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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Host pathogen interaction between Staphylococcus aureus ATCC25923 and murine RAW264.7 macrophage-like cells

ABSTRACT: Macrophages infected with S. aureus were subjected to gene expression profiling to undertake a complete understanding of the interaction induced gene expression changes in both, S.aureus and the RAW macrophages. Agilent one-color experiment, Agilent-021933 Genotypic designed Custom Staphylococcus aureus and Mus musculus 8x15k

ORGANISM(S): Mus musculus

SUBMITTER: Genotypic technology

PROVIDER: E-GEOD-23538 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Host pathogen interaction between Staphylococcus aureus ATCC25923 and murine RAW264.7 macrophage-like cells

Project description:Macrophages infected with S. aureus were subjected to gene expression profiling to undertake a complete understanding of the interaction induced gene expression changes in both, S.aureus and the RAW macrophages.

2010-08-11 | GSE23538 | GEO

Expression data of murine dermal macrophages

Project description:Dermal macrophages were sorted from the ears of CCR2-/- mice that were uninfected, injected with PBS or injected with S.aureus strain Newmann 107 CFU/ml live S. aureus was injecetd in 10µl PBS.

2020-07-15 | GSE145094 | GEO

Nitrogen-ion-beam implantation effect on rice dry seeds

Project description:Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam. Three sample groups—the controls, the ion-beam implanted samples and vacuum-treated samples. Three replicates were included in each sample group. Radiation induced gene expression rice seedlings was measured at 96 hours after germination of the seeds.

2012-03-01 | E-GEOD-36152 | biostudies-arrayexpress

Monitoring of protein thiol-oxidation in S.aureus USA300 under hypochlorite stress using OxICAT approach.

Project description:During infections, S. aureus has to cope with the oxidative burst of activated macrophages and neutrophils, including reactive oxygen and nitrogen species (RNS, ROS) and the strong oxidant hypochloric acid. We aimed to understand the global thiol-redox state in the major pathogen S. aureus and discover new NaOCl-sensitive proteins driven by thiol-switches. Thus, we performed a quantitative redox proteomics approach based on OxICAT and analyzed the percentages of thiol-oxidation levels in S.aureus before and after sub-lethal doses of 150 µM NaOCl stress. In parallel, we searched for protein S-bacillithiolation.

2016-12-22 | PXD004918 | Pride

Hypoxia-induced modulation of gene expression in human adipocytes - A microarray study

Project description:Obesity is characterised by expansion of white adipose tissue, accompanied by an inflamatory response. It has been proposed that the inflammatory state observed may be linked to relative hypoxia in clusters of adipocytes distant from vasculature. Adipose tissue hypoxia has been observed in both animal models and human studies in obesity, and has been linked to insulin resistance. This study has used Agilent whole-genome microarrays to examine the effects of acute hypoxia on the global gene expression in human adipocytes. Human adipocytes (Zen-bio cells) were incubated in hypoxic conditions (1% O2) for 24 h. Control human adipocytes were incubated under normoxic conditions (21% O2). Eight biological replicates were prepared for each experimental condition, and RNA was pooled from two biological replicates, giving a total of n=4 array replicates.

2012-03-09 | E-GEOD-34007 | biostudies-arrayexpress

Direct reprogramming of human fibroblasts to functional hepatocyte-like cells

Project description:Plasticity of differentiated cells has been proved by nuclear transfer, induced pluripotent cells and transdifferentiation. Here we show that by transduction of 3 factors (FOXA3, HNF1A and HNF4A), human fetal fibroblasts can be converted to hepatocyte-like cells (hiHep cells), expressing hepatic marker genes, and acquiring many mature hepatocyte functions in vitro and in vivo. Human fetal fibroblasts (HFF) were tranfected with 3 liver enriched transcription factors (FOXA3, HNF1A, HNF4A), and converted to hepatocyte-like cells (hiHep cells). HFF and primary human hepatocytes (PHH) serve as control.

