Similar Datasets
Project description:To understand signal transduction mechanism by MeJA in rice, we have analyzed transcription profile with 60K Rice Whole Genome Microarray after MeJA treatment. Gene transcripts were extracted from ten individual rice plants treated with 100 uM MeJA for 6 hrs. RNA samples from these plants were used to generate cyanine-3 (Cy3) and Cy5-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats independently.
2011-01-01 | GSE22757 | GEO
Project description:Brachypodium distachyon identification of MeJA responsive genes in wild type and MTL-overexpression plants
| PRJNA512201 | ENA
Project description:The aim was to determine the changes in cell wall composition and transcriptome changes following treatment with the stress hormone precursor methyl jasmonate (MeJA) in the model grass Brachypodium distachyon. The correlation between transcript changes and cell wall composition changes allowed identification of candidate genes responsible for grass-specific features of the cell wall that are specifically changed in response to MeJA.
2017-09-04 | E-MTAB-5413 | biostudies-arrayexpress
Project description:We used Affymetrix 1.0 ST arrays to compare the transcriptome of 4 weeks‐day‐old plants sprayed with 250uM of MeJA or mock (control). For the experiments we used wild-type (Col-0), phyB-9 and jaz10 single mutants and jaz10phyb double mutant. Samples were harvested after 3hours of induction with MeJA or mock. We performed a first analysis with the transcriptomes of wild‐type (Col-0) to identify those group of genes that are up‐ and down‐regulated by MeJA treatment (2 fold-changes). We founded 719 genes whose expression was statistically significantly different between the two treatments. To gain knowledge into the regulation of phyB over these set of 719 genes, we contrasted their expression levels against phyB transcriptome. By cluster analysis, we identified five major groups of genes, where in two of them the transcript levels increased in presence of MeJA (clusters 1 and 2) and three whose expression decrease after MeJA treatment (Cluster 3, 4 and 5).
2020-01-01 | GSE130255 | GEO
Project description:To understand signal transduction mechanism by MeJA in rice, we have analyzed transcription profile with 60K Rice Whole Genome Microarray after MeJA treatment. Gene transcripts were extracted from ten individual rice plants treated with 100 uM MeJA for 6 hrs. RNA samples from these plants were used to generate cyanine-3 (Cy3) and Cy5-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats independently. Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 kit (v. 2, Genisphere, Hatfield, PA). The microarray was scanned with Genepix 4000B (Axon Instruments, Union City, CA) and the quality of the chip data was analyzed with statistical R language and sma package in Bioconductor project (http://www.bioconductor.org/) implemented on Linux platform. Noncorrelation of signal and background intensities were confirmed by plotting base 2 log background intensity in x axis and base 2 log intensity subtracted with background intensity in y axis. Prior to normalization, normal distribution of Cy3 and Cy5 intensities were tested by qqplot function in R statistical language. The spatial effects on the chip during the hybridization process were checked with spatial func in sma package. The variance difference between Cy3 and Cy5 intensities within microarray was tested by the Student's t test under the assumptions firstly uniform and then nonuniform variances. The ANOVA difference of signal intensities between microarrays was performed by one-way ANOVA. Block-by-block Lowess normalization (Yang et al., 2002) and multivariate statistics such as clustering, principal component analysis, multidimensional scaling, etc. were analyzed with Acuity 3.1 (Axon Instruments). Spots with flag of 0 and a diameter greater than 51 pixel size were used for the analysis. Cy3 significant spots were determined when its log ratio is less than –0.67 [2**(–0.67) = 1.6-fold decrease] and its background subtracted intensity is higher than 500. On the contrary, Cy5 significant spots was determined when its log ratio is greater than 0.67 [2**0.67 = 1.6-fold increase] and its intensity is higher than 500. A preliminary microarray experiment using nontreated wild-type RNA labeled Cy3 and Cy5, respectively, gave less than 0.5% false positive signals in the analysis. To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNA
2011-01-01 | E-GEOD-22757 | biostudies-arrayexpress
Project description:Purpose: Understanding of MeJA, CK effect on regulation of gene expression patterns in Arabidopsis roots Total mRNA was extracted from 7-day-old Arabidopsis roots grown in MeJA (10uM), CK (50nM) and MeJA/CK-treated conditions. To generate cDNA libraries with TruSeq RNA library kit, 1 μg of total RNA was used. This step consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100 nt paired-end sequencing by Illumina HiSeq2000. 4,403 genes satisfying |fold change|â¥2 in at least one data set were collected.
2016-07-30 | E-GEOD-80188 | biostudies-arrayexpress
Project description: Not available
| S-EPMC3003816 | biostudies-other
Project description:Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments. Keywords = sugarcane Keywords = methyl jasmonate Keywords = nylon arrays Keywords: time-course
2004-07-23 | GSE1546 | GEO
Project description: Not available
| S-EPMC3898008 | biostudies-other
Project description:Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments. Keywords = sugarcane Keywords = methyl jasmonate Keywords = nylon arrays
2010-10-08 | E-GEOD-1546 | biostudies-arrayexpress