Comment[ArrayExpressAccession]	E-GEOD-45948
MAGE-TAB Version	1.1							
Public Release Date	2013-10-02
Investigation Title	Comparison between stationary phase S. cerevisiae H155 cells, exponential phase cells and stressed cells							
Comment[Submitted Name]	Comparison between stationary phase S. cerevisiae H155 cells, exponential phase cells and stressed cells
Experiment Description	The sensibility of the used low-density arrays was tested by applying the lab strain S. cerevisiae H155. Important abiotic parameters were tested as they were introduced as elevated osmotic, pH or ethanol stress to the cells. Results from one loop including samples from cells in five different conditions are summarized in this study. Microarrays were hybridized in a loop approach.							
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	Stahl	Bühligen	Rüdinger	Fetzer	Stahl	Scheper	Harms	Müller
Person First Name	Frank	Franziska	Philipp	Ingo	Frank	Thomas	Hauke	Susann
Person Email	stahl@iftc.uni-hannover.de							
Person Affiliation	Universität Hannover							
Person Phone	0511-7622968							
Person Address	Institut für Technische Chemie, Universität Hannover, Callinstr. 3, Hannover, Germany							
Person Roles	submitter							
Protocol Name	P-GSE45948-1	P-GSE45948-5	P-GSE45948-6	P-GSE45948-2	P-GSE45948-3	P-GSE45948-4	P-GSE45948-7	
Protocol Description	Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes. ID_REF =  VALUE = The values are normalized log2 Cy5/Cy3 F635 Median =  B635 =  F532 Median =  B532 =  Flags = 	The indirect labeling by the tyramide-signal-amplification method was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP/ Biotin-dCTP.	The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s recommendations.	Comparison between unstressed and stressed cells	S. cerevisiae H155 was batch-cultured in 100 ml Erlenmeyer flasks at 30°C, 150 rpm in 50 ml Schatzmann medium (pH 5.4).	The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied. The RNA of the 3 parallels of each condition with S. cerevisiae H155 was pooled in an equimolar manner.	The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.	
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol	
Experimental Factor Name	STRESS							
Experimental Factor Type	stress							
Publication Title	Sustainability of industrial yeast serial repitching practice studied by gene expression and correlation analysis.							
Publication Author List	B�hligen F, R�dinger P, Fetzer I, Stahl F, Scheper T, Harms H, M�ller S							
PubMed ID	24060829							
Publication DOI	10.1016/j.jbiotec.2013.09.008							
Comment[SecondaryAccession]	GSE45948							
Comment[GEOReleaseDate]	2013-10-02							
Comment[ArrayExpressSubmissionDate]	2013-04-10							
Comment[GEOLastUpdateDate]	2013-10-03							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-45948.sdrf.txt