title: Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
abstract: In multicellular organisms, biological function emerges when heterogeneous cell types form complex organs. Nevertheless, dissection of tissues into mixtures of cellular subpopulations is currently challenging. We introduce an automated massively parallel single-cell RNA sequencing (RNA-seq) approach for analyzing in vivo transcriptional states in thousands of single cells. Combined with unsupervised classification algorithms, this facilitates ab initio cell-type characterization of splenic tissues. Modeling single-cell transcriptional states in dendritic cells and additional hematopoietic cell types uncovers rich cell-type heterogeneity and gene-modules activity in steady state and after pathogen activation. Cellular diversity is thereby approached through inference of variable and dynamic pathway activity rather than a fixed preprogrammed cell-type hierarchy. These data demonstrate single-cell RNA-seq as an effective tool for comprehensive cellular decomposition of complex tissues.
authors: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
authors: Diego Adhemar
authors: DA
authors: Jaitin
authors: Ephraim
authors: E
authors: Kenigsberg
authors: Hadas
authors: H
authors: Keren-Shaul
authors: Naama
authors: N
authors: Elefant
authors: Franziska
authors: F
authors: Paul
authors: Irina
authors: I
authors: Zaretsky
authors: Alexander
authors: A
authors: Mildner
authors: Nadav
authors: N
authors: Cohen
authors: Steffen
authors: S
authors: Jung
authors: Amos
authors: A
authors: Tanay
authors: Ido
authors: I
authors: Amit
mesh_terms: D000818:Animals; D015415:Biomarkers; D003713:Dendritic Cells / Q000378:metabolism; D005260:Female; D006410:Hematopoiesis / Q000235:genetics; D008810:Mice, Inbred C57BL; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013154:Spleen / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger