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

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 infectio...

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Autores principales: Avital, Gal, Avraham, Roi, Fan, Amy, Hashimshony, Tamar, Hung, Deborah T., Yanai, Itai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658913/
https://www.ncbi.nlm.nih.gov/pubmed/29073931
http://dx.doi.org/10.1186/s13059-017-1340-x
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author Avital, Gal
Avraham, Roi
Fan, Amy
Hashimshony, Tamar
Hung, Deborah T.
Yanai, Itai
author_facet Avital, Gal
Avraham, Roi
Fan, Amy
Hashimshony, Tamar
Hung, Deborah T.
Yanai, Itai
author_sort Avital, Gal
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1340-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-56589132017-10-31 scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing Avital, Gal Avraham, Roi Fan, Amy Hashimshony, Tamar Hung, Deborah T. Yanai, Itai Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1340-x) contains supplementary material, which is available to authorized users. BioMed Central 2017-10-27 /pmc/articles/PMC5658913/ /pubmed/29073931 http://dx.doi.org/10.1186/s13059-017-1340-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Avital, Gal
Avraham, Roi
Fan, Amy
Hashimshony, Tamar
Hung, Deborah T.
Yanai, Itai
scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing
title scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing
title_full scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing
title_fullStr scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing
title_full_unstemmed scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing
title_short scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing
title_sort scdual-seq: mapping the gene regulatory program of salmonella infection by host and pathogen single-cell rna-sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658913/
https://www.ncbi.nlm.nih.gov/pubmed/29073931
http://dx.doi.org/10.1186/s13059-017-1340-x
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