Transcription profiling of human hepatocyte and neuron cell cultures following exposure to various chemical compounds
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Claude Reiss
PROVIDER: E-TOXM-31 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The function of the Staphylococcus aureus eukaryotic-like serine/threonine protein kinase PknB was investigated by transcriptome analysis using DNA-microarray technology and biochemical assays. The transcriptional profile reveals a strong regulatory impact of PknB on the expression of genes encoding proteins which are involved in purine and pyrimidine biosynthesis, cell wall metabolism, autolysis, and glutamine synthesis. To investigate the functional role of PknB in S. aureus DNA microarray experiments were performed. In this experiment, the impact of the deletion of PknB was investigated. Each experiment was performed 5 times including a dye swap resulting in five chips per competitive comparison to increase reproducibility. All hybridizations were done with equal amounts of cDNA probes.
2010-05-05 | E-GEOD-15346 | biostudies-arrayexpress
Project description:The transcription level of a rex-deficient S. aureus mutant in comparison to its parental strain S. aureus SH1000 was analyzed using DNA microarrays. S. aureus N315 microarrays were purchased from Scienion (Scienion AG, Berlin, Germany) and were produced by spotting 2,338 PCR products of the 2,593 ORFs comprising annotated genome of S. aureus N315 [reference identification: NC_002745] on a glass slide. Each ORF is present in duplicate on the microarray (further details can be found at http://www.scienion.com), cDNA was synthesized from total RNA with the LabelStar Array Kit from QIAGEN using the QIAGEN protocol with slight modifications: Random hexamer primer were used (Invitrogen, Karlsruhe, Germany) and Cy3- and Cy5-dCTP were purchased from Perkin-Elmer (Rodgau - Juegesheim, Germany). As recommended by Scienion, 10 µg RNA from either SH1000 or AK1 were used for cDNA synthesis. After hybridisation for 72 h, the microarrays were washed as recommended by the manufacturer. Data analysis. The hybridized microarrays were scanned with a GenePix 4000B microarray scanner (MDS Analytical Technologies GmbH, Ismaning, Germany). A geometric raster was laid over the resulting microarray picture to distinguish the signals from the background. After localization of single spots, intensities and global background were calculated automatically. The hybridization patterns and intensities were quantitatively analyzed using the Imagene 6 software (BioDiscovery, El Segundo, CA). The replicates were averaged, and the spots identified by Imagene 6 (BioDiscovery) as flawed were omitted. The data set was normalized by application of the LOWESS algorithm. In a next step, the intensity values of all arrays for each time point as well as for all time points combined were used for t tests. Genes with a change of <0.5- or â?¥2.0-fold were characterized as having significantly differing amounts of transcripts based on t tests with a P value cut-off of at least 0.05. Gene functions were assigned to the respective accession numbers and annotations as compiled on DOGAN, a web page for S. aureus N315 (http://www.bio.nite.go.jp/dogan/MicroTop?GENOME_ID=n315G1). The parental strain SH1000 and the Rex deficient mutant AK1 were applied on full-genome microarrays to get a detailed view on the differences in the transcriptional profiles which are caused â?? directly or indirectly â?? by the introduced mutation. More specifically, expression levels were compared at five time points, covering different growth phases. To highlight the general changes in the expression profile between SH1000 and the rex mutant, the microarray data of all five time points were also analyzed in a combined way using standard statistical methods. In further experiments, we focused on those genes, which seemed to flag the general difference between the investigated strains.
2010-05-16 | E-GEOD-17128 | biostudies-arrayexpress
Project description:The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the 'Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system' (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose (E-MTAB-799), in vivo repeat dosing, in vitro rat (E-MTAB-797) and in vitro human (E-MTAB-798). This submission comprises the in vivo, repeat dosing studies. If publishing results based on this data, please cite the full project name 'Toxicogenomics Project and Toxicogenomics Informatics Project', the database name 'Open TG-GATEs' and the URL 'http://toxico.nibio.go.jp'. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.
2012-02-10 | E-MTAB-797 | biostudies-arrayexpress
Project description:The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the 'Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system' (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose (E-MTAB-799), in vivo repeat dosing (E-MTAB-800), in vitro rat (E-MTAB-797) and in vitro human. This submission comprises the in vitro human studies. If publishing results based on this data, please cite the full project name 'Toxicogenomics Project and Toxicogenomics Informatics Project', the database name 'Open TG-GATEs' and the URL 'http://toxico.nibio.go.jp'. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.
2012-02-10 | E-MTAB-798 | biostudies-arrayexpress
Project description:Study of gene expression profiles of muscular and neuronal mouse mutant of spinal muscular atrophy(SMA). Pre and post symptomatic stage disease have been analyzed.
