Mapping the Mouse Cell Atlas by Microwell-Seq

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

View graph of relations


  • 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
  • Jin Xie
  • Qun Fang
  • Yibin Wang
  • Rui Yue
  • Tiefeng Li
  • He Huang
  • Stuart H. Orkin
  • Guo-Cheng Yuan
  • Ming Chen
  • Guoji Guo


Original languageEnglish
Pages (from-to)1091-1107
Journal / PublicationCell
Issue number5
Online published22 Feb 2018
Publication statusPublished - 22 Feb 2018
Externally publishedYes


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.

Research Area(s)

  • single cell RNA-seq, mouse cell atlas, Microwell-seq, scMCA analysis, mammalian cell map, cellular heterogeneity, cross-tissue cellular network, cell type classification, single-cell analysis

Citation Format(s)

Mapping the Mouse Cell Atlas by Microwell-Seq. / Han, Xiaoping; Wang, Renying; Zhou, Yincong; Fei, Lijiang; Sun, Huiyu; Lai, Shujing; Saadatpour, Assieh; Zhou, Ziming; Chen, Haide; Ye, Fang; Huang, Daosheng; Xu, Yang; Huang, Wentao; Jiang, Mengmeng; Jiang, Xinyi; Mao, Jie; Chen, Yao; Lu, Chenyu; Xie, Jin; Fang, Qun; Wang, Yibin; Yue, Rui; Li, Tiefeng; Huang, He; Orkin, Stuart H.; Yuan, Guo-Cheng; Chen, Ming; Guo, Guoji.

In: Cell, Vol. 172, No. 5, 22.02.2018, p. 1091-1107.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review