Investigation Title	Transcription profiling of Arabidopsis thaliana wild type Col-0) and Atpdr2 mutant roots.							
Comment[Submitted Name]	Pleiotropic effect of gene mutation							
Experimental Design	gene_mutation_design	co-expression_design	transcription profiling by array					
Experimental Design Term Source REF		The MGED Ontology	EFO					
Comment[AEExperimentType]	transcription profiling by array							
Comment[AEExperimentDisplayName]	Transcription profiling by array of Arabidopsis mutant for Atpdr2							
Comment[ArrayExpressReleaseDate]	2009-10-20							
Comment[SecondaryAccession]								
Comment[AEMIAMESCORE]	5							
Comment[ArrayExpressAccession]	E-TABM-821							
Comment[MAGETAB TimeStamp_Version]	2010-08-13 12:02:54 Last Changed Rev: 13058							
Experimental Factor Name	GENOTYPE							
Experimental Factor Type	genotype							
Experimental Factor Term Source REF								
Person Last Name	Vivanco							
Person First Name	Dayakar Badri/Jorge							
Person Mid Initials								
Person Email	dayakar@lamar.colostate.edu							
Person Phone								
Person Fax								
Person Address								
Person Affiliation	Colorado State university							
Person Roles	submitter							
Person Roles Term Source REF	The MGED Ontology							
Quality Control Type	dye_swap_quality_control							
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	2009-10-20							
PubMed ID	19854857							
Publication DOI	10.1104/pp.109.147462							
Publication Author List	Badri, Dayakar V.; Quintana, Naira; El Kassis, Elie G.; Kim, Hye Kyong; Choi, Young Hae; Sugiyama, Akifumi; Verpoorte, Robert; Martinoia, Enrico; Manter, Daniel K.; Vivanco, Jorge M.							
Publication Title	An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota							
Publication Status	published							
Publication Status Term Source REF	EFO							
Publication Status Term Accession Number	EFO_0001796							
Experiment Description	To determine the pleiotropic effect of the ABC transporter gene (Atpdr2) mutation, we performed the microarray analyses on the root tissues of Arabidopsis thaliana wild type (Col-0) and Atpdr2 mutant.							
Protocol Name	P-TABM-4361	P-TABM-4360	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6	Affymetrix:Protocol:ExpressionStat			
Protocol Type	grow	nucleic_acid_extraction	hybridization	feature_extraction	bioassay_data_transformation			
Protocol Description	Arabidopsis seeds were surface-sterilized with bleach for one minute followed by five rinses in sterile distilled water and plated on Murashige and Skoog (MS) ( Murashige & Skoog, 1962) salts supplemented with 3% sucrose and 0.8% Bacto agar in Petri dishes.  Plates were incubated in a growth chamber (Percival Scientific, IO, USA) at 25ï¾°C, with a photoperiod of 16h light/8h dark for germination.  To collect root exudates, seven-day-old seedlings were transferred to 6-well culture plates (VWR Scientific), each well containing 5 ml of liquid MS (MS basal salts supplemented with 1% sucrose), incubated on an orbital shaker at 90 rpm and illuminated under cool white fluorescent light (45 ï¾μmol m-2 s-1) with a photoperiod of 16h light/8h dark at 25ï¾°C. According to previously-published methods (Loyola-Vargas et al., 2007; Badri et al., 2008) when plants were 18 days old, they were washed with sterile water to remove the surface-adhering exudates and transferred to new 6-well plates containing 5 ml MS liquid media and incubated on an orbital shaker at 90 rpm and illuminated under cool white fluorescent light (45 ï¾μmol m-2 s-1) with a photoperiod of 16h light/8h dark at 25ï¾°C. The root tissue was collected from 20 day old seedlings.	Total RNA extration from root tissues were done by using Trizol regant	Title: Affymetrix Generic Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	Title: Affymetrix CHP Analysis (ExpressionStat). Description: 			
Protocol Parameters								
Protocol Hardware								
Protocol Software			MicroArraySuite 5.0	MicroArraySuite 5.0	MicroArraySuite 5.0			
Protocol Contact								
Protocol Term Source REF			mo					
SDRF File	E-TABM-821.sdrf.txt							
Term Source Name	Plant Ontology	NCBI Taxonomy	The MGED Ontology		ArrayExpress	The MGED Ontology	EFO	mo
Term Source File	http://www.plantontology.org/	http://www.ncbi.nlm.nih.gov/Taxonomy/	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/	http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version