Comment[ArrayExpressAccession]	E-GEOD-42994
MAGE-TAB Version	1.1					
Public Release Date	2012-12-19
Investigation Title	V. salmonicida wild type strain LFI1238 and isogenic DlitR mutant grown in suspension in SWT medium					
Comment[Submitted Name]	V. salmonicida wild type strain LFI1238 and isogenic DlitR mutant grown in suspension in SWT medium
Experiment Description	Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12M-BM-:C. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR deletion mutant were grown in suspension in SWT medium at 8M-BM-0C  with  200 rpm and harvested at OD=0.8. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.					
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl				
Person Last Name	Robertsen	Hansen	Ronessen	Bjelland	Robertsen	Willassen
Person First Name	Espen	Hilde	Maria	Ane-Mohn	Espen-Mikal	Nils-Peder
Person Mid Initials	Mikal					
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	University of Tromsoe					
Person Address	University of Tromsoe, Breivika, Tromsoe, Norway					
Person Roles	submitter					
Protocol Name	P-GSE42994-1	P-GSE42994-5	P-GSE42994-4	P-GSE42994-2	P-GSE42994-3	P-GSE42994-6
Protocol Description	ID_REF =  VALUE = Normalized log2 ratio wild type/mutant	Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.) Images were quantified using the GenePix v6.1 software	Samples were hybridised to the microarrays at 42M-:C on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in2M-CM-^WSSC/0.1% SDS for 5 min at 42M-:C, then once in 0.1M-CM-^WSSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1M-CM-^WSSC for 1 min at room temperature.	Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)	cDNA was generated and labelled with Cy3 and Cy5 by using 15 M-5g RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDyeM-bM-^DM-" Post-Labeling Reactive Dye Pack (GE Healthcare).	The quantified signals were background corrected using M-bM-^@M-^\normexpM-bM-^@M-^] (LIMMA) with offset value 50 and normalized using print-tip loess and between-array quantile normalization. The expression data were analysed using the LIMMA framework in Bioconductor (http://www.bioconductor.org).
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction
Experimental Factor Name	VARIATION					
Experimental Factor Type	variation					
Comment[SecondaryAccession]	GSE42994					
Comment[GEOReleaseDate]	2012-12-19					
Comment[ArrayExpressSubmissionDate]	2012-12-18					
Comment[GEOLastUpdateDate]	2012-12-20					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-42994.sdrf.txt