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A sample-to-sequence protocol for genus targeted transcriptomic profiling : application to marine Synechococcus

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Pitt, Frances Diana, Millard, Andrew D., Ostrowski, Martin, Dervish, Suat, Mazard, Sophie, Paulsen, Ian T., Zubkov, Mikhail V. and Scanlan, David J. (2016) A sample-to-sequence protocol for genus targeted transcriptomic profiling : application to marine Synechococcus. Frontiers in Microbiology, 7 . 1592. doi:10.3389/fmicb.2016.01592 ISSN 1664-302X.

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Official URL: http://dx.doi.org/10.3389/fmicb.2016.01592

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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.

Item Type: Journal Article
Subjects: Q Science > QH Natural history
Q Science > QR Microbiology
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Marine microbiology, Flow cytometry
Journal or Publication Title: Frontiers in Microbiology
Publisher: Frontiers Research Foundation
ISSN: 1664-302X
Official Date: 14 October 2016
Dates:
DateEvent
14 October 2016Published
22 September 2016Accepted
8 July 2016Submitted
Volume: 7
Article Number: 1592
DOI: 10.3389/fmicb.2016.01592
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 18 October 2016
Date of first compliant Open Access: 18 October 2016
Funder: Natural Environment Research Council (Great Britain) (NERC)
Grant number: NE/I00985X/1
Adapted As: R

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