2005-05-20 | E-MEXP-131 | biostudies-arrayexpress
Project description:Fibrillar α-Synuclein (α-Syn) is the principal component of Lewy bodies which are evident in individuals affected by Parkinson disease (PD). This neuropathologic form of α-Syn contributes to PD progression and propagation of exogeneous α-Syn between neurons has been demonstrated. In order to identify proteins interacting with extracellularly applied α-syn assemblies (either oligomeric or fibrillar α -syn) and identify in particular plasma membrane proteins exposed extracellularly, we exposed pure-neuronal cultures to oligomeric and fibrillar α-syn for 10 min, pulled down the complex, and identified the associated proteins using a proteomic-based approach. Using pull-down of whole cell lysates and MS, we have identified proteins interacting with extracellularly applied α-syn in three different conditions. Each condition consisted in three experimental replicates of cells exposed 10 min to α-syn assemblies and the non-treated cells used as controls.
2015-09-07 | PXD002260 | Pride
Project description:Fibrillar α-Synuclein (α-Syn) is the principal component of Lewy bodies which are evident in individuals affected by Parkinson disease (PD). This neuropathologic form of α-Syn contributes to PD progression and propagation of exogeneous α-Syn between neurons has been demonstrated. In order to identify proteins interacting with extracellularly applied α-syn assemblies (either oligomeric or fibrillar α -syn) and identify in particular plasma membrane proteins exposed extracellularly, we exposed pure-neuronal cultures to oligomeric and fibrillar α-syn for 10 min, pulled down the complex, and identified the associated proteins using a proteomic-based approach. Using pull-down of whole cell lysates and MS, we have identified proteins interacting with extracellularly applied α-syn in three different conditions. Each condition consisted in three experimental replicates of cells exposed 10 min to α-syn assemblies and the non-treated cells used as controls.
2015-09-07 | PXD002257 | Pride
Project description:Fibrillar α-Synuclein (α-Syn) is the principal component of Lewy bodies which are evident in individuals affected by Parkinson disease (PD). This neuropathologic form of α-Syn contributes to PD progression and propagation of exogeneous α-Syn between neurons has been demonstrated. In order to identify proteins interacting with extracellularly applied α-syn assemblies (either oligomeric or fibrillar α -syn) and identify in particular plasma membrane proteins exposed extracellularly, we exposed pure-neuronal cultures to oligomeric and fibrillar α-syn for 10 min, pulled down the complex, and identified the associated proteins using a proteomic-based approach. Using pull-down of whole cell lysates and MS, we have identified proteins interacting with extracellularly applied α-syn in three different conditions. Each condition consisted in three experimental replicates of cells exposed 10 min to α-syn assemblies and the non-treated cells used as controls
2015-09-07 | PXD002259 | Pride
Project description:Fibrillar α-Synuclein (α-Syn) is the principal component of Lewy bodies which are evident in individuals affected by Parkinson disease (PD). This neuropathologic form of α-Syn contributes to PD progression and propagation of exogeneous α-Syn between neurons has been demonstrated. In order to identify proteins interacting with extracellularly applied α-syn assemblies (either oligomeric or fibrillar α -syn) and identify in particular plasma membrane proteins exposed extracellularly, we exposed pure-neuronal cultures to oligomeric and fibrillar α-syn for 10 min, pulled down the complex, and identified the associated proteins using a proteomic-based approach. Using pull-down of whole cell lysates and MS, we have identified proteins interacting with extracellularly applied α-syn in three different conditions. Each condition consisted in three experimental replicates of cells exposed 10 min to α-syn assemblies and the non-treated cells used as controls.
2015-09-07 | PXD002258 | Pride
Project description:Fibrillar α-Synuclein (α-Syn) is the principal component of Lewy bodies which are evident in individuals affected by Parkinson disease (PD). This neuropathologic form of α-Syn contributes to PD progression and propagation of exogeneous α-Syn between neurons has been demonstrated. In order to identify proteins interacting with extracellularly applied α-syn assemblies (either oligomeric or fibrillar α -syn) and identify in particular plasma membrane proteins exposed extracellularly, we exposed pure-neuronal cultures to oligomeric and fibrillar α-syn for 10 min, pulled down the complex, and identified the associated proteins using a proteomic-based approach. Using pull-down of whole cell lysates and MS, we have identified proteins interacting with extracellularly applied α-syn in three different conditions. Each condition consisted in three experimental replicates of cells exposed 10 min to α-syn assemblies and the non-treated cells used as controls
2015-09-07 | PXD002256 | Pride