Transcriptome in yeast by exposure of 7 transition metals
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE9466 | GEO | 2008/11/01
SECONDARY ACCESSION(S): PRJNA103237
REPOSITORIES: GEO
Similar Datasets
Project description:To get an insight into the time-resolved gene expression response elicited by different heavy metals, we treated the cell line 1321N1 with cadmium, mercury or arsenic for 1.5h, 3h, 6h, 12h and 24h and performed QuantSeq 3'-mRNA sequencing.
2024-11-16 | GSE281225 | GEO
Project description:We are investigating the response of human lymphoblastoid cells to low-dose exposure of environmental metals We used microarrays to detail the global programme of gene expression upon response to low-dose metals Keywords: dose TK6 cells were grown to mid log-phase and exposed to low-doses of arsenic and cadmium. RNA was collected 24 hrs after exposure.
2010-04-14 | E-GEOD-20320 | biostudies-arrayexpress
Project description:Metal toxicity is a global environmental challenge. Fish are particularly prone to metal exposure, which can be lethal or can cause sublethal physiological impairments. The objective of this study was to improve our understanding on how adverse effects of essential and non-essential metals in early life stage zebrafish may be explained by changes in the transcriptome after exposure to non-toxic levels. We therefore studied the effects of three different metals at low concentrations in zebrafish embryos by transcriptomics analysis. The study design compared exposure effects caused by different metals at different developmental stages (pre-hatch and post-hatch). Wild-type embryos were exposed to solutions of low concentrations of copper (CuSO4), cadmium (CdCl2) and cobalt (CoSO4) until 96 h post-fertilization (hpf) and microarray experiments were carried out to determine transcriptome profiles at 48 and 96 hpf. We found that the toxic metal cadmium affected the expression of more genes at 96 hpf than 48 hpf. The opposite effect was observed for the essential metals cobalt and copper, which also showed enrichment of different GO terms. Genes involved in neuromast and motor neuron development, were significantly enriched, agreeing with our previous results showing motor neuron and neuromast damage in the embryos. Our data provide evidence that the response of the transcriptome of fish embryos to metal exposure differs for essential and non-essential metals.
2017-12-27 | GSE80957 | GEO
Project description:Heavy metals have been postulated as significant nitrification inhibitor in wastewater treatment plant. The effect of heavy metals such as Cd2+, Cu2+ and Hg2+ to nitrifying bacterium, Nitrosomonas europaea, was studied in pseudo-steady state batch reactor. Under incubation of Nitrosomonas europaea with 1 ?M CdCl2 for 1 hour, transcripts for 66 of 2460 genes were found at high level, yet transcripts of 50 genes were found at low level. Mercury resistance genes (merACDPT) showed 277-fold up regulation. Keywords: cadmium, stress response, global transcription, mercury resistance genes, merA, The 1 uM CdCl2 caused more than 50 % inhibition in physiological response for 1 hour incubation. Transcriptional levels of the cells inhibited by cadmium were compared with the cells under control condition.
2010-05-25 | E-GEOD-9221 | biostudies-arrayexpress
Project description:Heavy metals have been postulated as significant nitrification inhibitor in wastewater treatment plant. The effect of heavy metals such as Cd2+, Cu2+ and Hg2+ to nitrifying bacterium, Nitrosomonas europaea, was studied in pseudo-steady state batch reactor. Under incubation of Nitrosomonas europaea with 1 ?M CdCl2 for 1 hour, transcripts for 66 of 2460 genes were found at high level, yet transcripts of 50 genes were found at low level. Mercury resistance genes (merACDPT) showed 277-fold up regulation. Keywords: cadmium, stress response, global transcription, mercury resistance genes, merA,
2008-03-22 | GSE9221 | GEO
Project description:From the result of comparative the gene expression analyses of human hepatoma cell line, HepG2 following exposures of three heavy metals; arsenic, cadmium and nickel and three carcinogens; N-dimethylnitrosoamine (DMN), 12-O-tetradecanoylphorbol-13-acetate (TPA) and tetrachloroethylene (TCE), 31-55% of the genes altered by As, Cd and Ni exposure were overlapped with those by three model carcinogen exposures in our experiments. In particular, three heavy metals shared certain characteristics with TPA and TCE in remarkable up-regulations of the genes associated with progression of cell cycle, which might play a central role in heavy metal carcinogenesis. In addition, this characteristic of gene expressions alteration was counteracted by intracellular accumulation of vitamine C in As-exposed cells but not in Cd- and Ni-exposed cells. These results suggest that the cell proliferative responses are caused by reactive oxygen species mainly in As exposure, while other mechanisms would be involved in these responses in Cd and Ni exposures. Experiment Overall Design: In this study, we examined the gene expression alteration in human hepatoma cell line, HepG2 following exposures of three heavy metals; arsenic, cadmium and nickel and three carcinogens; N-dimethylnitrosoamine (DMN), 12-O-tetradecanoylphorbol-13-acetate (TPA) and tetrachloroethylene (TCE) using DNA microarray with 8795 human genes. Furthermore, we also performed the DNA microarray analyses for the heavy metal exposed-cells that were loaded with vitamine C beforehand to examine the effects of antioxidant molecule to heavy metal exposures.
