Investigation Title	Transcription profiling of yeast grown in media with and without amino acids	
Comment[Submitted Name]	Ernst - S.cerevisiae - Ino4 AA	
Experimental Design	binding_site_identification_design	growth_condition_design	transcription profiling by array	
Experimental Design Term Source REF	The MGED Ontology	mo	EFO	
Comment[ArrayExpressReleaseDate]	2006-11-16	
Comment[AEMIAMESCORE]	5	
Comment[ArrayExpressAccession]	E-MEXP-906	
Comment[MAGETAB TimeStamp_Version]	2010-08-11 16:33:53 Last Changed Rev: 13058	
Experimental Factor Name	growth condition	time	
Experimental Factor Type	growth_condition	time	
Experimental Factor Term Source REF	
Person Last Name	Bar-Joseph	Harbison	Vainas	Simon	Ernst	
Person First Name	Ziv	Christopher	Oded	Itamar	Jason	
Person Mid Initials		T	
Person Email			odedvainas@yahoo.com	
Person Phone			972-2-6757906	
Person Fax	
Person Address			Hadasa Ein Karem Hospital	
Person Affiliation	Carnegie Mellon University	 Institute for Biomedical Research	Molecular Biology	Hebrew University Medical School	Carnegie Mellon University	
Person Roles			submitter	
Person Roles Term Source REF			The MGED Ontology	
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	2006-11-16	
PubMed ID	17224918	
Publication DOI	17224918	
Publication Author List	Jason Ernst; Oded Vainas; Christopher Harbison; Itamar Simon; Ziv Bar-Joseph	
Publication Title	Reconstructing dynamic regulatory maps	
Publication Status	journal_article	
Publication Status Term Source REF	
Experiment Description	Effect of Amino Acid Starvation on Ino4 Binding.  Comparing SCD conditions to 4hrs of Amino Acid starvation	
Protocol Name	P-MEXP-34518	P-MEXP-34517	P-MEXP-34520	P-MEXP-34523	P-MEXP-34521	P-MEXP-34524	P-MEXP-34525	P-MEXP-34528	
Protocol Type	specified_biomaterial_action	grow	nucleic_acid_extraction	labeling	labeling	hybridization	feature_extraction	bioassay_data_transformation	
Protocol Description	Cells were grown in complete minimal medium (SCD) to early-log phase in 30°C until the culture reached an OD600 of 0.8 – 1.0. Cells were collected by centrifugation and resuspend in an equal volume of minimal medium lacking amino acids and adenine (YNB AA, 2% glucose, 20 mg/L uracil) and allowed to grow for 4 hours and than were collected. 	SCD media, Temperature 30C, cells grown reaching OD600 of 0.6-1.0	After finishing the treatement, cells were cross-link with formaldehyde for 20 minutes, centrifuged and sheared with sonication. Sample of total DNA (WCE) was kept and the rest was incubated with agarose conjugated anti-human-cMyc Ab (9E11 Santa Cruse). The sample was then reversed cross-link, and the DNA was purified (IP). The purified DNA went under ligate-mediated PCR with Amino-Allyl.  	The Amino-Allyl ligate-mediated PCR products were incubated with CyDye post labaling Cy5 dye (Amersham) for 1 hour in 9 microL of 0.1M NaHCO3 pH ~8.7. The labeled DNA was purified with PCR purification kit (Qiagene) and was ethanol percipitated.	The Amino-Allyl ligate-mediated PCR products were incubated with CyDye post labaling Cy3 dye (Amersham) for 1 hour in 9 microL of 0.1M NaHCO3 pH ~8.7. The labeled DNA was purified with PCR purification kit (Qiagene) and was ethanol percipitated.	The slide was incubated in 50ml 3.5X SSC, 0.1% SDS, 10 mg/ml BSA in room temprature for 20 minutes and then in 50°C for another 20 minutes in the same pre-heated solution. The slide was centrifuged for drying. The labeled DNA was suspended in 60 microL 3X SSC, 0.1% SDS and 4 microL Yeast tRNA 8mg/microL and was incubated in 95°C for 5 minutes. The suspended labeled DNA was added to the slide in the chamber,the slide was covered and incubated for 16 hours.  	The slide was scanned with GenePix 4000B scanner with wavelengths of 532nm (Cy3) and 635nm (Cy5). 	The background intensity was subtracted from the spot intensity to give the final calculated spot intensity. The intensities of all of the spots from the Cy5 and Cy3 scans were summed, and the ratio of total Cy5/Cy3 intensity was set equal to one. For each spot the ratio of corrected Cy5/Cy3 intensity was computed. An error model described in (Roberts et al., Science 2000) was implemented on the corrected spots' values. Lowess normalization was performed before the error model.	
Protocol Parameters		max temperature;stop time;min temperature;start time;	Extracted product;Amplification;	Label used;Amplification;Amount of nucleic acid labeled;	Amount of nucleic acid labeled;Label used;Amplification;	Quantity of label target used;time;Volume;Chamber type;temperature;	
Protocol Hardware							GenePix 4000B [Axon Instruments]	
Protocol Software							GenePix Pro [Axon Instruments]	
Protocol Contact	
Protocol Term Source REF	mo			mo	mo		The MGED Ontology	The MGED Ontology	
SDRF File	E-MEXP-906.sdrf.txt	
Term Source Name	mo		ncbitax	The MGED Ontology	ArrayExpress	The MGED Ontology	mo	EFO	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version