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Five genome-wide microarrays were used to indentify gene expression in exposure to Tributyltin, Dichlorodiphenyltrichloroethane and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin.

ABSTRACT: Five genome-wide microarrays were used to indentify gene expression in exposure to Tributyltin, Dichlorodiphenyltrichloroethane and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin. The three environmental chemicals are persistent in environment and cause continuous toxical effects on human and aquatic life. Tetrahymena thermophila has the potential as a toxical model. The genome-wide microarray in Tetrahymena thermophila exposed to these toxicants was analyzed. First, genes differentially expressed under the treatment of each toxicant were identified and then their functions were categorized using GO enrichment analysis. The results may suggest that Tetrahymena thermophila is able to reflect different mechanism of different toxic-type toxicants which are similar to those in multicellular organisms. Regarding the complexity of TCDD effects, context likelihood of relatedness method (CLR) was applied to construct a TCDD-relevant network. General functions of the network are related to the epigenetic mechanism of TCDD. Based on the network analysis, a model of TCDD effect on T. thermophila was infered. Thus, Tetrahymena has the potential to be a good unicellular eukaryotic model for toxic mechanism research at genome level.

ORGANISM(S): Tetrahymena thermophila

PROVIDER: GSE26515 | GEO | 2011/06/30

SECONDARY ACCESSION(S): PRJNA136701

REPOSITORIES: GEO

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Five genome-wide microarrays were used to indentify gene expression in exposure to Tributyltin, Dichlorodiphenyltrichloroethane and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin.

Project description:Five genome-wide microarrays were used to indentify gene expression in exposure to Tributyltin, Dichlorodiphenyltrichloroethane and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin. The three environmental chemicals are persistent in environment and cause continuous toxical effects on human and aquatic life. Tetrahymena thermophila has the potential as a toxical model. The genome-wide microarray in Tetrahymena thermophila exposed to these toxicants was analyzed. First, genes differentially expressed under the treatment of each toxicant were identified and then their functions were categorized using GO enrichment analysis. The results may suggest that Tetrahymena thermophila is able to reflect different mechanism of different toxic-type toxicants which are similar to those in multicellular organisms. Regarding the complexity of TCDD effects, context likelihood of relatedness method (CLR) was applied to construct a TCDD-relevant network. General functions of the network are related to the epigenetic mechanism of TCDD. Based on the network analysis, a model of TCDD effect on T. thermophila was infered. Thus, Tetrahymena has the potential to be a good unicellular eukaryotic model for toxic mechanism research at genome level. Tetrahymena thermophila CU428 cells were cultured using 1XSPP, 30 degree, 100 rpm shaking, until 300,000 cells/ml. Cells at 300,000 cells/ml was incubated in SPP medium were treated. Two microarrays were used 4.02μl DMSO per ml SPP as the solvent and control; One microarray for 5 ppb TBT treatment 24 hours; One microarray for 1 ppb TCDD treatment 24 hours; One microarray for 4ppm DDT treatment for 24 hours.

2011-06-30 | E-GEOD-26515 | biostudies-arrayexpress

Gene expression of Tetrahymena thermophila SB210 under the arsenic exposure

Project description:To identified the differential expressed genes between the arsenic exposure cells and wild type cells As is a well- known carcinogen, it receives special attention. Due to its ubiquitous distribution in the environment, a unicellular model system related to the environment will be useful in toxicological research of arsenic. The eukaryotic protist Tetrahymena thermophila is a well-established model in classical toxicology and now a potential model at genomic level. In the present study, Tetrahymena thermophila was inbred with arsenate. With the use of microarray technique, the genes differentially expressed at 4 time points in exposure to arsenate were screened out. The major biological processes involved and their changes over time were identified with enrichment analysis and transformed expression data. Characteristics of arsenic toxicity and response to arsenic were identified, proving T. thermophila a good unicellular model for arsenic toxicological research at genomic level.

2019-12-01 | GSE53836 | GEO

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Project description:We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote. RNA-seq for six samples of Tetrahymena growth, starvation and conjugation.

2012-03-15 | E-GEOD-27971 | biostudies-arrayexpress

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Project description:Tetrahymena thermophila

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Genome-Wide Microarray Analysis of Gene Expression During Starvation in Tetrahymena thermophila

Project description:Two genome-wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila were used to study gene expression in starved cells (starvation 0 hour and starvation 24 hour). Combining these two microarrays with 50 microarrays described in Miao et al. (2009) and 15 other microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human. For starvation, CU428 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 24 hours (referred to as S-0 and S-24, respectively).

2011-06-13 | E-GEOD-26384 | biostudies-arrayexpress

Genome-Wide Microarray Analysis of Gene Expression During Starvation in Tetrahymena thermophila

Project description:Four genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in starved cells (Starvation 0 hour and Starvation 9 hour, each two replicates). Combined these four microarrays with 50 microarrays described in Miao et al (2009, PMID: 19204800; GSE11300) and other 13 microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human. For starvation, CU427 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 9 hours (referred to as S-0 and S-9, respectively).

2011-06-13 | E-GEOD-26385 | biostudies-arrayexpress

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