Investigation Title Transcription profiling of chinese cabbage exposed to prolonged cold Comment[Submitted Name] Prolonged cold Experimental Design stimulus_or_stress_design transcription profiling by array Experimental Design Term Source REF mo EFO Comment[ArrayExpressReleaseDate] 2006-10-25 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-MEXP-190 Comment[MAGETAB TimeStamp_Version] 2011-06-28 19:36:14 Last Changed Rev: 14857 Experimental Factor Name Temperature Time Experimental Factor Type temperature time Experimental Factor Term Source REF Person Last Name Chung Lee Hong Yun Hong Jin Lim Lim Cho Lim Person First Name Woo Sik Sang Yeol Jong Chan Dae-Jin Joon Ki Zheng Lu Chan Ju Chae Oh Moo Je Chae Oh Person Mid Initials Person Email colimpbl@naver.com Person Phone +82-55-6255 Person Fax Person Address #900, Jinju, Gyeongnam, 660-701, South Korea Person Affiliation Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Molecular Biology Molecular Biology, Gyeongsang National University Molecular Biology, Gyeongsang National University Person Roles submitter Person Roles Term Source REF Quality Control Type technical_replicate biological_replicate Quality Control Term Source REF mo The MGED Ontology Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2006-10-25 PubMed ID Publication DOI Publication Author List Kyung Ae Yang; Chan Ju Lim; Joon Ki Hong; Zheng Lu Jin; Jong Chan Hong; Dae-Jin Yun; Woo Sik Chung; Sang Yeol Lee; Moo Je Cho; Chae Oh Lim Publication Title Identification of Chinese cabbage genes up-regulated by prolonged cold by using microarray analysis Publication Status Publication Status Term Source REF Experiment Description Identification of Chinese cabbage genes up-regulated by prolonged cold by using cDNA microarray. Protocol Name P-MEXP-5862 P-MEXP-5863 P-MEXP-5847 P-MEXP-5853 P-MEXP-5857 P-MEXP-5856 P-MEXP-5859 P-MEXP-5864 Protocol Type grow grow grow nucleic_acid_extraction labeling labeling hybridization bioassay_data_transformation Protocol Description Four-day old Chinese cabbage seedlings were incubated in a cold chamber (4C) for 1 week. Four-day old Chinese cabbage seedlings were incubated in a cold chamber (4C) for 4 weeks. Chinese cabbage seeds were sown on MSO medium (Duchefa) containg 0.25% phyta-gel and incubated at 4C for 3 days under short-day condition to induce synchronous germination. They were then transferred to a growth chamber and grown at 22C for 4 days under long-day condition. 0.1 g of Chinese cabbage seedlings were homogenized with 2 ml of guanidinium thiocyanate homogenization buffer. By centrifugation (9000 rpm for 5 min) at room temperature, cell debris had been removed from the suspension. To the suspension solution, an equal volume of chloroform was added and vortexed for 5 min, then centrifuged. 700 ul of the cushion of CsCl was added in a new tube and 1.2 ml of supernatant was carefully added above it. The tubes were centrifuged for 14 hrs at 45,000 rpm (Beckman). Following centrifugation, fluid above the 0.5 cm above was removed, and the bottom of the tube filled with 500 ul of 70% ethanol for washing the remnant, and then the pellet was dissolved in 300 ul of 0.1% DEPC water containing 0.1% SDS. The equal volume of water saturated water was added to the solution and vortexed for 5 min then centrifuged. The supernatant was taken and added to an equal volume of chloroform. It was vortexed for 5 min and the surpernatant was taken and RNA was precipitated with 2.5 volume of ethanol and 0.1% of 3M NaOAc then stored -20C for 2 hr. It was centrifuged for 20 mins at 4C and the pellet was washed with 70% ethanol. The surpernatant was removed by gentle aspiration and then dried for 15-20 mins. RNA was dissolved with 30 ul of DEPC-H2O. The yield of RNA was calculated by measuring the absorbance of the RNA solution at 260 nm and 280 nm. OD 260/280 ratio of RNA solution between 1.8 ~ 2.1 was used for hybridizations. Genisphere 3DNA Array 50 kit protocol provied by the manufacturer was used without modifications. cDNA synthesis was primed with a 3DNA Array 50 kit Cy5 primer and reverse transcript was performed with TOYOBO AceTra MMLV reverse transcriptase. Genisphere 3DNA Array 50 kit protocol provided by the manufacturer was used without modifications. cDNA synthesis was primed with a 3DNA Array 50 kit Cy3 primer and reverse transcript was performed with TOYOBO AceTra MMLV reverse transcriptase. First hybridization was perfomed following 3DNA Array kit protocol provided by the manufacturer. All material generated from 40 ug of total RNA was labeled. Hybridization was carried out overnight (16h) at 55C in a Big Shot (Boekel scientific) hybridization chamber. To dry the washed slides, we put a slide in a slide jar and centrifuged it at 800 rpm. Then, slides were stored in the dark until scanned. Intensities were background-subtracted and normalized using housekeeping gene intensities. Normalization was performed using the "To total (intensity - background) method provided by the QuantArray software package (Packard BioScience, Billerica, MA, USA). Protocol Parameters start time;min temperature;stop time;media;max temperature; Amplification;Extracted product; Amount of nucleic acid labeled;Amplification;Label used; Amount of nucleic acid labeled;Label used;Amplification; Chamber type;Quantity of label target used;time;Volume;temperature; Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF mo mo SDRF File E-MEXP-190.sdrf.txt Term Source Name mo ArrayExpress mo The MGED Ontology 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://www.ebi.ac.uk/efo/ Term Source Version