title: Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
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.
authors.affiliation: Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Saiful
authors.initials: S
authors.lastname: Islam
authors.forename: Una
authors.initials: U
authors.lastname: Kjällquist
authors.forename: Annalena
authors.initials: A
authors.lastname: Moliner
authors.forename: Pawel
authors.initials: P
authors.lastname: Zajac
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Peter
authors.initials: P
authors.lastname: Lönnerberg
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000235:genetics; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D016678:Genome; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger