Investigation Title	Candida glabrata oxidative stress	
Comment[Submitted Name]	Candida glabrata oxidative stress	
Experimental Design	dose_response_design	compound_treatment_design	co-expression_design	in_vitro_design	transcript_identification_design	transcription profiling by array	
Experimental Design Term Source REF		The MGED Ontology	The MGED Ontology			EFO	
Comment[SecondaryAccession]		
Comment[ArrayExpressReleaseDate]	2011-01-01	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressAccession]	E-MEXP-2915	
Comment[MAGETAB TimeStamp_Version]	2010-09-22 14:55:34 Last Changed Rev: 13833	
Experimental Factor Name	COMPOUND	DOSE	GENOTYPE	
Experimental Factor Type	compound	dose	genotype	
Experimental Factor Term Source REF	
Person Last Name	Schuller	
Person First Name	Christoph	
Person Mid Initials	
Person Email	Christoph.Schueller@univie.ac.at	
Person Phone	+43 1 4277 52815	
Person Fax	
Person Address	Department f.r Biochemie, Dr.Bohr-Gasse 9, Vienna, Vienna, A-1030, Austria	
Person Affiliation	University and BioCenter Vienna	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	dye_swap_quality_control	
Quality Control Term Source REF	The MGED Ontology	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2011-01-01	
PubMed ID	
Publication DOI	
Publication Author List	
Publication Title	
Publication Status	
Publication Status Term Source REF	
Experiment Description	Investigating the oxidative stress response: Candida glabrata strains were stressed with hydrogen peroxide and menadione (causing oxygen radicals) to induce the oxidative stress regulon, which is thought to be upregulated during the oxidative burst inside of phagocytic cells.	
Protocol Name	P-MTAB-17100	P-MTAB-17097	P-MTAB-17096	P-MTAB-17099	P-MTAB-17092	P-MTAB-17102	P-MTAB-17101	P-MTAB-17098	P-MTAB-17095	P-MTAB-17093	
Protocol Type	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	pool	grow	labeling	labeling	hybridization	bioassay_data_transformation	
Protocol Description	Cells were grown to OD 1 and harvested.	Candida glabrata cells from stationary overnight cultures were diluted in fresh YPD and grown to log phase (form OD600=0.1 to 1). Freshly prepared Menadione solution was added to a final concentration of 0.1mM. All treatments were done at 30°C for 20 minutes. Untreated and treated cells were then harvested by centrifugation at 4°C (2 minutes, 4000g). Cell pellets were washed once with ice cold water, harvested as before and immediately frozen at -20°C.	Cells grown in liquid culture in early logarithmic phase (OD =1). Cultures were treated with 0.4mM H2O2 and incubation was continued at 30° for 20 minutes. Treated cells were harvested at 4° for 2 minutes at 4000g. Cell pellets were washed once with ice cold water, harvested at 4° for 2 minutes at 4000g and immediately frozen at -20°C.	Cells were grown over night diluted to OD600=0.1 in fresh medium, grown to OD600 of 1 and treated as described. Cells were harvested by centrifugation and frozen immediately. For each RNA extraction 25ml of yeast cells were collected. Frozen pellets were resuspended in RNA isolation buffer (50mM Tris pH7.5 / 5mM EDTA / 5% SDS / 130mM NaCl), 200µl PCI solution (Roth) and glass beads (2/3 of total volume) were added and total RNA was extracted using FastPrep (2 x 12’’, speed 6, Thermo Savant).(Parameters: Extracted product = total_RNA, Amplification = none)	RNA was hydrolysed in 50mM NaOH at 65°C for 20 minutes, the solution was neutralized with acetic acid. cDNA was purified using a GFX purification kit (GE Healthcare). Labelled cDNAs were concentrated via SpeedVac to about 5-7µl each and pooled.	