Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

TLDR

Large‑scale gene expression studies have advanced tissue development knowledge, yet bulk profiling masks cell‑type‑specific expression patterns. The authors introduce a novel strategy to dissect complex tissues at single‑cell resolution. They generated single‑cell RNA‑seq profiles, clustered them into a two‑dimensional cell map that integrates population, subpopulation, and single‑cell levels without relying on known markers. Feasibility was shown by profiling 85 single cells of two distinct types, and the method is expected to enable unbiased discovery of natural cell types in development, physiology, and disease.

Abstract

Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constituent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data were projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves—all without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the transcriptomes of 85 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology, and disease.