Investigation Title	Transcription profiling of S. cerevisiae temperature sensitive eIF5A mutant shows accumulation of transcripts targeted to the Nonsense Mediated Decay pathway	
Comment[Submitted Name]	Temperature sensitive eIF5A mutant shows accumulation of transcripts targeted to the Nonsense Mediated Decay pathway	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressReleaseDate]	2008-06-13	
Comment[SecondaryAccession]	GSE5290	
Comment[ArrayExpressAccession]	E-GEOD-5290	
Comment[MAGETAB TimeStamp_Version]	2010-08-06 15:55:46 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Schrader	
Person First Name	Rainer	
Person Mid Initials	
Person Email	schrader@biochem.mpg.de	
Person Phone	
Person Fax	
Person Address	Prof. Lottspeich, Proteinanalytics, Max-Planck-Institut for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany	
Person Affiliation	Max-Planck-Institut for Biochemistry	
Person Roles	submitter	
Person Roles Term Source REF		
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2008-06-13	
PubMed ID	16987817	
Publication DOI	16987817	
Publication Author List	Rainer Schrader, Craig Young, Detlef Kozian, Reinhard Hoffmann, Friedrich Lottspeich	
Publication Title	Temperature-sensitive eIF5A mutant accumulates transcripts targeted to the nonsense-mediated decay pathway.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	The highly conserved protein eIF5A found in archaea and all eucaryotes uniquely contains the posttranslationally formed amino acid hypusine. Despite being essential the functions of this protein and its modification remain unclear. To gain more insight into these functions temperature sensitive mutants of the human EIF5A1 were characterized in the yeast Saccharomyces cerevisiae. EIF5A is proposed to be an RNA binding protein. Thus, we used microarrays to identify special RNA subsets of up- and downregulation that are influenced by a limited eIF5A function in strains expressing a point mutated form of eIF5A. Experiment Overall Design: Wild-type and mutant yeast strains were grown at 25°C following total RNA extraction and hybridization on Affymetrix microarrays. cRNA probes derived from RNA preparations were obtained from four isogenic, haploid strains from each of the wild-type and the mutant. This ensured that changes in the transcriptome could be attributed to the impaired HYP function of V81G rather than to differences in the genetic background. Therefore, two groups of 4 datasets (per wild-type W303-WT and mutant W303-V81G strains) were generated after hybridisation to the micro arrays.	
Protocol Name	P-G5290-1	P-G5290-3	P-G5290-2	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6	
Protocol Type	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	Strains were cultured at 25°C (permissive temperature) until reaching the early lorarithmic phase of growth. 2*10^8 cells of each strain were harvested by centrifugation and briefly rinsed with 1 volume of water (4°C), cells were either frozen at -80°C or directly subjected to the isolation of total RNA.	Hot phenol extraction of total RNA was performed according to the literature.	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Title: Affymetrix Generic Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software				MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF				mo	
SDRF File	E-GEOD-5290.sdrf.txt	
Term Source Name	The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	mo	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version