Comment[ArrayExpressAccession]	E-GEOD-48956
MAGE-TAB Version	1.1					
Public Release Date	2013-07-18
Investigation Title	Wild-type yeast vs Desl1/Desl2 mutant strain					
Comment[Submitted Name]	Wild-type yeast vs Desl1/Desl2 mutant strain
Experiment Description	Transcript profiling of the double  Desl1/Desl2 mutant versus wild-type growning at log phase in rich meda. During its natural life cycle, budding yeast (Saccharomyces cerevisiae) has to adapt to drastically changing environments, but how environmental sensing pathways are linked to adaptive gene expression changes remains incompletely understood. Here, we describe two closely related yeast hEST1A-B (SMG5-6)-like proteins termed Esl1 and Esl2 that contain a 14-3-3-like domain and a putative PIN ribonuclease domain.  We found that, unlike their metazoan orthologues, Esl1/2 were not involved in nonsense-mediated mRNA decay or telomere maintenance pathways. However, in genome-wide expression array analyses, absence of Esl1 and Esl2 led to >2-fold deregulation of ~50 transcripts, most of which were expressed inversely to the appropriate metabolic response to environmental nutrient supply; for instance, normally glucose-repressed genes were de-repressed in esl1M-NM-^T esl2M-NM-^T double mutants during growth in a high-glucose environment. Likewise, in a genome-wide synthetic gene array screen, esl1M-NM-^T esl2M-NM-^T double mutants were synthetic sick with null mutations for Rim8 and Dfg16, which form the environmental sensing complex of the Rim101 pH response gene expression pathway. Overall, these results suggest that Esl1 and Esl2 contribute to the regulation of adaptive gene expression responses of environmental sensing pathways. 3 biological replicates of each strain (wt & mutant) were analysed by competitive hybridisation.  One dye-swap exeperiment was additionally performed.					
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	Beilharz	Beilharz	Heierhorst			
Person First Name	traude	Traude	JM-CM-6rg			
Person Mid Initials	Helene					
Person Email	traude.beilharz@monash.edu					
Person Affiliation	Monash University					
Person Phone	++61 3 99029183					
Person Address	Biochemistry & Molecular Biology, Monash University, Monash University, Clayton, Victoria, Australia					
Person Roles	submitter					
Protocol Name	P-GSE48956-1	P-GSE48956-4	P-GSE48956-5	P-GSE48956-2	P-GSE48956-3	P-GSE48956-6
Protocol Description	Lowess normalisation (gene-spring) ID_REF =  VALUE = normalized log2 ratio Desl1/ Desl2 LogRatioError = 	500ng of total RNA was labelled using T7 polymerase (Agilent Quick Amp Two Colour Labeling kit protocol version 5.7, March 2008). Agilent RNA spikes were included to monitor labelling	300ng of Cy3 labelled cRNA and 300ng of Cy5 labelled cRNA were co-hybridised to Agilent 8 x 15K custom arrays. Arrays were hybridised at 65C for 17 hours. Arrays were washed according to manufacture's instructions.	Experiments were carried out in YPD medium (1% yeast extract, 2% peptone, 2% glucose) at 30M-0C. Yeast cells were harvested during log phase	RNA was extracted using the hot-phenol method	Arrays were scanned on an Agilent G2565CA Scanner at a 5um resolution. Data was extracted from the image files using Agilent Feature Extraction Software 9.5.3 using protocol GE2 QCMT Feb07
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GENOTYPE					
Experimental Factor Type	genotype					
Comment[SecondaryAccession]	GSE48956					
Comment[GEOReleaseDate]	2013-07-18					
Comment[ArrayExpressSubmissionDate]	2013-07-17					
Comment[GEOLastUpdateDate]	2013-07-20					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-48956.sdrf.txt