Comment[ArrayExpressAccession]	E-GEOD-28741
Public Release Date	2011-04-21
Investigation Title	sncRNAs in E. faecalis V538								
Comment[Submitted Name]	sncRNAs in E. faecalis V538
Experiment Description	Small non coding RNA molecules (sncRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sncRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. Enterococcus faecalis. We characterized 11 sncRNAs by tiling microarray analysis, 5’ and 3’ RACE-PCR, and Northern blot analysis. Six sncRNAs were specifically expressed at exponential phase, two sncRNAs were observed at stationary phase, and three were detected during both phases. This is the first experimental genome-wide identification of sncRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen. Identification of sncRNA candidates transcribed by E. faecalis V583 was undertaken with two samples of cells harvested in mid-log growth phase and  stationary phase after 24h of incubation at 37°C in M17 glucose media.								
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Term Source Name	EFO
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Term Source File	http://bar.ebi.ac.uk:8080/trac/browser/branches/curator/ExperimentalFactorOntology/ExFactorInOWL/currentrelease/eforelease/efo.owl								
Person Last Name	giard	Shioya	Michaux	Kuenne	Hain	Verneuil	Hartsch	Hartke	Giard
Person First Name	jean-christophe	Kouki	Charlotte	Carsten	Torsten	Nicolas	Thomas	Axel	Jean-Christophe
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Person Email	jean-christophe.giard@unicaen.fr								
Person Affiliation	Université de Caen								
Person Phone	33 231 565 410								
Person Fax	33 231 565 311								
Person Address	Université de Caen, esplanade de la paix, Caen, France								
Person Roles	submitter								
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Protocol Name	P-GSE28741-1	P-GSE28741-6	P-GSE28741-3	P-GSE28741-8	P-GSE28741-7	P-GSE28741-2	P-GSE28741-4	P-GSE28741-5	
Protocol Description	ID_REF = <br>VALUE = Quantile normalized data	Production, hybridization and data collecting were carried out by Febit biomed GmbH Company (Heidelberg, Germany).	E. faecalis V583 strain cells were grown at 37ºC in M17 0.5% glucose medium and collected at exponential phase (OD600 = 0.5) and at 24h stationary phase.	Genedata Expressionist software (version 5.3) was used for data processing. Raw data were Quantile normalized applying standard settings  (Averaging: Logarithmic Mean) of Expressionist Analyst.	Production, hybridization and data collecting carried out by Febit biomed GmbH Company (Heidelberg, Germany) on the Febit Geniom platform.	Harvested by centrifugation	For total RNA extraction cells were resuspended into 200 µl of “max bacterial enhancement reagent” (Invitrogen), transferred into micro tubes containing glass beads and 400 µl acid phenol (Ambion, Austin, TX) followed by  mechanically lysation in Mixer Mill 200 (30/s, 30 min, Retsch, Haan, Germany). After centrifugation 10 min at 14,000 g at 4ºC, aqueous phase  transferred to 2 ml tubes containing 1 ml Trizol reagent, 5 min incubation at room temperature (RT). Added 200 µl chloroform, mixed, incubated for 3 min at RT. Centrifugation for 15 min at 12,000 g at 4ºC; aqueous phase transferred into 2 ml tubes containing 200 µl chloroform, mixed gently and centrifuged again. RNAs contained in the Aqueous phase with RNAs precipitated by addition of 500 µl isopropanol, incubated for 10 min at RT. After centrifugation, RNA pellets washed with 75% ethanol, dried at RT. RNA pellets resuspended in DEPC-treated pure water. To enrich sncRNAs, 10µg RNA fractionated using flashPAGE Fractionator (Applied Biosystems, Foster City, CA).	Fractionated RNA labelled using mirVana labelling kit (Applied Biosystems) hybridized onto the tiling array.	
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Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling	
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Experimental Factor Name	PHASE								
Experimental Factor Type	phase								
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Comment[SecondaryAccession]	GSE28741								
Comment[GEOLastUpdateDate]	2011-04-21
Comment[AEExperimentType]	transcription profiling by array								
Comment[GEOReleaseDate]	2011-04-20
Comment[ArrayExpressSubmissionDate]	2011-04-19
SDRF File	E-GEOD-28741.sdrf.txt