Comment[ArrayExpressAccession]	E-GEOD-34899
MAGE-TAB Version	1.1						
Public Release Date	2013-07-22
Investigation Title	Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid						
Comment[Submitted Name]	Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid
Experiment Description	Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid. Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 50 ppm ferulic acid (FA) during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 FA-treated replicates (short and long exposures).						
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	Chi	Chi	Chen	Hsiung	Chou	Huang	
Person First Name	Wen-Chang	Wen-Chang	Yun-An	Yu-Chywan	Chang-Hung	Hao-Jen	
Person Email	wenji0918177774@yahoo.com.tw						
Person Affiliation	National Cheng Kung University						
Person Phone	+886918177774						
Person Address	Life Science, National Cheng Kung University, No.1, University Road, Tainan City, Tainan, Taiwan, Taiwan						
Person Roles	submitter						
Protocol Name	P-GSE34899-1	P-GSE34899-5	P-GSE34899-6	P-GSE34899-2	P-GSE34899-3	P-GSE34899-4	P-GSE34899-7
Protocol Description	An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method. ID_REF =  VALUE = Normalized log2 ratio (Cy5/Cy3) representing test/reference	0.5 M-NM-<g of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after ferulic acid treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 M-NM-<g of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.	Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4M-CM-^W44K Microarray (Agilent Technologies, USA) at 60M-0C for 17 h.	Control and rice seedlings were exposed to to 50 ppm ferulic acid during short (pooled from 1- and 3-h treatments) exposures or long (24 h) exposures	6-day-old seedlings	Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.	After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TIME	COMPOUND					
Experimental Factor Type	time	compound					
Publication Title	Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.						
Publication Author List	Chi WC, Chen YA, Hsiung YC, Fu SF, Chou CH, Trinh NN, Chen YC, Huang HJ						
PubMed ID	23705659						
Publication DOI	10.1186/1471-2164-14-351						
Comment[SecondaryAccession]	GSE34899						
Comment[GEOReleaseDate]	2013-07-22						
Comment[ArrayExpressSubmissionDate]	2012-01-06						
Comment[GEOLastUpdateDate]	2013-07-22						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-34899.sdrf.txt