Transcription profiling of ray aortic tissue from different hypertensive models
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
SUBMITTER: Lynn Amon
PROVIDER: E-GEOD-7483 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Folsomia candida (Collembola) is able to survive dryer conditions by absorbing water vapour from its surroundings. To unravel the genomic responses underlying this intriguing water-absorption mechanism, we exposed the species to 98.2% Relative Humidity (eight, 27, 53 and 174 hours respectively) and subjected it to microarray based transcription profiling. About twenty-five 25-27 day old animals were placed in plastic containers that had a Relative Humidity of 98.2% (desiccated groups; n=16) or 100% RH (reference groups; n=16). After 8, 27, 53 and 174 hours four reference and four desiccation treated groups were snap-frozen (in liquid nitrogen) and stored at â80 °C until further analysis. Total RNA was obtained for each of the 32 samples. 500ng total RNA was labelled with the Agilent Low-Input Fluorescent Linear Amplification Kit. A pair-wise reference design was applied, implying that samples originating from desiccated groups were hybridized onto arrays with samples from reference groups that were exposed for the same duration; 8, 27, 53 or 174 hours). Dyes were swapped over the biological replicates.
2010-05-06 | E-GEOD-16127 | biostudies-arrayexpress
Project description:Histologically normal breast epithelium and stroma were laser capture microdissected from breast reduction specimens and from specimens of invasive ductal carcinoma. The objective of the study was to compare normal reduction tissues to tissues adjacent to I.D.C. to determine whether adjacent normal tissues contained expression profiles correlated with characteristics of the primary tumor and to identify markers of normal epithelium and stroma. Experiment Overall Design: common reference design. 66 samples replicated twice as dye swaps generating 132 arrays.
2008-06-13 | E-GEOD-4823 | biostudies-arrayexpress
Project description:A common bacterial strategy for monitoring environmental challenges is to use two-component systems, which consist of a sensor histidine kinase (HK) and a response regulator (RR). In the food-borne pathogen Bacillus cereus, the alternative sigma factor ÏB is activated by the RR RsbY. Here we present strong indications that the PP2C-type phosphatase RsbY receives its input from the multi-sensor hybrid kinase BC1008 (renamed RsbK). Genome analyses revealed that, across bacilli, rsbY and rsbK are located in a conserved gene cluster. A B. cereus rsbK deletion strain was shown to be incapable of inducing ÏB upon stress conditions and was impaired in its heat adaptive response. Comparison of the wild-type and rsbK mutant transcriptomes upon heat shock revealed that RsbK was primarily involved in the activation of the ÏB-mediated stress response. Truncation of the RsbK RR receiver domain demonstrated the importance of this domain for ÏB induction upon stress. The domain architecture of RsbK suggests that in the B. cereus group and in other bacilli, environmental and intracellular stress signalling routes are combined into one single protein. This strategy is markedly different from the ÏB activation pathway in other low-GC Grampositives. Two different comparisons were performed (both in duplo and Cy5-Cy3 dye-swapped): (1) B. cereus WT 30°C versus B. cereus WT 42°C (10 min heat shock) (2) B. cereus WT 42°C versus B. cereus FM1404 42°C Data from comparisons (2) were subsequently compared with transcriptome data obtained previously by Van Schaik et al., 2007
2010-06-24 | E-GEOD-14589 | biostudies-arrayexpress
Project description:A comparative transcriptome approach was used to assess genes involved in metabolism and pathogenesis that are specifically activated during anaerobic growth of the spore-forming food-borne human pathogen Bacillus cereus ATCC 14579. Growth under anaerobic conditions in Brain Heart Infusion broth revealed a reduced growth rate and a lower yield as compared to that under aerobic conditions. Comparative transcriptome analysis of cells harvested at early- and mid-exponential growth phase, transition phase and stationary phase, subsequently showed hundreds of genes to be induced under anaerobic condition. These included novel genes identified for anaerobic growth of B. cereus, encoding metabolic pathways, such as the arginine deiminase pathway (ArcABDC), a formate dehydrogenase (FdhF) and a pyruvate fomate lyase (Pfl), and alternative respiratory proteins, such as arsenate reductases. Furthermore, the nitrosative stress response was induced in the anaerobic transition phase of growth, conceivably due to the production of nitric oxide as a by-product of nitrite and nitrate respiration. Notably, both hemolytic enzyme and enterotoxin encoding genes were activated in different oxygen limiting conditions, i.e. hemolytic enzyme encoding genes were induced during anaerobic growth, whereas enterotoxin encoding genes were induced in the transition and stationary phase of aerobic cultures reaching a high cell density. These data point to metabolic rearrangements, stress adaptation and activation of the virulent status of B. cereus under anaerobic conditions, such as encountered in the human GI-tract. B. cereus ATCC 14579 was grown in BHI in 50 ml. Aerobic in a Erlenmeyer flask, shaking at 200 rpm. Anaerobic in a closed flask, flushed with Nitrogen-gas for 30 min, also shaking at 200 rpm. Transcriptome analyses Phase compared to mid-exponential phase Anaerobic (OD600) 0.2 compared to 0.4 Early-exponential 1.0 compared to 0.4 Transition 1.1 compared to 0.4 Stationary Aerobic (OD600) 0.2 compared to 0.8 Early-exponential 4.0 compared to 0.8 Transition 8.0 compared to 0.8 Stationary Aerobic to anaerobic (OD600) Anaerobic 0.6 to aerobic 0.6
2008-05-11 | E-GEOD-9846 | biostudies-arrayexpress
Project description:Abstract BACKGROUND: The basal-like breast cancer (BLBC) subtype is characterized by positive staining for basal mammary epithelial cytokeratin markers, lack of hormone receptor and HER2 expression, and poor prognosis with currently no approved molecularly-targeted therapies. The oncogenic signaling pathways driving basal-like tumorigenesis are not fully elucidated. METHODS: One hundred sixteen unselected breast tumors were subjected to integrated analysis of phosphoinositide 3-kinase (PI3K) pathway related molecular aberrations by immunohistochemistry, mutation analysis, and gene expression profiling. Incidence and relationships between molecular biomarkers were characterized. Findings for select biomarkers were validated in an independent series. Synergistic cell killing in vitro and in vivo tumor therapy was investigated in breast cancer cell lines and mouse xenograft models, respectively. RESULTS: Sixty-four % of cases had an oncogenic alteration to PIK3CA, PTEN, or INPP4B; when including upstream kinases HER2 and EGFR, 75 % of cases had one or more aberration including 97 % of estrogen receptor (ER)-negative tumors. PTEN-loss was significantly associated to stathmin and EGFR overexpression, positivity for the BLBC markers cytokeratin 5/14, and the BLBC molecular subtype by gene expression profiling, informing a potential therapeutic combination targeting these pathways in BLBC. Combination treatment of BLBC cell lines with the EGFR-inhibitor gefitinib plus the PI3K pathway inhibitor LY294002 was synergistic, and correspondingly, in an in vivo BLBC xenograft mouse model, gefitinib plus PI3K-inhibitor PWT-458 was more effective than either monotherapy and caused tumor regression. CONCLUSIONS: Our study emphasizes the importance of PI3K/PTEN pathway activity in ER-negative and basal-like breast cancer and supports the future clinical evaluation of combining EGFR and PI3K pathway inhibitors for the treatment of BLBC. Gene expression profiles were generated for 95 breast tumors using Agilent Human 44K v5 microarrays following the manufacturer protocol. Stratagene Universal Human Reference RNA was used as the common control sample.
2016-08-21 | E-GEOD-74667 | biostudies-arrayexpress
Project description:The fathead minnow (Pimephales promelas) is a small fish species widely used for ecotoxicology research and regulatory testing in North America. This study used a 2000 gene oligonucleotide microarray to evaluate the effects of the aromatase inhibitor, fadrozole, on gene expression in the liver and brain tissue of exposed females. Reproductive measures, plasma vitellogenin, and gene expression data for the brain isoform of aromatase (CYP19B), vitellogenin precursors, and transferrin all provided evidence supporting the efficacy of the fadrozole exposure. Unsupervised analysis of the microarray results identified 20 genes in brain and 41 in liver as significantly up-regulated and 7 genes in brain and around 45 in liver as significantly down-regulated. Differentially expressed genes were associated with a broad spectrum of biological functions, many with no obvious relationship to aromatase inhibition. However, in brain, fadrozole exposure elicited significant up-regulation of several genes involved in the cholesterol synthesis, suggesting it as one potentially impacted pathway. Gene ontology-based analysis of expression changes in liver suggested overall down-regulation of protein biosynthesis. While real-time PCR analyses supported some of the microarray responses, others could not be verified. Overall, results of this study provide a foundation for developing novel hypotheses regarding the system-wide effects of fadrozole, and other chemical stressors with similar modes of action, on fish biology. Keywords: chemical stress response --Fadrozole exposure-- Treatments: 0, 60 ug fadrozole/L Replication: 4 replicate tanks per treatment, 2 replicate pairs (1 male, one female per pair) per tank for a total of 8 male, 8 female per treatment. Route of exposure: Waterborne, continuous flow through, without the use of carrier solvents, flow rate approx. 45 ml/min. Tanks: 20 L tanks containing 10 L of exposure water Fadrozole (purity ⥠99%; Dr. H. Cooper Eckhardt, Summit, NJ, USA). Fish: Adult (ca. 6 month old) male (4.65±0.93 g) and female (1.90±0.44 g) Conditions: (25°C, 16:8 light:dark photoperiod, fed adult brine shrimp twice daily) Duration: 7 d (± 4 h) Sampling: Fish humanely euthanized in tricaine methanesulfonate (Finquel; Argent, Redmond, WA, USA). Liver, and brain samples transferred directly to pre-weighed vials of RNAlater® (Sigma, St. Louis, MO). Plasma samples were stored frozen at -80°C. Average water quality characteristics (±SD): temperature 25.5±0.1 °C; pH 7.21±0.04; dissolved oxygen 5.74±0.52 mg/L. --Microarray analysis-- n=3 microarrays per treatment and tissue Experimental samples: total RNA pooled from n=2 fish from the same treatment and replicate (except for pooled sample BC3 which included fish from two different replicate tanks). Reference sample: pooled liver, brain, and gonad samples from adult male and female fathead minnows Microarray design: Two color, reference design Hybridization: Experimental samples Cy5, reference sample Cy3
