Shenzhen
    University of Chinese Academy of Sciences)

  • Haorong Lu

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Bo Wang

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Xiaofeng Wei

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Fengzhen Chen

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Tao Yang

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Wensi Du

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Jing Chen

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Shibo Xu

    (Nanjing Medical University)

  • Juan An

    (Chinese Academy of Sciences
    University of Science and Technology of China)

  • Carl Ward

    (Chinese Academy of Sciences)

  • Zongren Wang

    (Sun Yat-sen University)

  • Zhong Pei

    (Sun Yat-sen University)

  • Chi-Wai Wong

    (Huazhen Biosciences)

  • Xiaolei Liu

    (Jilin University)

  • Huafeng Zhang

    (Tianjin Medical University General Hospital)

  • Mingyuan Liu

    (Jilin University)

  • Baoming Qin

    (Chinese Academy of Sciences)

  • Axel Schambach

    (Hannover Medical School
    Harvard Medical School)

  • Joan Isern

    (Spanish National Center for Cardiovascular Research (CNIC))

  • Liqiang Feng

    (Chinese Academy of Sciences)

  • Yan Liu

    (Nanjing Medical University)

  • Xiangyu Guo

    (Jinan University
    Hubei Topgene Biotechnology Co., Ltd)

  • Zhen Liu

    (Chinese Academy of Sciences)

  • Qiang Sun

    (Chinese Academy of Sciences)

  • Patrick H. Maxwell

    (University of Cambridge)

  • Nick Barker

    (A*STAR Institute of Molecular and Cell Biology)

  • Pura Muñoz-Cánoves

    (Pompeu Fabra University (UPF), ICREA and CIBERNED)

  • Ying Gu

    (BGI-Shenzhen)

  • Jan Mulder

    (KTH–Royal Institute of Technology
    Karolinska Institute)

  • Mathias Uhlen

    (KTH–Royal Institute of Technology
    Karolinska Institute)

  • Tao Tan

    (Kunming University of Science and Technology)

  • Shiping Liu

    (BGI-Shenzhen
    BGI-Beijing
    Shenzhen Bay Laboratory)

  • Huanming Yang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Sciences)

  • Jian Wang

    (BGI-Shenzhen
    James D. Watson Institute of Genome Sciences)

  • Yong Hou

    (BGI-Shenzhen
    BGI-Beijing
    Shenzhen Bay Laboratory
    Zhengzhou University)

  • Xun Xu

    (BGI-Shenzhen
    BGI-Beijing
    Zhengzhou University
    Guangdong Provincial Key Laboratory of Genome Read and Write)

  • Miguel A. Esteban

    (Jilin University
    Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Longqi Liu

    (BGI-Shenzhen
    BGI-Beijing
    Shenzhen Bay Laboratory
    Zhengzhou University)

Abstract

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell–cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.

Suggested Citation

  • Lei Han & Xiaoyu Wei & Chuanyu Liu & Giacomo Volpe & Zhenkun Zhuang & Xuanxuan Zou & Zhifeng Wang & Taotao Pan & Yue Yuan & Xiao Zhang & Peng Fan & Pengcheng Guo & Yiwei Lai & Ying Lei & Xingyuan Liu , 2022. "Cell transcriptomic atlas of the non-human primate Macaca fascicularis," Nature, Nature, vol. 604(7907), pages 723-731, April.
    • Handle: RePEc:nat:nature:v:604:y:2022:i:7907:d:10.1038_s41586-022-04587-3
    DOI: 10.1038/s41586-022-04587-3
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    Citations

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    Cited by:

    1. Jiao Qu & Fa Yang & Tao Zhu & Yingshuo Wang & Wen Fang & Yan Ding & Xue Zhao & Xianjia Qi & Qiangmin Xie & Ming Chen & Qiang Xu & Yicheng Xie & Yang Sun & Dijun Chen, 2022. "A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    2. Yuyao Song & Zhichao Miao & Alvis Brazma & Irene Papatheodorou, 2023. "Benchmarking strategies for cross-species integration of single-cell RNA sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    4. Jessica M. Vanslambrouck & Sean B. Wilson & Ker Sin Tan & Ella Groenewegen & Rajeev Rudraraju & Jessica Neil & Kynan T. Lawlor & Sophia Mah & Michelle Scurr & Sara E. Howden & Kanta Subbarao & Melissa, 2022. "Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
    5. Yueli Yang & Wenqi Jia & Zhiwei Luo & Yunpan Li & Hao Liu & Lixin Fu & Jinxiu Li & Yu Jiang & Junjian Lai & Haiwei Li & Babangida Jabir Saeed & Yi Zou & Yuan Lv & Liang Wu & Ting Zhou & Yongli Shan & , 2024. "VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    6. Shixuan Liu & Camille Ezran & Michael F. Z. Wang & Zhengda Li & Kyle Awayan & Jonathan Z. Long & Iwijn De Vlaminck & Sheng Wang & Jacques Epelbaum & Christin S. Kuo & Jérémy Terrien & Mark A. Krasnow , 2024. "An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    7. Di-Xian Wang & Zhao-Jun Dong & Sui-Xin Deng & Ying-Ming Tian & Yu-Jie Xiao & Xinran Li & Xiao-Ru Ma & Liang Li & Pengxiao Li & Hui-Zhong Chang & Longqi Liu & Fan Wang & Yang Wu & Xiang Gao & Shuang-Sh, 2023. "GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
    8. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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