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Series GSE74507

Query DataSets for GSE74507

Status

Public on Feb 09, 2017

Title

The dynamic transcriptome of natural competence in Streptococcus suis

Organism

Streptococcus suis

Experiment type

Expression profiling by array

Summary

Streptococcus suis is a major pig pathogen as well as an emerging zoonotic pathogen. In a previous study (Zaccaria et al. Plos One DOI: 10.1371/journal.pone.0099394) we identified the natural pheromone-induced competence system of S. suis. To identify the mechanisms enabling competence, gene expression analysis of bacteria induced or not for competence, and in presence or absence of exogenous DNA, was assessed at 5, 15 and 45 minutes after pheromone addition. The transcriptomes showed how competence was induced and eventually shut down, and which metabolic pathways were repressed or induced when competence was active or shut down.

Overall design

In this experiment, S. suis bacteria were grown in THB, exposed to three different conditions and RNA was extracted at three different timepoints: 5, 15 and 45 minutes after the zer timepoint which was essentially the induction of competence. The three conditions were: bacteria were (i) either growing in THB with no other additions, or (ii) grown in THB in the presence of competence-inducing pheromone but without exogenously added DNA, or (iii) grown in presence of pheromone and exogenous DNA. RNA samples extracted from the bacteria were hybridised once per array.
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The samples above refer to the raw array data shown in the Matrix worksheet. The corresponding biological comparisons and their statistics are shown in the separate worksheet, Array Results.
The samples are as follows:
Sample 1: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA
Sample 2: suis WT O.D. 0.04 + DNA 15’ (No peptide) VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide (No DNA)
Sample 3: suis WT O.D. 0.04 + DNA 45’ (No peptide) VS suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA
Sample 4: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + DNA 15’ (No peptide)
Sample 5: suis WT O.D. 0.04 + Pep 15’ (no DNA) VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA
Sample 6: suis WT O.D. 0.04 + DNA 15’ (No peptide) VS suis WT O.D. 0.04 + DNA 45’ (No peptide)
Sample 7: suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA
Sample 8: suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA

Contributor(s)

van Baarlen P, Zaccaria E, Wels M

Citation(s)

27149631, 28066332

Submission date

Oct 29, 2015

Last update date

Feb 09, 2017

Contact name

Peter van Baarlen

E-mail(s)

peter.vanbaarlen@wur.nl

Organization name

Wageningen University

Department

Animal Sciences

Lab

Host-Microbe Interactomics

Street address

De Elst 1

City

Wageningen

ZIP/Postal code

6708 WD

Country

Netherlands

Platforms (1)

GPL16024

Agilent SSU 8 x 15K (Feature Number version)

Samples (16)

More...

GSM1921961	Edoardo_251914810017-1_1.txt #1 control
GSM1921962	Edoardo_251914810017-1_1.txt #1 target
GSM1921963	Edoardo_251914810017-1_2.txt #1 control

Relations

BioProject

PRJNA300576

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE74507_RAW.tar	5.8 Mb	(http)(custom)	TAR (of TXT)
GSE74507_array_results.xlsx	1.5 Mb	(ftp)(http)	XLSX
Processed data included within Sample table