2008-06-16 | E-GEOD-8865 | biostudies-arrayexpress
Project description:Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the of toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays. We identified both common and unique biological responses to exposure to the three metals. Nickel, cadmium, chromium all induced oxidative stress with both similar and unique genes and pathways responding to this stress. Although all three metals are known to be genotoxic, evidence for DNA damage in our study only exists in response to chromium. Nickel induced a hypoxic response as well as inducing genes involved in chromatin structure, perhaps by replacing iron in key proteins. Cadmium distinctly perturbed genes related to endoplasmic reticulum stress and invoked the unfolded protein response leading to apoptosis. With these studies, we have completed the first gene expression comparative analysis of nickel, cadmium, and chromium in H4-II-E-C3 cells.
2011-08-19 | GSE31503 | GEO
Project description:From the result of comparative the gene expression analyses of human hepatoma cell line, HepG2 following exposures of three heavy metals; arsenic, cadmium and nickel and three carcinogens; N-dimethylnitrosoamine (DMN), 12-O-tetradecanoylphorbol-13-acetate (TPA) and tetrachloroethylene (TCE), 31-55% of the genes altered by As, Cd and Ni exposure were overlapped with those by three model carcinogen exposures in our experiments. In particular, three heavy metals shared certain characteristics with TPA and TCE in remarkable up-regulations of the genes associated with progression of cell cycle, which might play a central role in heavy metal carcinogenesis. In addition, this characteristic of gene expressions alteration was counteracted by intracellular accumulation of vitamine C in As-exposed cells but not in Cd- and Ni-exposed cells. These results suggest that the cell proliferative responses are caused by reactive oxygen species mainly in As exposure, while other mechanisms would be involved in these responses in Cd and Ni exposures. Keywords: other
2007-12-31 | GSE8865 | GEO
Project description:Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the of toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays. We identified both common and unique biological responses to exposure to the three metals. Nickel, cadmium, chromium all induced oxidative stress with both similar and unique genes and pathways responding to this stress. Although all three metals are known to be genotoxic, evidence for DNA damage in our study only exists in response to chromium. Nickel induced a hypoxic response as well as inducing genes involved in chromatin structure, perhaps by replacing iron in key proteins. Cadmium distinctly perturbed genes related to endoplasmic reticulum stress and invoked the unfolded protein response leading to apoptosis. With these studies, we have completed the first gene expression comparative analysis of nickel, cadmium, and chromium in H4-II-E-C3 cells. H4-II-E-C3 cells were were exposed to nickel (II) chloride (NiCl2), cadmium chloride (CdCl2), or sodium dichromate (Na2Cr2O7) for 24 hours. The cells were treated with a low, mid, and high concentration of each chemical and shared a control for each biological replicated, and we exposed 4 biologcial replicates for a total of 44 samples.
2011-08-18 | E-GEOD-31503 | biostudies-arrayexpress
Project description:Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms such as springtails, supplement traditional ecotoxicological research, but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. We used the uncorrelated shrunken centroid (USC) method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants.
2010-02-05 | GSE19353 | GEO