2010-05-22 | E-GEOD-10722 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE13711: Comparative transcriptome and phenotype analysis of acid-stressed Bacillus cereus strain ATCC 14579 GSE13729: Comparative transcriptome and phenotype analysis of acid-stressed Bacillus cereus strain ATCC 10987 Refer to individual Series
2010-06-25 | E-GEOD-13773 | biostudies-arrayexpress
Project description:The food-borne human pathogen Bacillus cereus is found in environments that often have a low pH, such as food and soil. The physiological response upon exposure to several levels of acidity were investigated of B. cereus model strain ATCC 14579, to elucidate the response of B. cereus to acid stress. pH 5.4, pH 5.0, pH 4.8 and pH 4.5 were selected to conduct microarray analyses, based on the differences in physiological response upon exposure to the acid conditions. The transcriptome data revealed response specific profiles. Showing mechanisms induced upon all the different acid down-shocks, such as nitrate reductase and energy production genes, and several genes specifically expressed differentially in mild or lethal levels of acidity, such as F1F0-ATPase and cydAB. Furthermore, mechanisms involved in oxidative stress response were found highly up-regulated in response to both mild and lethal acid stress. The induction of oxidative stress related genes may be a response to the formation of reactive oxygen species by a perturbation of the electron transport chain. Therefore, the formation of hydroxyl radicals and/ or peroxynitrite was monitored upon exposure to the different levels of acidity with a fluorescent probe in a flow cytometer. The formation of these oxidative compounds was shown to be specific for lethal pHs and a model to relate radical formation with the observed transcriptome profiles was proposed. Per acid down-shock three exposure times (i.e., 10, 30 and 60 min) were each compared with non-exposed cells (i.e., t0). In total 4 different acid down-shocks were applied, pH 5.4, pH 5.0, pH 4.8 and pH 4.5. The experiments were performed in duplicate and the duplicate samples were hybridised with a dye-swap.
2010-06-25 | E-GEOD-13711 | biostudies-arrayexpress
Project description:Here, the role of σM and its regulon in stress response and survival of B. cereus ATCC 14579 was assessed by comparative transciptome and phenotypic analysis of this strain and its sigM deletion strain. Exposure of B. cereus ATCC 14579 to a wide range of stresses revealed expression of sigM, encoding σM, to be up-regulated mainly in the presence of ethanol and after alkaline pH-shock. Next to this, disc diffusion tests showed the sigM deletion strain to be more sensitive to oxidizing agents and to be more resistant to cell-wall targeting antibiotics than the wild-type strain. The σM regulon was subsequently determined by comparative transcriptional analyses of the wild-type and its sigM-deletion strain after exposure to ethanol. The putative σM-regulon was shown to consist of 29 genes, several of these genes are predicted to be involved in counteracting oxidative stress, such as an NADH oxidase, a ferredoxin, and a lysine decarboxylase or could encode enzymes involved in methionine metabolism, leading toward L-cysteine production, including luxS. Screening of promoter upstream regions allowed for the assessment of a B. cereus consensus promoter binding site for σM. Since the consensus promoter binding site for B. cereus ATCC 14579 σM, its regulon and the predicted functionalities are different from the corresponding features in B. subtilis, it can be concluded that σM plays a unique role in B. cereus stress response and survival. The sigM deletion strain of B. cereus ATCC 14579 was cultured to an OD600 of ~0.6. Here the first RNA sample was taken, 0 min. After sampling 4% of ethanol was added (v/v), and samples were taken after 10, 30 and 60 minutes of exposure. Comparisons performed were 0 min - 10 min, 0 min - 30 min, and 0 min - 60 min.
2008-05-11 | E-GEOD-9856 | biostudies-arrayexpress
Project description:The stress response of B. cereus ATCC 14579 is monitored true time, showing an enormous response in gene expression. The wild-type strain of B. cereus ATCC 14579 was cultured to an OD600 of ~0.6. Here the first RNA sample was taken, 0 min. After sampling 4% of ethanol was added (v/v), and samples were taken after 10, 30 and 60 minutes of exposure. Comparisons performed were 0 min - 10 min, 0 min - 30 min, and 0 min - 60 min.
2008-05-11 | E-GEOD-9855 | biostudies-arrayexpress