Mapping the Mouse Cell Atlas by Microwell-Seq

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, researchers at Zhejiang University School of Medicine have developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, they 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). They reveal a single-cell hierarchy for many tissues that have not been well characterized previously. The researchers 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.


Availability – the mouse cell atlas website at

Han X et al. (2018) Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172(5):1091-1107.[article]

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