Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression time series of Arabidopsis thaliana Col-0 and rcd1 genotypes in ozone and control

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 Salojarvi

PROVIDER: E-MTAB-662 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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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:Q fever, a zoonosis due to Coxiella burnetii infection, exhibits sexual dimorphism; men are affected more frequently and severely than women for a given exposure. Here we explore whether the severity of C. burnetii infection in mice is related to differences in male and female gene expression profiles. Mice were infected with C. burnetii for 24 hours, and gene expression was measured in liver cells using microarrays. Multiclass analysis identified 2,777 probes for which expression was specifically modulated by C. burnetti infection. Only 14% of the modulated genes were sex-independent, and the remaining 86% were differentially expressed in males and females. Castration of males and females showed that sex hormones were responsible for more than 60% of the observed gene modulation, and this reduction was most pronounced in males. Using functional annotation of modulated genes, we identified four clusters enriched in males that were related to cell-cell adhesion, signal transduction, defensins and cytokine/Jak-Stat pathways. Up-regulation of the IL-10 and Stat-3 genes may account for the high susceptibility of men with Q fever to C. burnetii infection and autoantibody production. Two clusters were identified in females, including the circadian rhythm pathway, which consists of positive (Clock, Arntl) and negative (Per) limbs of a feedback loop. We found that Clock and Arntl were down-modulated whereas Per was up-regulated; these changes may be associated with efficient bacterial elimination in females but not in males, in which an exacerbated host response would be prominent. This large-scale study revealed for the first time that circadian rhythm plays a major role in the anti-infectious response of mice, and it provides a new basis for elucidating the role of sexual dimorphism in human infections. Liver transcriptome was analyzed using whole genome microarray. Forty mice were divided into 8 groups of five mice upon three binary factors: sex, infection and castration. Four Samples were excluded from final analysis (see Data Processing for additional details).

Dataset Information

Gene expression time series of Arabidopsis thaliana Col-0 and rcd1 genotypes in ozone and control

Publications

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

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