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Genome Biol. 2017 Oct 27;18(1):200. doi: 10.1186/s13059-017-1340-x.

scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing.

Author information

1
Institute for Computational Medicine and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.
2
Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel.
3
Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
4
Present address: Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
5
Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.
6
Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
7
Institute for Computational Medicine and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA. Itai.Yanai@nyumc.org.

Abstract

The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously captures both host and pathogen transcriptomes. We use it to study the process of infection of individual mouse macrophages with the intracellular pathogen Salmonella typhimurium. Among the infected macrophages, we find three subpopulations and we show evidence for a linear progression through these subpopulations, supporting a model in which these three states correspond to consecutive stages of infection.

PMID:
29073931
PMCID:
PMC5658913
DOI:
10.1186/s13059-017-1340-x
[Indexed for MEDLINE]
Free PMC Article

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