Project description:The cytopheno project studies cytoplasmic-nucleus interactions by characterizing cytolines (same nucleus but different cytoplasm, and conversely) at several levels (growth, germination, transcriptomic, proteomic, metabolomic) notably in response to nitrogen deficiency. For this project, there are 48 hybridizations performed as following, on leaf samples from hydroponically grown plants. bioadapt2011_cytopheno - bioadapt2011_cytopheno - Evaluation of the impact of nucleo-cytoplasmic co-adaptation disruptions on nuclear genome expression in Arabidopsis - Obtaining samples by hydroponic culture.
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'. This dataset is part of the TransQST collection.
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'.
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'.
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'. This dataset is part of the TransQST collection.
Project description:As part of a larger conifer genomics project, we developed a new 21.8K cDNA microarray containing 21,843 spotted ESTs from spruce (Picea spp.). To evaluate the performance of the array we conducted four technical replicate self-self hybridizations using untreated control bark RNA pooled from four biological replicates. The objectives were to determine: 1) the linear dynamic range of expression detection of the array; 2) the level of non-specific hybridization to negative control elements on the array; and 3) the overall technical reproducibility of the array. Keywords: Array performance evaluation using self-self hybridizations.
Project description:ChIP-seq and input sequence data used in the development and evaluation of the BEADS normalization method. Examination of ChIP and input sequence reads across the worm genome