2014-03-06 | E-GEOD-42643 | biostudies-arrayexpress

Microarray Analysis of Genes Regulated by Macrophage-Conditioned Media Treatment of Human Pre-Adipocytes

Project description:A major development in the study of obesity is the recognition that the condition is characterised by chronic mild inflammation. Within adipose tissue, this involves the infiltration of macrophages, as well as the direct inflammatory response of the adipocytes and pre-adipocytes. This study has used Agilent whole-genome microarrays to examine the effects of macrophage-conditioned medium on the global inflammatory response of human pre-adipocytes. Human pre-adipocytes (SGBS cells) were treated with macrophage (U937 cells) conditioned medium for 24 h. Control pre-adipocytes were treated with unconditioned medium (control) or RPMI-1640 media alone to control for differences in media used to culture the U937 cells. There were 5 biological replicates per group.

2011-12-21 | E-GEOD-27503 | biostudies-arrayexpress

Comparative genomics of Staphylococcus aureus and the application of a “pan-genome” for assigning RNA-Seq transcript reads from divergent strains and in vivo human nasal samples

Project description:in vitro comparison between two MRSA grown in rich (BHI) and poor media (SNM), compared with the nasal metatranscriptome reads of S. aureus. Global expression profile of two MRSA strains of S.aureus harvested in two different growth phases and compared with a metatranscriptome nose sample of a S. aureus carrier.

2015-01-05 | E-GEOD-56294 | biostudies-arrayexpress

Placental growth factor as potential target against hepatocellular carcinoma in an orthotopic mouse model.

Project description:The placental growth factor (PlGF) is member of the vascular endothelial growth factor (VEGF)-family known to stimulate endothelial cell growth, migration and survival, attract angiocompetent macrophages and bone marrow progenitor cells and determine the metastatic niche. Unlike VEGF, genetic studies have shown that PlGF is specifically involved in the pathologic angiogenesis, thus its inhibition would not affect healthy blood vessels, providing an attractive drug candidate with a good safety profile. In this study, we assess whether inhibition of PlGF could be used as a potential therapy against hepatocellular carcinoma (HCC), by using PlGF-knock out mice and monoclonal antibodies targeting PlGF in an orthotopic model for HCC. In addition, the effect of PlGF-antibodies is compared to that of Sorafenib, as well as the combination of both therapies. In our study we have found that both in a transgenic knock out model as in a treatment model, silencing or inhibition of PlGF significantly decreased tumour burden, not only by inhibiting the vascularisation, but also by decreasing hepatic macrophage recruitment and by normalizing the remaining blood vessels, thereby decreasing hypoxia and thus, reducing the pro-metastatic potential of HCC. Conclusion: considering its favourable safety profile and its pleiotropic effect on vascularisation, metastasis and inflammation, targeting PlGF could become a valuable therapeutic strategy against HCC. Hybridisation on the Mouse Gene Expression Microarray (Agilent) was performed in a single sample per chip and in a monocolore mode, using cyanine-3 (Cy3) labeling. Following conditions were assessed: 25W DEN + 5W αPlGF tumour tissue (n = 5), 25W DEN + 5W αPlGF surrounding tissue (n = 4), 25W DEN + 5W IgG tumour tissue (n = 5), 25W DEN + 5W IgG surrounding tissue (n = 4), 25W saline + 5W αPlGF (n = 3) and 25W saline + 5W IgG (n = 3).

2014-12-23 | E-GEOD-35289 | biostudies-arrayexpress

Response of Candida glabrata to low pH

Project description:To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH 2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains. To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ delta cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains Agilent one-color experiment,Organism: Yeast ,Agilent-026378 Genotypic designed Custom Candida glabrata 8x15k , Labeling kit: Agilent Quick-Amp labeling

2011-01-10 | E-GEOD-24267 | biostudies-arrayexpress

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