Candida glabrata from stationary overnight cultures were diluted in fresh YPD medium to A600 of 0.1 and grown until an A600 of 1 to 1.1 was reached. Temperature 30°, Volume 50ml, 190rpm (Parameters: time unit = seconds, temperature unit = C, media = YPD)	Labeling protocol description- Labeling protocol description: Protocol from: Microarray Centre Clinical Genomics Centre University Health Network 200 Elizabeth Street MBRC 5R414 Toronto, Ontario, M5G 1L7 Reaction volume is 40 µl. Combine the following on ice: 8.0 µL 5X First Strand reaction buffer (Superscript II, Invitrogen) 1.5 µL AncT mRNA primer (5’-T20VN, 100 pmol/µl) 3.0 µL dNTP (-dCTP) (6.67 mM each of dATP, dGTP, dTTP) 1.0 µL 2 mM dCTP 1.0 µL 1 mM Cyanine 5-dCTP (NEN) 4.0 µL 0.1 M DTT 0.1 – 20 µg RNA (0.1-0.5 µg mRNA or 10-20 µg total RNA) to 40 µL dH20 Incubate the labeling reaction at 65°C for 5 minutes, then at 42°C for 5 minutes. Add 2µL of reverse transcriptase (Superscript III, Invitrogen). Incubate at 42 °C for 2 to 3 hours. Add 4 µL of 50 mM EDTA (pH 8.0), and 2 µL of 10 N NaOH. Incubate at 65°C for 20 minutes. Add 4 µL of 5M acetic acid. cDNA was purified using a GFX purification kit (GE Healthcare). Labelled cDNAs were concentrated in a speed vac to 5µl.(Parameters: Mass unit = Micro gram, Amplification = none)	Labeling protocol description- Protocol from: Microarray Centre Clinical Genomics Centre University Health Network 200 Elizabeth Street MBRC 5R414 Toronto, Ontario, M5G 1L7 Reaction volume is 40 µl. Combine the following on ice: 8.0 µL 5X First Strand reaction buffer (Superscript II, Invitrogen) 1.5 µL AncT mRNA primer (5’-T20VN, 100 pmol/µl) 3.0 µL dNTP (-dCTP) (6.67 mM each of dATP, dGTP, dTTP) 1.0 µL 2 mM dCTP 1.0 µL 1 mM Cyanine 3-dCTP (NEN) 4.0 µL 0.1 M DTT 0.1 – 20 µg RNA (0.1-0.5 µg mRNA or 10-20 µg total RNA) to 40 µL dH20 Incubate the labeling reaction at 65°C for 5 minutes, then at 42°C for 5 minutes. Add 2µL of reverse transcriptase (Superscript III, Invitrogen). Incubate at 42 °C for 2 to 3 hours. Add 4 µL of 50 mM EDTA (pH 8.0), and 2 µL of 10 N NaOH. Incubate at 65°C for 20 minutes. Add 4 µL of 5M acetic acid. cDNA was purified using a GFX purification kit (GE Healthcare). Labelled cDNAs were concentrated in a speed vac to 5µl.(Parameters: Mass unit = Micro gram, Amplification = none)	To each 100 µL of DIG Easy Hyb solution (Roche), add 75µg sonicated salmon sperm DNA (Sigma). Incubate the mixture at 65°C for 2 minutes and cool to room temperature. Mix the hyb solution with the labeled-cDNA, incubate at 65°C for 2 minutes, and cool to room temperature. Add Mix to Yeast-array, cover with coverslip. Incubate on a level surface in a 37 °C incubator.(Parameters: Chamber type =  custom, Quantity of label target used = 20, Mass unit = Micro gram, time = 14, Tiny time unit = hours, Volume = 60, Volume unit = Micro litre, temperature = 37)	Normalization protocol description: Normalization protocol description: Features containing control and dubious ORF DNA were excluded. Remaining values were log2-transformed and normalized. Colour inversion experiments were converted. Genes reported have been selected by 2 criteria: >1 present values and a CV <1 for at least one tested condition. Single values have no SD and CV. Mean value, standard deviation and coefficient of variance are included.	
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	The MGED Ontology	The MGED Ontology	The MGED Ontology	
SDRF File	E-MEXP-2915.sdrf.txt	
Term Source Name	The MGED Ontology		ArrayExpress	NCI_thesaurus	The MGED Ontology	EFO	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ebi.ac.uk/arrayexpress	ncithesaurus.obo.alt	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version