Investigation Title	Transcription profiling of Capsicum fruit ripening process	
Comment[Submitted Name]	Fruit ripening analysis	
Experimental Design	development_or_differentiation_design	reference_design	transcription profiling by array	
Experimental Design Term Source REF	mo:1.3.1.1	mo	EFO	
Comment[ArrayExpressReleaseDate]	2005-03-01	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-MEXP-260	
Comment[MAGETAB TimeStamp_Version]	2010-08-10 13:42:21 Last Changed Rev: 13058	
Experimental Factor Name	organism	developmental_stage	
Experimental Factor Type	organism	developmental_stage	
Experimental Factor Term Source REF	
Person Last Name	Byun	Chung	Shin	Lee	Choi	Hur	
Person First Name	Sang-Jin	Eun-Joo	Yoonhee	Sanghyeob	Doil	Cheol-Goo	
Person Mid Initials	
Person Email				sol6793@kribb.re.kr	
Person Phone				+82-42-860-4342	
Person Fax	
Person Address				52 Oun-dong, Yusong-gu, Taejon, 305-333, South Korea	
Person Affiliation	KRIBB	KRIBB	KRIBB	Plant Genomics Lab	KRIBB	KRIBB	
Person Roles				submitter	
Person Roles Term Source REF					
Quality Control Type	technical_replicate	biological_replicate	dye_swap_quality_control	
Quality Control Term Source REF	mo	The MGED Ontology	The MGED Ontology	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2005-03-01	
PubMed ID	20435701	
Publication DOI	20435701	
Publication Author List	Sanghyeob Lee; Eun-Joo Chung; Yoonhee Shin; Sang-Jin Byun; Cheol-Goo Hur; Doil Choi	
Publication Title	Expression Analysis of Fruit-related Genes in Tomato (Lycopersicon esculentum cv. Micro-tom) and Pepper (Capisicum annuum cv. Bukang) Reveals Conservation Between Climacteric and Non-climacteric Fruit Ripening Processes	
Publication Status	
Publication Status Term Source REF	
Experiment Description	Pepper fruits at four different developmental stages were collected: early fruit [EF; 1 cm long; 7 days after pollination (dap)], mature green fruit (MG; 6-7 cm length; 20 dap), breaking or turning red fruit (BR; fruit are partially red; 35 dap), and red ripe fruit (RR; fully red; 40 dap). Tomato fruits at corresponding developmental stages were also collected: EF (less than 1cm; 7 dap), MG (40 dap), BR (50 dap), and RR (55 dap). For the monitoring of fruit-specific and fruit ripening-related genes, we did array hybridization by using the leaves as a common reference and each corresponding fruit developmental stage sample.	
Protocol Name	P-MEXP-6951	P-MEXP-6939	P-MEXP-6991	P-MEXP-7040	P-MEXP-6940	P-MEXP-7043	P-MEXP-6988	P-MEXP-6987	P-MEXP-6989	P-MEXP-6986	P-MEXP-6992	P-MEXP-6990	P-MEXP-7358	P-MEXP-7039	P-MEXP-6945	P-MEXP-6946	P-MEXP-6947	
Protocol Type	grow	grow	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	pool	labeling	labeling	hybridization	
Protocol Description	Tomato (Lycopersicon esculentum cv. Micro-Tom) plants were grown in a controlled environment room at 26C with a photoperiod of 16hr light.	Pepper (Capsicum annuum cv. Bukang) plants were grown in a controlled environment room at 26 ±1C with a photoperiod of 16 hours light.	Tomato breaking or turning red fruit (BR; 50 dap) were collected.	Tomato leaves from 10-week old plants were collected.	Pepper fruits were collected at early fruit stage [EF; 1 cm long; 7 days after pollination (dap)].	Pepper leaves from 10-week old plants were collected.	Pepper red ripe fruit (RR; fully red; 40 dap) were collected.	Pepper breaking or turning red fruit (BR; fruit are partially red; 35 dap) were collected.	Tomato early fruit [EF; 1 cm long; 7 days after pollination (dap)] were collected.	Pepper mature green fruit (MG; 6-7 cm length; 20 dap) were collected.	Tomato red ripe fruit (RR; fully red; 55 dap) were collected.	Tomato mature green fruit (MG; 6-7 cm length; 40 dap) were collected.	50 ug of total RNA was isolated by using TRIzol reagent following the manufacturer's protocol.	Six leaves were pooled and total RNA was isolated.	Probe labeling was performed by using a 3DNA Array 50 kit as described by the manufacturer (Genisphere Inc., Hatfield, PA, USA). The labeling process was done by using Cy5-dUTP.	Probe labeling was performed by using a 3DNA Array 50 kit as described by the manufacturer (Genisphere Inc., Hatfield, PA, USA). The labeling process was done by using Cy3-dUTP.	cDNA and 3DNA hybridization was performed using 25 ul of 2X formamide-based hybridization buffer at 42C overnight and 50C for 6 hr, respectively. This was followed by post cDNA and 3DNA hybridization washing performed according to the manufacturer's instructions except that the first washing was performed at 50C.	
Protocol Parameters													Amplification;Extracted product;		Amount of nucleic acid labeled;Amplification;Label used;	Amplification;Label used;Amount of nucleic acid labeled;	Volume;time;Quantity of label target used;Chamber type;temperature;	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF													mo	mo	mo	mo	mo	
SDRF File	E-MEXP-260.sdrf.txt	
Term Source Name		mo	po_structure_ontology1.1	ArrayExpress	mo	The MGED Ontology	mo:1.3.1.1	EFO	
Term Source File		http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version							1.3.1.1