Name: Transcription profiling by array of Arabidopsis thaliana Col-0 and rcd1 genotypes after ozone and control treatments
Keywords: transcription profiling by array

Dataset Information

Transcription profiling by array of Arabidopsis thaliana Col-0 and rcd1 genotypes after ozone and control treatments

ABSTRACT: Wild-type Columbia (Col-0) and rcd1-1 seeds were sown on 1:1 peat:vermiculite mixture, stratified for 2 days and grown in controlled environment chambers (Weiss Bio1300; Weiss Gallenkamp, (http://www.weiss-gallenkamp.com/) with 12-h/12-h day/night cycle, temperature 22 °C/19 °C, relative humidity 70%/90%. 1-week old plants were transplanted into individual pots (5x5cm) and subirrigated twice a week. O3 experiments (6 hours of 350 nL L-1) were performed with 3-week old plants. Control and O3-treated plants (x-10 individuals) were collected at 0, 1, 2, 4, 8 and 24h after the start of the O3 treatment. The experiment was repeated 3 times, in addition to which a fourth identical repeat was used as the common reference RNA. cDNA synthesis, sample labeling, microarray hybridization, washing of the slides as well as image scanning were performed as described in Jaspers et al. (2009; PMID:19548978). The 50-mer oligo microarrays were identical to the Jaspers et al. 2009. In prerocessing, the 50mer probes were reannoated to TAIR9 with BLASTn algorithm. Data was analysed with linear mixed models using scripts in R.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jarkko T Salojarvi

PROVIDER: E-MTAB-662 | ArrayExpress | 2014-05-02

REPOSITORIES: ArrayExpress

ACCESS DATA

Publications

Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1.

Brosché Mikael M Blomster Tiina T Salojärvi Jarkko J Cui Fuqiang F Sipari Nina N Leppälä Johanna J Lamminmäki Airi A Tomai Gloria G Narayanasamy Shaman S Reddy Ramesha A RA Keinänen Markku M Overmyer Kirk K Kangasjärvi Jaakko J

PLoS genetics 20140213 2

Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). ...[more]

PMID: 24550736

Similar Datasets

Project description:Background: The mechanisms underlying ozone (O3)-induced pulmonary inflammation remain unclear. Interleukin (IL)-10 is an anti-inflammatory cytokine that is known to inhibit inflammatory mediators. Objectives: The current study investigated the molecular mechanisms underlying IL-10-mediated attenuation of O3-induced pulmonary inflammation in mice. Methods: Il10-deficient (Il10-/-) and wild type (Il10+/+) mice were exposed to 0.3-ppm O3 or filtered air for 24, 48 or 72 hr. Immediately following exposure, differential cell counts, and total protein (a marker of lung permeability) were assessed from bronchoalveolar lavage fluid (BALF). mRNA and protein levels of cellular mediators were determined from lung homogenates. We also utilized global mRNA expression analyses of lung tissue with Ingenuity Pathway Analyses (IPA) to identify patterns of gene expression through which IL-10 modifies O3-induced inflammation. Results: Mean numbers of BALF polymorphonuclear leukocytes (PMNs) were significantly greater in Il10-/- mice than in Il10+/+ mice after exposure to O3 at all time points tested. O3-enhanced nuclear NF-kB translocation was elevated in the lungs of Il10-/- compared to Il10+/+ mice. Gene expression analyses revealed several key IL-10 and O3-dependent mediators, including IL-6, MIP-2, IL-1 and CD86. Conclusions: Results indicated that IL-10 protects against O3-induced pulmonary neutrophilic inflammation and cell proliferation. Moreover, gene expression analyses identified three response pathways and several novel genetic targets (e.g. Ccr1, Socs3, Il33, Hat1, and Gale) through which IL10 may modulate the innate and adaptive immune response. These novel mechanisms of protection against the pathogenesis of O3-induced pulmonary inflammation may also provide potential therapeutic targets to protect susceptible individuals. PARALLEL study design with 26 samples. Biological replicates: 2 to 3 replicates per group with wild type air exposed animals as controls for each time point (24, 48, 72 hours). Time-Course, Dose-Response, Strain comparison

Project description:A combined approach of evaluating ozone (O3)-caused foliar injury symptom and global gene expression profiling was used to identify potential genes associated with severity of injury on leaves of O3 (200 ppb)-fumigated (1, 12, 24, 48, and 72 h) two-week-old rice (cv. Nipponbare) seedling along with appropriate control. Foliar injuries were evaluated up to 72 h using both qualitative visual scale and quantitative RGB (red-green-blue) image analysis methods. The (R-G)/(R+G) was found as the optimal quantitative RGB parameter to assess the foliar injury. Large-scale transcript profiling of leaves identified 270 genes linked with foliar injury. Of these genes, the expression levels of 139 genes showed significant differences (P < 0.05) between leaves without and with injury symptoms. When a rigorous correlation test was applied on these genes for their expression changes and relative (R-G)/(R+G) parameters, the expression of 93 genes were found to increase with increased foliar severity up to 72 h, showing a positive, tight correlation between a subset of gene expression and commonly observed O3-triggerred symptom of foliar injury with correlation coefficient below -0.80. Of 93 genes, genes involved in metabolism (29%) formed a major functional category. Reconstruction of the metabolic networks with identified metabolic genes provided insight into the cellular responses such as photorespiration, biosynthesis of secondary metabolites, and detoxification. The O3 effect on these cellular responses has been previously reported based on physiological and biochemical studies, validating our approach used in this study to globally identify O3-responsive biomarkers tightly linked with foliar injury symptom. This study provides evidence for the presence of large number of genes associated with the foliar injury symptom than thought before, and could serve as a resource of potential biomarkers to study mechanisms of visible injury development by O3. Comparison between healthy rice seedling leaves and ozone treated (for 48 h and 72 h) rice seedling leaves was performed. Three biological replicates (5 leaves in each replicate; pooled) were used, and dye-swaped.