Mapping the Mouse Cell Atlas by Microwell-Seq

doi:10.1016/j.cell.2018.02.001

. 2018 Feb 22;172(5):1091-1107.e17.

doi: 10.1016/j.cell.2018.02.001.

Mapping the Mouse Cell Atlas by Microwell-Seq

Xiaoping Han¹, Renying Wang², Yincong Zhou³, Lijiang Fei², Huiyu Sun², Shujing Lai², Assieh Saadatpour⁴, Ziming Zhou², Haide Chen², Fang Ye², Daosheng Huang⁵, Yang Xu⁵, Wentao Huang⁵, Mengmeng Jiang², Xinyi Jiang², Jie Mao⁶, Yao Chen⁷, Chenyu Lu⁸, Jin Xie⁹, Qun Fang¹⁰, Yibin Wang¹¹, Rui Yue¹¹, Tiefeng Li⁶, He Huang¹², Stuart H Orkin¹³, Guo-Cheng Yuan⁴, Ming Chen³, Guoji Guo¹⁴

Affiliations

¹ 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.
² Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
³ College of Life Sciences, Zhejiang University, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
⁴ Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA.
⁵ Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
⁶ Institute of Applied Mechanics, Zhejiang University, Hangzhou 310027, China.
⁷ Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
⁸ Research Center of Infection and Immunity, Zhejiang University School of Medicine, Hangzhou 310058, China.
⁹ State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China.
¹⁰ Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
¹¹ Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
¹² Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
¹³ Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁴ 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.

PMID: 29474909
DOI: 10.1016/j.cell.2018.02.001

Free article

Mapping the Mouse Cell Atlas by Microwell-Seq

Xiaoping Han et al. Cell. 2018.

Free article

. 2018 Feb 22;172(5):1091-1107.e17.

doi: 10.1016/j.cell.2018.02.001.

Authors

Affiliations

¹ 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.
² Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
³ College of Life Sciences, Zhejiang University, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
⁴ Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA.
⁵ Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
⁶ Institute of Applied Mechanics, Zhejiang University, Hangzhou 310027, China.
⁷ Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
⁸ Research Center of Infection and Immunity, Zhejiang University School of Medicine, Hangzhou 310058, China.
⁹ State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China.
¹⁰ Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
¹¹ Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
¹² Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
¹³ Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁴ 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.

PMID: 29474909
DOI: 10.1016/j.cell.2018.02.001

Erratum in

Mapping the Mouse Cell Atlas by Microwell-Seq.
Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G. Han X, et al. Cell. 2018 May 17;173(5):1307. doi: 10.1016/j.cell.2018.05.012. Cell. 2018. PMID: 29775597 No abstract available.

Abstract

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.

Keywords: Microwell-seq; cell type classification; cellular heterogeneity; cross-tissue cellular network; mammalian cell map; mouse cell atlas; scMCA analysis; single cell RNA-seq; single-cell analysis; transcriptome analysis.

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Mapping the Mouse Cell Atlas by Microwell-Seq

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Mapping the Mouse Cell Atlas by Microwell-Seq

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