Investigation Title	Transcription profiling, Rpd3 ChIP-chip and histone H4 and TATA binding protein ChIP-chip of wild type, cti6 and sfl1 yeast mutants	
Comment[Submitted Name]	A Toggle Involving Cis Interfering Noncoding RNAs Controls Variegated Gene Expression in Yeast	
Experimental Design	genetic_modification_design	tiling_path_design	in_vivo_design	transcription profiling by array	
Experimental Design Term Source REF	The MGED Ontology			EFO	
Comment[SecondaryAccession]		
Comment[ArrayExpressReleaseDate]	2010-03-29	
Comment[AEMIAMESCORE]	2	
Comment[ArrayExpressAccession]	E-MEXP-2269	
Comment[MAGETAB TimeStamp_Version]	2010-08-10 12:03:15 Last Changed Rev: 13058	
Experimental Factor Name	IMMUNOPRECIPITATE	GENOTYPE	EXTRACT MATERIAL	
Experimental Factor Type	immunoprecipitate	genotype	material_type	
Experimental Factor Term Source REF	
Person Last Name	Dowell	
Person First Name	Robin	
Person Mid Initials	D	
Person Email	rdd@mit.edu	
Person Phone	(617)-253-3031	
Person Fax	
Person Address	CSAIL, 32 Vassar St, Cambridge, MA, 02139, USA	
Person Affiliation	
Person Roles	
Person Roles Term Source REF	
Quality Control Type	
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Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2010-03-29	
PubMed ID	19805129	
Publication DOI	19805129	
Publication Author List	Stacie L. Bumgarner, Robin D. Dowell, Paula Grisafi, David K. Gifford, and Gerald R. Fink	
Publication Title	Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Effects of genetic modification of trans-acting transcription factors and a chromatin remodeler on noncoding RNA transcription and trans-acting factor binding at loci in yeast.	
Protocol Name	P-MTAB-4833	P-MTAB-4837	P-MTAB-4830	P-MTAB-4832	P-MTAB-4836	P-MTAB-4834	P-MTAB-4835	P-MTAB-4838	
Protocol Type	nucleic_acid_extraction	nucleic_acid_extraction	nucleic_acid_extraction	nucleic_acid_extraction	grow	labeling	labeling	hybridization	
Protocol Description	Total RNA isolated by hot phenol extraction. Contaminant DNA was eliminated with TURBO DNase from Ambion (AM2238).  First strand cDNA was synthesized using an oligo dT(16) primer (TaqMan Reverse Transcription Reagents N8080234) using the protocol described in: http://research.nhgri.nih.gov/microarray/sample_labeling.shtml<br>(Parameters: Extracted product = total_RNA, Amplification = none)	DNA cross-linked to protein is then sheared by sonication. Cross-linked material was then subjected to immunoprecipitation with a rabbit polyclonal antibody against the yeast TATA binding protein (TBP) (Santa Cruz SC-33736) (IP sample only). Cross-links in both the IP and WCE samples were reversed, protein and RNA were digested, DNA isolated and purified.<br><br><br>(Parameters: Extracted product = genomic_DNA, Amplification = none)	DNA cross-linked to protein is then sheared by sonication.  Cross-linked material was then subjected to immunoprecipitation with a monocolonal antibody against the c-myc epitope tag (9e11 Covance Cat No MMS-164P) (IP sample only).  Cross-links in both the IP and WCE samples were reversed, protein and RNA were digested and DNA isolated.<br>(Parameters: Extracted product = genomic_DNA, Amplification = none)	DNA cross-linked to protein is then sheared by sonication. Cross-linked material was then subjected to immunoprecipitation with a rabbit monoclonal antibody against histone H4 (pan) (Upstate-Millipore 05-858) (IP sample only). Cross-links in both the IP and WCE samples were reversed, protein and RNA were digested, DNA isolated and purified.<br>(Parameters: Extracted product = genomic_DNA, Amplification = none)	Cells were grown overnight in YPD liquid, diluted 1:50 in YPD liquid, and grown to OD600 0.8-1.2<br>(Parameters: time unit = seconds, temperature unit = C)	See: http://research.nhgri.nih.gov/microarray/sample_labeling.shtml<br>(Parameters: Mass unit = Micro gram, Amplification = none)	IP and WCE samples were amplified and labeled (Cy5-IP, Cy3-WCE) by ligation-mediated PCR.  <br>(Parameters: Amplification = PCR, Mass unit = Micro gram)	Standard Agilent Protocol.<br>(Parameters: Chamber type = OTHER: Agilent, Quantity of label target used = 5, Mass unit = Micro gram, Tiny time unit = seconds, Volume unit = Nano litre, temperature = 65)	
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SDRF File	E-MEXP-2269.sdrf.txt	
Term Source Name	mo		The MGED Ontology	ArrayExpress	The MGED Ontology	EFO	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version