Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye, Daosheng Huang, Yang Xu, Wentao Huang, Mengmeng Jiang, Xinyi Jiang, Jie Mao, Yao Chen, Chenyu Lu, Jin Xie, Qun Fang, Yibin Wang, Rui Yue, Tiefeng Li, He Huang, Stuart H Orkin, Guo-Cheng Yuan, Ming Chen, Guoji Guo
Author Information
Xiaoping Han: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China. Electronic address: xhan@zju.edu.cn.
Renying Wang: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Yincong Zhou: College of Life Sciences, Zhejiang University, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Lijiang Fei: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Huiyu Sun: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Shujing Lai: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Assieh Saadatpour: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA.
Ziming Zhou: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Haide Chen: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Fang Ye: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Daosheng Huang: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
Yang Xu: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
Wentao Huang: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
Mengmeng Jiang: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Xinyi Jiang: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Jie Mao: Institute of Applied Mechanics, Zhejiang University, Hangzhou 310027, China.
Yao Chen: Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
Chenyu Lu: Research Center of Infection and Immunity, Zhejiang University School of Medicine, Hangzhou 310058, China.
Jin Xie: State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China.
Qun Fang: Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
Yibin Wang: Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Rui Yue: Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Tiefeng Li: Institute of Applied Mechanics, Zhejiang University, Hangzhou 310027, China.
He Huang: Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Stuart H Orkin: Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Guo-Cheng Yuan: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA.
Ming Chen: College of Life Sciences, Zhejiang University, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
Guoji Guo: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China. Electronic address: ggj@zju.edu.cn.
Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current cell-type classification system. However, a transcriptome-based single-cell atlas has not been achieved for complex mammalian systems. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we analyzed more than 400,000 single cells covering all of the major mouse organs and constructed a basic scheme for a mouse cell atlas (MCA). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously. We built a web-based "single-cell MCA analysis" pipeline that accurately defines cell types based on single-cell digital expression. Our study demonstrates the wide applicability of the Microwell-seq technology and MCA resource.
