Comment[ArrayExpressAccession]	E-GEOD-42029				
MAGE-TAB Version	1.1				
Public Release Date	2013-09-05				
Investigation Title	Silencing of OsMADS29 in Oryza sativa var. PB1				
Comment[Submitted Name]	Silencing of OsMADS29 in Oryza sativa var. PB1				
Experiment Description	RNAi mediated suppression of MADS29 severely affects seed set; the surviving seeds are smaller in size with reduced grain filling, abnormal starch grains and aberrant embryo development. To identify the affected pathways  due to suppression of this transcription factor in the transgenic seeds, transcriptome analysis using microarray was carried out. Three biological replicates of MADS29 RNAi (silencing) lines and Wild Type PB1 (control) plants were used for microarray study				
Term Source Name	ArrayExpress	EFO			
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Kapoor	Nayar	Sharma	Tyagi	Kapoor
Person First Name	Sanjay	Saraswati	Rita	Akhilesh	Sanjay
Person Mid Initials				K	
Person Email	saraswati.nayar@gmail.com				
Person Affiliation	University of Delhi, South Campus				
Person Address	Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Huarez MArg, New Delhi, India				
Person Roles	submitter				
Protocol Name	P-GSE42029-1	P-GSE42029-3	P-GSE42029-4	P-GSE42029-2	P-GSE42029-5
Protocol Description	First-order analysis was performed using Affymetrix® GeneChip® Command Console® 3.0. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5.1 (Stratagene, CA, USA) ID_REF =  VALUE = GC-RMA normalised signal values	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450	Trizol extraction of total RNA was performed according to the manufacturer's instructions.	GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	RNA interference				
Experimental Factor Type	RNA interference				
Publication Title	Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis.				
Publication Author List	Nayar S, Sharma R, Tyagi AK, Kapoor S				
PubMed ID	23929654				
Publication DOI	10.1093/jxb/ert231				
Comment[SecondaryAccession]	GSE42029				
Comment[GEOReleaseDate]	2013-09-05				
Comment[ArrayExpressSubmissionDate]	2012-11-05				
Comment[GEOLastUpdateDate]	2013-09-05				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-42029.sdrf.txt