Investigation Title	A compendium of antibiotic-induced transcription profiles reveals broad regulation of P. multocida virulence genes	
Comment[Submitted Name]	A compendium of antibiotic-induced transcription profiles reveals broad regulation of P. multocida virulence genes	
Experimental Design	transcription profiling by array	
Experimental Design Term Source REF	EFO	
Comment[AEMIAMESCORE]	3	
Comment[SecondaryAccession]		
Comment[SecondaryAccession]	GSE10051	
Comment[ArrayExpressReleaseDate]	2008-06-01	
Comment[Publication DOI]	10.1016/j.vetmic.2008.03.007	
Comment[ArrayExpressAccession]	E-GEOD-10051	
Comment[MAGETAB TimeStamp_Version]	2010-10-22 19:47:44 Last Changed Rev: 14857	
Experimental Factor Name	TREATMENT	
Experimental Factor Type	Treatment	
Experimental Factor Term Source REF	
Person Last Name	Selzer	Spehr	Duszenko	Melnikow	Schoenfeld	Warrass	Gunkel	Ullrich	
Person First Name	Paul	Volker	Michael	Elena	Caroline	Ralf	Nikolas	Heinz	
Person Mid Initials	M							J	
Person Email				Elena.Melnikow@intervet.com	
Person Phone				+49 (6130) 948 339	
Person Fax				+49 (6130) 948 517	
Person Address				Drug Discovery, Intervet Innovation GmbH, Zur Propstei, Schwabenheim, Germany	
Person Affiliation				Intervet Innovation GmbH	
Person Roles				submitter	
Person Roles Term Source REF				The MGED Ontology	
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2008-06-01	
PubMed ID	18501535	
Publication DOI	18501535	
Publication Author List	Melnikow E, Schoenfeld C, Spehr V, Warrass R, Gunkel N, Duszenko M, Selzer PM, Ullrich HJ	
Publication Title	A compendium of antibiotic-induced transcription profiles reveals broad regulation of Pasteurella multocida virulence genes.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Treatment of bacteria with antibiotics at or close to the inhibitory concentration leads to specific transcriptional responses often affecting target genes and targets pathways. A dataset of transcriptional profiles (compendium) induced by antibiotics with known mode-of-action (MoA) can be used to gain information on the putative MoA of novel substances with unknown MoAs. We used a Pasteurella multocida microarray to generate a compendium of transcriptional profiles and to obtain information on the putative MoA of a novel antibiotic compound. We also show a strong impact of the bacteriostatic antibiotics on P. multocida virulence gene transcription. Keywords: antibiotica treatment, time course Midlog-grown cultures of P. multocida were treated for 10 or 30 min with 8 different antibiotics and one novel compound (thiazin) at minimal inhibitory concentrations (MICs) and were harvested. Control bacteria were not-treated and harvested at approximately the same optical density an OD578 of ~ 0.5. Total RNA was extracted from these samples and labelled with biotin. P. multocida whole genome transcriptional profiling was performed by hybridization on the custom-made Affymetrix microarray according to the manufacturer’s instructions. The experiments were done in triplicates.	
Protocol Name	P-GSE10051-3	P-GSE10051-4	P-GSE10051-2	P-GSE10051-5	P-GSE10051-6	P-GSE10051-7	P-GSE10051-8	P-GSE10051-1	
Protocol Type	grow	nucleic_acid_extraction	specified_biomaterial_action	labeling	hybridization	image_aquisition	feature_extraction	bioassay_data_transformation	
Protocol Description	P. multocida was cultured in 40 ml BHI medium for 3h at 37°C by 200 rpm.	Extraction of total RNA was performed usind RNAeasy Midi Kit (Qiagen) according to the manufacturer's instructions.	1xMIC of each antibiotic was added to the P. multocida culture for 10 min and 30 min at an optical density of approximately 0.5. The bacteria were harvested by centifugation for 5 min at 5000 rpm at 4 °C.	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Following fragmentation, 2.5 ug of cDNA were hybridized for 16 hr at 45°C on a custom-made GeneChip Genome Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	GeneChips were scanned using the Agilent GeneArray Scanner.	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.	ID_REF = <br>VALUE = MAS5.0 signal intensity<br>ABS_CALL = <br>DETECTION P-VALUE =	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology		The MGED Ontology	The MGED Ontology	
SDRF File	E-GEOD-10051.sdrf.txt	
Term Source Name	The MGED Ontology		ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version