Comment[ArrayExpressAccession]	E-GEOD-51563
MAGE-TAB Version	1.1					
Public Release Date	2013-10-23
Investigation Title	Gene expression profile of a S. cerevisiae strain deleted in CSN5/RRI1 gene (systematic name YDL216C)					
Comment[Submitted Name]	Gene expression profile of a S. cerevisiae strain deleted in CSN5/RRI1 gene (systematic name YDL216C)
Experiment Description	The COP9 signalosome (CSN) is a highly conserved eukaryotic protein complex which regulates the Cullin-RING family of ubiquitin ligases and carries out a deneddylase activity that resides in subunit 5 (CSN5). The budding yeast CSN is biochemically active and deletion mutants of each of its subunits exhibit deficiency in deneddylation of cullins, although the biological context of this activity is still unknown in this organism. To further characterize CSN function in budding yeast, we present here a transcriptomic analysis of a S. cerevisiae strain deleted in CSN5/RRI1 gene (hereafter referred to as CSN5), coding for the only canonical subunit of the complex. We show that Csn5 is involved in the modulation of the genes controlling aminoacid and lipid metabolism, and especially ergosterol biosynthesis. These alterations in gene expression correlate with the lower ergosterol levels and increased intracellular zinc content which we observed in csn5 null mutant cells. Two biological replicates, csn5 deleted strain vs. isogenic wild-type strain W303					
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	Licursi	Licursi	Salvi	De Cesare	Negri	
Person First Name	Valerio	Valerio	Chiara	Virginia	Rodolfo	
Person Email	valerio.licursi@uniroma1.it					
Person Affiliation	UniversitM-CM-  di Roma "Sapienza"					
Person Address	Biologia e Biotecnologie "C. Darwin", UniversitM-CM-  di Roma "Sapienza", via dei Sardi, 70, Roma, Italy					
Person Roles	submitter					
Protocol Name	P-GSE51563-1	P-GSE51563-4	P-GSE51563-5	P-GSE51563-2	P-GSE51563-3	P-GSE51563-6
Protocol Description	LOWESS normalized, median background intensity subtraction, with Goulphar script running on R software. We filtered the data to exclude artifacts, saturated spots, and low signal spots ID_REF =  VALUE = Normalized log2 ratio (HyPer5/Cy3) representing csn5 mutant cells/WT cells	20 M-NM-<g of total RNA extracted from cell culture as described above was mixed with 2 M-NM-<g of 16mers oligo dT and incubated at 70 M-0C for 10 min. cDNA was synthesized in a final volume of 40 M-NM-<l with 25 mM each of dATP, dCTP and dGTP, 15 mM of dTTP, 10 mM of aminoallyl-dUTP, 10 mM DTT and 400U of SuperScript III reverse transcriptase (Life Technologies, Carlsbad, California) in 1M-CM-^W reaction buffer. The samples were incubated for 2 hours at 42M-0C. cDNA was labeled with Cy3 and HyPer5 Post-Labeling Reactive Dye (GE Healthcare cod. 28-9224-19, Little Chalfont, United Kingdom) according to manufacturerM-bM-^@M-^Ys protocol.	cDNA Microarray Yeast 6.4k ver. 7 purchased from UHN Microarray Centre were pre-hybridized at 42 M-0C for at least 45 min in a solution containing, 5M-CM-^W saline sodium citrate buffer (SSC), 0.1% SDS and 0.1% BSA. The labeled cDNAs (Cy3 sample and HyPer5 sample mixed) were added to an equal volume of hybridization buffer containing 50% formamide, 10M-CM-^W SSC, 0.2% SDS pre-heated at 70M-0C for 3 min. Hybridization was carried out for 16 h at 42 M-0C and unbound DNA was washed off using 3 steps with solutions containing: 1) 1XSSC 0.2% SDS pre-heated at 42 M-0C; 2) 0.1X SSC 0.2 % SDS at room temperature; 3) two times 0.1X SSC at room temperature	strains were grown in YPD medium at 30M-0C	Total RNA was extracted from S. cerevisiae cell cultures at 1 OD600/mL with hot acid phenol extraction method	Scanned on an PerkinElmer ScanArray Lite scanner. Images were quantified using ScanArray Express and GenePix Pro 6.1 software
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	STRAIN OR LINE					
Experimental Factor Type	strain or line					
Comment[SecondaryAccession]	GSE51563					
Comment[GEOReleaseDate]	2013-10-23					
Comment[ArrayExpressSubmissionDate]	2013-10-22					
Comment[GEOLastUpdateDate]	2013-10-23					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-51563.sdrf.txt