Investigation Title	Transcription profiling of tomato seedlings Condine wild type vs. Divaricata a-DOX2 mutant	
Comment[Submitted Name]	Tomato seedlings Condine wild type vs. Divaricata a-DOX2 mutant	
Experimental Design	individual_genetic_characteristics_design	co-expression_design	replicate_design	transcription profiling by array	
Experimental Design Term Source REF		The MGED Ontology	The MGED Ontology	EFO	
Comment[AEMIAMESCORE]	5	
Comment[SecondaryAccession]		
Comment[ArrayExpressReleaseDate]	2009-09-25	
Comment[ArrayExpressAccession]	E-MEXP-2265	
Comment[MAGETAB TimeStamp_Version]	2010-08-10 11:40:32 Last Changed Rev: 13058	
Experimental Factor Name	GENOTYPE	
Experimental Factor Type	genotype	
Experimental Factor Term Source REF	
Person Last Name	Martinez	
Person First Name	Marta	
Person Mid Initials	
Person Email	mmmtnez@cnb.csic.es	
Person Phone	(+34) 91 585 45 31	
Person Fax	
Person Address	Genetica Molecular Plantas, Darwin  3 Cantoblanco, Madrid, Madrid, 28049, Spain	
Person Affiliation	CNB-CSIC	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	biological_replicate	
Quality Control Term Source REF	The MGED Ontology	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2009-09-25	
PubMed ID	19759339	
Publication DOI	19759339	
Publication Author List	Bannenberg, Gerard; Martinez, Marta; Rodriguez, Maria Jose; Lopez, Miguel Angel; de Leon, Ines Ponce; Hamberg, Mats; Castresana., Carmen	
Publication Title	Functional analysis of {alpha}-DOX2, an active {alpha}-dioxygenase critical for normal development in tomato plants.	
Publication Status	submitted	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Gene expression of Condine wild type tomato seedling aerial parts grown on MS medium was compared with that of alpha-dioxygenase2 Divaricata (div) mutant	
Protocol Name	P-MTAB-4811	P-MTAB-4814	P-MTAB-4816	P-MTAB-4815	P-MTAB-4809	P-MTAB-4810	P-AFFY-6	P-MTAB-4812	
Protocol Type	pool	nucleic_acid_extraction	specified_biomaterial_action	grow	labeling	hybridization	feature_extraction	bioassay_data_transformation	
Protocol Description	Hypocotyls and cotyledons 15 7-d-old tomato seedling were excised and pooled per each sample.	Total RNA was isolated using RNeasy plant mini kit (QIAGEN, Hilden, Germany). RNA was quantified by use of a Nanodrop ND-1000 UV-Vis Spectrophotometer (Nanodrop Technology, Wilminton, DE) and assessed using an Agilent 2100 Bioanalyzer (Agilent Technology, Palo Alto, CA). <br>(Parameters: Extracted product = total_RNA, Amplification = none)	Hypocotyls and cotyledons of 7-d-old tomato seedlings grown on MS medium were excised and used to compared gene expression.	Sterilized tomato seeds were grown in vertically oriented square Petri Dishes, containing described MS medium, in chamber. Growth conditions were 16 h of light, 8 h of dark.<br>(Parameters: start time = 7, time unit = days, min temperature = 22, temperature unit = C, media = 0.5X Murashige-Skoog (MS) pH 6.0; 2%Sucrose (w/v) and 1.5% (w/v) agar )	cDNA was synthesized from 4 microg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA. The cRNA preparation (15 microg)was fragmented at 94ºC for 35 min into 35-200 bases in length.<br>(Parameters: Amount of nucleic acid labeled = 4, Amplification = none, Mass unit = Micro gram)	Three biological replicates for each condition were independently hybridized. If the quality control was correct 5 microg of fragmented cRNA were hybridized to the Tomato Genome Array. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 microg/ml. Hybridization was performed for 16h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).<br>(Parameters: Chamber type = Affymetrix- GeneChip Hyb Oven 640, Quantity of label target used = 5, Mass unit = Micro gram, time = 16, Tiny time unit = hours, Volume unit = Nano litre, temperature = 45)	Title: Affymetrix CEL analysis. Description: 	Differentially expressed transcripts were determined using the rank products method (Breitling et al., 2004). The multiple testing problem inherent to microarray experiments was corrected using the false discovery method (FDR) (Benjamini and Hochberg, 1995; Reiner et al., 2003). <br>Data preprocessed by: RMA<br>Normalization between slides: Quantile<br>p values calculated by: Limma (Linear models and empirical Bayes methods)<br>p values calculated by: Rank Products (permutations: 250)<br>p values adjustment: fdr	
Protocol Parameters	
Protocol Hardware	
Protocol Software							MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF	The MGED Ontology							The MGED Ontology	
SDRF File	E-MEXP-2265.sdrf.txt	
Term Source Name	The MGED Ontology		tair_dev:1.27	ArrayExpress	The MGED Ontology	EFO	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.arabidopsis.org/info/ontologies/	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version			1.27