Investigation Title	Gene expression profiling of Arabidopsis Atwrky12 mutants stems						
Comment[Submitted Name]	Gene expression profiling of Arabidopsis Atwrky12 mutants stems						
Experimental Design	genetic_modification_design	co-expression_design	replicate_design	transcription profiling by array			
Experimental Design Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	EFO			
Comment[AEExperimentType]	transcription profiling by array						
Comment[AEExperimentDisplayName]	Gene expression profiling of Arabidopsis Atwrky12 mutants stems						
Comment[AEMIAMESCORE]	5						
Comment[SecondaryAccession]							
Comment[ArrayExpressReleaseDate]	2011-06-01						
Comment[ArrayExpressAccession]	E-MEXP-2792						
Comment[MAGETAB TimeStamp_Version]	2010-08-10 14:23:12 Last Changed Rev: 13058						
Experimental Factor Name	genotype						
Experimental Factor Type	genotype						
Experimental Factor Term Source REF							
Person Last Name	Tang						
Person First Name	Yuhong						
Person Mid Initials							
Person Email	ytang@noble.org						
Person Phone	5802246645						
Person Fax							
Person Address	"2510 Sam Noble Pkwy, Ardmore, Oklahoma, 73401, USA"						
Person Affiliation	The Samuel Robert Noble Foundation						
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	2011-06-01						
PubMed ID	21135241						
Publication DOI	10.1073/pnas.1016436107						
Publication Author List	"Wang H, Avci U, Nakashima J, Hahn MG, Chen F, Dixon RA"						
Publication Title	Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants						
Publication Status	published						
Publication Status Term Source REF	EFO						
Publication Status Term Accession Number	EFO_0001796						
Experiment Description	Gene expression profile in Arabidopsis stems of T-DNA insertion lines Atwrky12-1 and Atwrky12-2 were compared with Columbia wild-type plants at 45 days after germination.						
Protocol Name	P-MTAB-15816	P-MTAB-15813	P-MTAB-15814	P-AFFY-2	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6	P-MTAB-15815
Protocol Type	grow	nucleic_acid_extraction	specified_biomaterial_action	labeling	hybridization	feature_extraction	bioassay_data_transformation
Protocol Description	"Arabidopsis thaliana wild-type Col-0 and T-DNA insert lines were grown in growth chambers at 22 oC under long day condition (16 hrs light). Stems of 45 days old plants were used for all experiments.<br><br><br>(Parameters: start time = 45, time unit = days, min temperature = 22, temperature unit = C, media = Potting soil mix)"	"Total RNA was extracted using TRIZOL reagent, treated with DNaseI (Ambion), and column purified with an RNeasy MinElute CleanUp kit (Qiagen).<br>(Parameters: Extracted product = total_RNA, Amplification = none)"	"For Arabidopsis, 1/3 of the bottom part of stems of Atwrky12-1 and Atwrky12-2 homozygous plants and Columbia wild type plants were used."	Title: Affymetrix in vitro transcription. Description: 	Title: Affymetrix Generic Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	The normalized data was obtained by using RMA. All chips were normalized together using robust multichip average.  Median polish was used for the probe level summary.
Protocol Parameters							
Protocol Hardware							
Protocol Software					MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact							
Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology		The MGED Ontology		The MGED Ontology
SDRF File	E-MEXP-2792.sdrf.txt						
Term Source Name	The MGED Ontology	EFO					
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/					
Term Source Version