Mapping the Mouse Cell Atlas by Microwell-Seq

Cell. 2018 Feb 22;172(5):1091-1107.e17. doi: 10.1016/j.cell.2018.02.001.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3T3 Cells
  • Animals
  • Costs and Cost Analysis
  • Female
  • High-Throughput Nucleotide Sequencing / economics
  • Mice
  • Organ Specificity
  • Reproducibility of Results
  • Sequence Analysis, RNA* / economics
  • Single-Cell Analysis* / economics