Mapping the Mouse Cell Atlas by Microwell-Seq

Highlights

• Development of Microwell-seq, a high-throughput and low-cost scRNA-seq platform

• Construction of a single-cell mouse cell atlas (scMCA) covering major cell types

• Characterization of cellular heterogeneity with minimal batch effect

• Characterization of cross-tissue cellular network at the single-cell level

Summary

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.