A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus.

Pitt, FD; Millard, A; Ostrowski, M; Dervish, S; Mazard, S; Paulsen, IT; Zubkov, MV; Scanlan, DJ

A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus.

Pitt, FD Millard, A Ostrowski, M

Dervish, S Mazard, S Paulsen, IT Zubkov, MV Scanlan, DJ

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Publisher:: FRONTIERS MEDIA SA
Publication Type:: Journal Article
Citation:: Front Microbiol, 2016, 7, (OCT), pp. 1592
Issue Date:: 2016

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Field	Value	Language
dc.contributor.author	Pitt, FD
dc.contributor.author	Millard, A
dc.contributor.author	Ostrowski, M https://orcid.org/0000-0002-4357-3023
dc.contributor.author	Dervish, S
dc.contributor.author	Mazard, S
dc.contributor.author	Paulsen, IT
dc.contributor.author	Zubkov, MV
dc.contributor.author	Scanlan, DJ
dc.date.accessioned	2022-02-23T20:43:55Z
dc.date.available	2016-09-22
dc.date.available	2022-02-23T20:43:55Z
dc.date.issued	2016
dc.identifier.citation	Front Microbiol, 2016, 7, (OCT), pp. 1592
dc.identifier.issn	1664-302X
dc.identifier.issn	1664-302X
dc.identifier.uri	http://hdl.handle.net/10453/154811
dc.description.abstract	Recent studies using whole community metagenomic and metatranscriptomic approaches are revealing important new insights into the functional potential and activity of natural marine microbial communities. Here, we complement these approaches by describing a complete ocean sample-to-sequence protocol, specifically designed to target a single bacterial genus for purposes of both DNA and RNA profiling using fluorescence activated cell sorting (FACS). The importance of defining and understanding the effects of a sampling protocol are critical if we are to gain meaningful data from environmental surveys. Rigorous pipeline trials with a cultured isolate, Synechococcus sp. BL107 demonstrate that water filtration has a well-defined but limited impact on the transcriptomic profile of this organism, whilst sample storage and multiple rounds of cell sorting have almost no effect on the resulting RNA sequence profile. Attractively, the means to replicate the sampling strategy is within the budget and expertise of most researchers.
dc.format	Electronic-eCollection
dc.language	eng
dc.publisher	FRONTIERS MEDIA SA
dc.relation	Natural Environment Research CouncilNE/I00985X/1
dc.relation.ispartof	Front Microbiol
dc.relation.isbasedon	10.3389/fmicb.2016.01592
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0502 Environmental Science and Management, 0503 Soil Sciences, 0605 Microbiology
dc.title	A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus.
dc.type	Journal Article
utslib.citation.volume	7
utslib.location.activity	Switzerland
utslib.for	0502 Environmental Science and Management
utslib.for	0503 Soil Sciences
utslib.for	0605 Microbiology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access	*
dc.date.updated	2022-02-23T20:43:51Z
pubs.issue	OCT
pubs.publication-status	Published online
pubs.volume	7
utslib.citation.issue	OCT

Abstract:

Recent studies using whole community metagenomic and metatranscriptomic approaches are revealing important new insights into the functional potential and activity of natural marine microbial communities. Here, we complement these approaches by describing a complete ocean sample-to-sequence protocol, specifically designed to target a single bacterial genus for purposes of both DNA and RNA profiling using fluorescence activated cell sorting (FACS). The importance of defining and understanding the effects of a sampling protocol are critical if we are to gain meaningful data from environmental surveys. Rigorous pipeline trials with a cultured isolate, Synechococcus sp. BL107 demonstrate that water filtration has a well-defined but limited impact on the transcriptomic profile of this organism, whilst sample storage and multiple rounds of cell sorting have almost no effect on the resulting RNA sequence profile. Attractively, the means to replicate the sampling strategy is within the budget and expertise of most researchers.

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http://hdl.handle.net/10453/154811