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E-MEXP-2740
Saccharomyces cerevisiae
8 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
The experiment describes the transcriptional response of Saccharomyces cerevisiae BY4741 and of the deletion mutant Δhaa1 following an incubation in the presence of 50 mM acetic acid (at pH 4.0)
Publication Title
Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid.
Sample Metadata Fields
Compound
View Samples- Saccharomyces cerevisiae
- 36 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
This study focus a comparative toxicogenomic analysis of the effects of four herbicides (alachlor, ALA, S-metolachlor, S-MET, diuron, DIU, and MCPA-methyl ester, MCPA-ME), one insecticide (carbofuran, CAB), and one fungicide (pyrimethanil, PYR), in the model yeast Saccharomyces cerevisiae, to predict potential cytotoxic effects of these xenobiotics while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. The six model pesticides selected have been used worldwide in agricultural activities, at the present time or in the past, and have different modes of action on their target-organisms. Moreover, some of them are currently in Annex 1 of EC Directive 1107/2009 (repealing 91/414), that is they are in use in the EU, but having some ecotoxicological concerns (e.g. S-MET, PYR, MCPA-ME), others have their use restricted and/or are priority substances under the Water Framework Directive (e.g. ALA, DIU), and one was banned (e.g. CAB).
Publication Title
Comparative analysis of transcriptomic responses to sub-lethal levels of six environmentally relevant pesticides in Saccharomyces cerevisiae.
Sample Metadata Fields
Treatment
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The world-wide used herbicide alachlor is among the priority substances listed in the European Water Framework Directive. We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes.
Publication Title
Transcriptional profiling in Saccharomyces cerevisiae relevant for predicting alachlor mechanisms of toxicity.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 9 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes.
Publication Title
Potential mechanisms underlying response to effects of the fungicide pyrimethanil from gene expression profiling in Saccharomyces cerevisiae.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 54 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Down syndrome (DS) is the most frequent cause of human congenital mental retardation. Cognitive deficits in DS result from perturbations of normal cellular processes both during development and in adult tissues, but the mechanisms underlying DS etiology remain poorly understood. To assess the ability of iPSCs to model DS phenotypes, as a prototypical complex human disease, we generated bona-fide DS and wild-type (WT) non-viral iPSCs by episomal reprogramming. DS iPSCs selectively overexpressed chromosome 21 genes, consistent with gene dosage, which was associated with deregulation of thousands of genes throughout the genome. DS and WT iPSCs were neurally converted at >95% efficiency, and had remarkably similar lineage potency, differentiation kinetics, proliferation and axon extension at early time points. However, at later time points DS cultures showed a two-fold bias towards glial lineages.
Publication Title
Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Cell line
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To understand the transcriptional program by which GR regulates skin development, we performed a microarray analysis using the skin of E18.5 GR-/- and GR+/+ mouse embryos.
Publication Title
Glucocorticoid receptor regulates overlapping and differential gene subsets in developing and adult skin.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 261 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To select signatures of ccRCC, 265 ccRCC samples were obtained from the Van Andel Research Institute.
Publication Title
Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma.
Sample Metadata Fields
Sex, Specimen part, Disease stage
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
MicroRNA-10b pleiotropically regulates invasion, angiogenicity and apoptosis of tumor cells resembling mesenchymal subtype of glioblastoma multiforme.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
There is an evident, unmet need to develop a commercially available in vitro system that can model inflammatory states of the liver and predict immune-mediated hepatotoxicity of drugs and xenobiotics taken under inflamed conditions. Hepatocyte-Kupffer cell co-cultures can model inflammation-mediated hepatotoxicity; however, Kupffer cell (KC) source remains an important bottleneck for the development of such models. Primary human Kupffer cells (PHKCs) are costly, limited in availability and exhibit donor variability. An alternative cell source for KCs has not been reported. Important paradigm shift from the classical dogma of adult blood-circulating monocyte-derived macrophages to intrahepatic precursor/fetal monocyte-derived macrophages has shed new light into the origin of KCs in vivo. Based on these recent findings, we report here, a novel method to generate human KCs in vitro from stem cells (hPSC-KCs) via fetal monocytes. hPSC-KCs expressed macrophage markers, CD11, CD14, CD68, CD163 and CD32 at gene and protein level and exhibited functional properties such as phagocytosis and Interleukin-6 and Tumor Necrosis Factor-4alpha production upon activation. Importantly, molecular signature, liver-macrophage specific CLEC-4F expression and cytokines production levels of hPSC-KCs were similar to PHKCs but different from non-liver macrophages. We used an inflammatory liver co-culture model to demonstrate that activated hPSC-KCs, but not non-liver macrophages, were able to recapitulate effects of PHKCs when stimulated with paradigm hepatotoxicants. hPSC-KCs developed in this study offer a renewable human cell source for liver-specific macrophages which can be used to develop in vitro systems for modelling the inflammatory state of the liver.
Publication Title
Generation of mature kupffer cells from human induced pluripotent stem cells.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 8 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Recombinant baculoviral vectors efficiently transduce several types of cells in the brain. To characterize host responses to viral challenge, thus verifying the suitability of using the virus for the development of gene therapy strategies in the central nervous system, we used cDNA microarray technology to examine in vitro and in vivo global cellular gene expression profiles after viral transduction. We demonstrated that the transduction induced host antiviral responses as a major reaction in all three types of samples profiled, including the rat brain, cultured human astrocytes and human neuronal cells. The related genes were mainly those associated with innate immunity. Several genes of the major histocompatibility complex molecules, an important component of the host adaptive immunity to exogenous pathogens, were up-regulated in the rat brain and human astrocytes, but not in neuronal cells. We also observed that genes related to cell death and apoptosis were up-regulated and genes related cell cycle regulation were down-regulated in neuronal cells, but not obviously affected in astrocytes. These findings should be useful in understating the molecular basis for neural cell response to baculoviral transduction and guiding rational applications of baculoviral vectors in the central nervous systems
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples