Comment[ArrayExpressAccession] E-GEOD-52378 MAGE-TAB Version 1.1 Public Release Date 2014-07-18 Investigation Title Comparison between all runs of a serial repitching in brewery A Comment[Submitted Name] Comparison between all runs of a serial repitching in brewery A Experiment Description The aim of this study was to identify differently expressed genes between all 6 runs of brewery A. A run describes the industrial fermentation of brewery wort. By the end of fermentation the yeast slurry is cropped. These cells are reused for inoculation of another cylindro-conical vessel (CCVs). Results from two loops of two different breweries are summarized in this study. The samples were taken from two serial repitchings of a two breweries. 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 Patrick Fetzer Stahl Scheper Harms Müller Person First Name Frank Franziska Lindner 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-GSE52378-1 P-GSE52378-5 P-GSE52378-6 P-GSE52378-2 P-GSE52378-3 P-GSE52378-4 P-GSE52378-7 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. successive runs varied from 1 to 6 Beer brewery process, industrial serial repitching 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 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 RUN POOL Experimental Factor Type run pool Publication Title Analysis of aging in lager brewing yeast during serial repitching. Publication Author List B�hligen F, Lindner P, Fetzer I, Stahl F, Scheper T, Harms H, M�ller S PubMed ID 25026460 Publication DOI 10.1016/j.jbiotec.2014.07.002 Comment[SecondaryAccession] GSE52378 Comment[GEOReleaseDate] 2014-07-18 Comment[ArrayExpressSubmissionDate] 2013-11-14 Comment[GEOLastUpdateDate] 2014-07-20 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-52378.sdrf.txt