Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells

Abstract Dual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcrip...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Regan J. Hayward, Michael S. Humphrys, Wilhelmina M. Huston, Garry S. A. Myers
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fe8a5218d62e4a1f995962750e59e982
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:fe8a5218d62e4a1f995962750e59e982
record_format	dspace
spelling	oai:doaj.org-article:fe8a5218d62e4a1f995962750e59e9822021-12-02T16:49:46ZDual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells10.1038/s41598-021-89921-x2045-2322https://doaj.org/article/fe8a5218d62e4a1f995962750e59e9822021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-89921-xhttps://doaj.org/toc/2045-2322Abstract Dual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 h), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host–pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.Regan J. HaywardMichael S. HumphrysWilhelmina M. HustonGarry S. A. MyersNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Regan J. Hayward Michael S. Humphrys Wilhelmina M. Huston Garry S. A. Myers Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
description	Abstract Dual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 h), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host–pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.
format	article
author	Regan J. Hayward Michael S. Humphrys Wilhelmina M. Huston Garry S. A. Myers
author_facet	Regan J. Hayward Michael S. Humphrys Wilhelmina M. Huston Garry S. A. Myers
author_sort	Regan J. Hayward
title	Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
title_short	Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
title_full	Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
title_fullStr	Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
title_full_unstemmed	Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells
title_sort	dual rna-seq analysis of in vitro infection multiplicity and rna depletion methods in chlamydia-infected epithelial cells
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fe8a5218d62e4a1f995962750e59e982
work_keys_str_mv	AT reganjhayward dualrnaseqanalysisofinvitroinfectionmultiplicityandrnadepletionmethodsinchlamydiainfectedepithelialcells AT michaelshumphrys dualrnaseqanalysisofinvitroinfectionmultiplicityandrnadepletionmethodsinchlamydiainfectedepithelialcells AT wilhelminamhuston dualrnaseqanalysisofinvitroinfectionmultiplicityandrnadepletionmethodsinchlamydiainfectedepithelialcells AT garrysamyers dualrnaseqanalysisofinvitroinfectionmultiplicityandrnadepletionmethodsinchlamydiainfectedepithelialcells
_version_	1718383253440692224

Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells

Ejemplares similares