Dataset Information


Gene expression in S1 panicles of Ubi1:AtJMT transgenic plants and drought-treated nontransgenic rice plants

ABSTRACT: To identify genes that are regulated by MeJA and drought, global expression profilings were performed on panicles from Ubi1:AtJMT, drought-treated NT, and untreated NT plants. The underlying assumption of this approach was that high levels of MeJA produced either by overexpression of AtJMT in the transgenic panicles or by drought treatment in the NT panicles regulates genes that are involved in spikelet and/or panicle development. Profiling was conducted using the Rice 3’-Tiling Microarray (GreenGene Biotech, Yongin, Korea). RNA samples from S1 panicles of Ubi1:AtJMT, drought-treated NT and untreated NT plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database ( Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. ( Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in Ubi1:AtJMT, drought-treated NT, and untreated NT plants. Cy3-labeled target cDNA fragments were synthesized from S1 panicles using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.

ORGANISM(S): Oryza sativa  

SUBMITTER: Nam-gun Kim  

PROVIDER: E-GEOD-14508 | ArrayExpress | 2009-07-09



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Methyl jasmonate reduces grain yield by mediating stress signals to alter spikelet development in rice.

Kim Eun Hye EH   Kim Youn Shic YS   Park Su-Hyun SH   Koo Yeon Jong YJ   Choi Yang Do YD   Chung Yong-Yoon YY   Lee In-Jung IJ   Kim Ju-Kon JK  

Plant physiology 20090211 4

Jasmonic acid (JA) is involved in plant development and the defense response. Transgenic overexpression of the Arabidopsis (Arabidopsis thaliana) jasmonic acid carboxyl methyltransferase gene (AtJMT) linked to the Ubi1 promoter increased levels of methyl jasmonate (MeJA) by 6-fold in young panicles. Grain yield was greatly reduced in Ubi1:AtJMT plants due to a lower numbers of spikelets and lower filling rates than were observed for nontransgenic (NT) controls. Ubi1:AtJMT plants had altered numb  ...[more]

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